Contacts of the helix formed by residues 538 - 565 (chain A) in PDB entry 1W7A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 538 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PHE* 5.4 3.6 - + + -
402A GLU* 5.7 3.6 + - - -
403A LEU* 3.6 41.0 - - + +
534A LEU 3.7 19.0 + - - -
535A LEU 3.0 8.2 + - - +
536A LEU 3.0 1.0 - - - -
537A PRO* 1.3 89.0 - - + +
539A LEU* 1.3 65.0 + - - +
540A GLU* 3.1 3.8 + - - -
541A ALA* 3.1 12.3 + - + +
542A LEU* 2.9 25.2 + - + +
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO* 4.0 13.5 - - + -
254A HIS* 4.0 14.1 - - + +
256A ARG* 3.7 15.5 - - - +
352A LEU* 4.2 26.7 - - + +
355A LEU* 4.5 14.8 - - + -
356A ALA* 3.8 25.4 - - + -
535A LEU 3.7 1.3 + - - -
536A LEU* 2.8 25.7 + - + +
537A PRO 3.4 0.8 + - - -
538A HIS* 1.3 76.2 - - - +
540A GLU* 1.3 57.3 + - - +
542A LEU* 3.2 6.4 + - - +
543A GLN* 2.9 49.0 + - + +
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 3.7 48.4 + - - +
537A PRO 5.0 2.4 + - - +
538A HIS 3.2 1.0 - - - -
539A LEU* 1.3 79.8 - - - +
541A ALA* 1.3 62.6 + - - +
543A GLN* 3.4 3.8 + - - +
544A GLN* 3.3 30.5 + - + +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LYS 4.7 1.7 - - - +
400A PHE* 3.7 20.3 - - + -
538A HIS* 3.1 14.2 + - + +
540A GLU* 1.3 77.6 - - - +
542A LEU* 1.3 64.0 + - - +
544A GLN* 3.4 8.6 + - - +
545A SER* 3.1 21.8 + - - -
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Residues in contact with LEU 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.9 3.8 - - + +
352A LEU* 3.4 38.3 - - + +
355A LEU* 4.7 7.4 - - + -
368A MET* 5.3 2.9 - - - -
372A PHE* 3.4 37.9 - - + -
400A PHE* 3.8 24.2 - - + -
403A LEU* 4.0 16.4 - - + -
535A LEU* 4.2 10.1 - - + +
538A HIS* 2.9 27.5 + - + +
539A LEU* 3.2 7.6 + - - +
541A ALA* 1.3 78.7 - - - +
543A GLN* 1.3 60.4 + - - +
545A SER* 3.2 4.1 + - - -
546A ALA 3.1 18.0 + - - -
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Residues in contact with GLN 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER 3.3 22.5 - - - +
254A HIS* 3.6 26.1 + - - +
256A ARG* 3.1 41.2 - - - +
352A LEU* 4.2 13.9 - - + -
539A LEU* 2.9 31.7 + - + +
540A GLU 3.4 4.2 + - - +
541A ALA 3.3 0.2 - - - -
542A LEU* 1.3 73.0 - - - +
544A GLN* 1.3 70.7 + - - +
546A ALA* 3.3 3.3 + - - +
547A SER* 2.9 25.5 + - - -
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 6.2 1.6 - - - +
396A LYS* 3.3 48.7 + - + +
540A GLU* 3.3 20.7 + - + +
541A ALA* 3.7 11.7 - - - +
542A LEU 3.3 0.2 - - - -
543A GLN* 1.3 80.3 - - - +
545A SER* 1.3 62.0 + - - +
547A SER* 3.4 4.5 + - - -
548A ALA 3.0 18.0 + - - -
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Residues in contact with SER 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.6 4.7 - - - +
375A LEU* 4.7 2.1 - - - +
396A LYS 3.6 10.7 + - - -
397A MET* 2.6 27.8 + - - +
400A PHE* 3.6 18.2 - - - -
541A ALA 3.1 14.3 + - - -
542A LEU* 3.4 9.4 - - - -
543A GLN 3.1 0.2 - - - -
544A GLN* 1.3 77.2 - - - +
546A ALA* 1.3 57.7 + - - +
548A ALA* 3.1 3.8 + - - +
549A LEU* 2.9 44.1 + - - +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET* 3.7 7.3 - - - +
348A LEU* 4.0 7.2 - - + +
349A GLU* 4.0 27.4 - - + +
352A LEU* 4.0 17.7 - - + -
542A LEU 3.1 14.9 + - - +
543A GLN* 3.9 4.3 - - - +
545A SER* 1.3 75.6 - - - +
547A SER* 1.3 57.8 + - - +
549A LEU* 3.6 12.1 - - - +
550A ALA* 2.9 30.7 + - - +
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Residues in contact with SER 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A MET* 3.8 15.4 - - - +
349A GLU* 6.0 1.3 - - - -
396A LYS* 3.5 17.8 + - - -
543A GLN 2.9 17.3 + - - -
544A GLN* 3.6 9.6 - - - -
546A ALA* 1.3 79.1 - - - +
548A ALA* 1.3 55.4 + - - +
550A ALA* 3.5 4.2 + - - -
551A GLU* 3.1 28.1 + - - +
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Residues in contact with ALA 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 3.9 26.1 - - + +
396A LYS* 3.7 30.9 - - + +
397A MET* 4.0 6.3 - - + +
544A GLN 3.0 16.8 + - - +
545A SER 3.6 3.8 - - - +
547A SER* 1.3 74.9 - - - +
549A LEU* 1.3 61.0 + - - +
551A GLU* 3.8 1.5 - - - +
552A LEU* 2.8 36.8 + - - +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A THR* 5.4 0.2 - - - +
302A MET* 3.7 13.9 - - + -
342A LEU* 4.4 12.8 - - + +
345A VAL* 3.6 28.9 - - + -
348A LEU* 3.8 15.0 - - + -
371A ALA* 5.9 0.2 - - + -
375A LEU* 4.3 9.6 - - + -
378A LEU* 3.8 17.0 - - + -
397A MET* 3.6 33.9 - - + -
545A SER* 2.9 33.9 + - - +
546A ALA* 3.6 4.7 - - - +
548A ALA* 1.3 76.9 - - - +
550A ALA* 1.3 55.8 + - - +
552A LEU* 3.5 6.3 + - + +
553A ASP* 3.1 27.0 + - - +
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Residues in contact with ALA 550 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A MET* 3.8 36.5 - - + +
303A GLY* 4.0 3.5 - - - -
306A MET* 3.7 23.6 - - + -
349A GLU* 5.2 3.1 - - - +
546A ALA 2.9 17.7 + - - +
547A SER* 3.8 0.9 - - - +
549A LEU* 1.3 74.8 - - - +
551A GLU* 1.3 59.8 + - - +
553A ASP* 3.2 8.8 + - - +
554A VAL* 3.0 30.1 + - - +
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Residues in contact with GLU 551 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A MET* 3.6 14.2 - - + +
310A TRP* 3.9 24.9 - - + -
324A ARG* 4.9 7.1 + - - +
393A LEU* 3.9 22.2 - - + +
396A LYS* 4.3 12.3 + - - -
547A SER* 3.1 17.7 + - - +
548A ALA 3.4 3.8 + - - +
550A ALA* 1.3 72.9 - - - +
552A LEU* 1.3 66.2 + - - +
554A VAL* 3.1 2.5 + - - +
555A LEU* 2.9 50.0 + - + +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A THR* 5.8 0.4 - - + -
331A LEU* 4.7 14.1 - - + -
338A LEU* 6.1 0.2 - - + -
342A LEU* 4.4 13.9 - - + -
378A LEU* 5.7 1.1 - - + -
382A LEU* 4.1 31.6 - - + -
390A VAL* 5.3 3.1 - - + +
393A LEU* 3.9 36.7 - - + +
397A MET* 4.1 25.8 - - + -
548A ALA 2.8 24.4 + - - +
549A LEU* 3.6 10.1 - - + +
551A GLU* 1.3 75.8 - - - +
553A ASP* 1.3 57.3 + - - +
555A LEU* 4.2 2.2 - - - +
556A VAL* 2.8 40.3 + - + +
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Residues in contact with ASP 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.3 16.2 - - - -
299A VAL* 3.1 29.4 + - - +
300A THR* 2.9 45.1 + - + +
303A GLY* 3.5 3.2 - - - -
339A GLN* 5.1 1.9 - - - +
342A LEU* 4.0 15.6 - - + +
549A LEU 3.1 14.3 + - - +
550A ALA 3.2 9.6 + - - +
552A LEU* 1.3 75.5 - - - +
554A VAL* 1.3 62.9 + - - +
556A VAL* 4.1 0.7 - - - +
557A ASN* 3.0 23.2 + - - +
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Residues in contact with VAL 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 4.4 7.0 - - - -
303A GLY 3.4 23.8 - - - +
306A MET* 3.8 14.8 - - + -
307A LEU* 3.8 26.0 - - + +
310A TRP* 3.5 35.9 - - + -
550A ALA 3.0 18.3 + - - +
551A GLU* 3.1 8.7 + - - +
553A ASP* 1.3 78.7 - - - +
555A LEU* 1.3 57.7 + - - +
557A ASN* 3.4 2.8 - - - +
558A LEU* 2.8 38.1 + - + +
----------------------------------------------------------
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Residues in contact with LEU 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A TRP* 3.6 29.2 - - + -
324A ARG* 4.2 23.1 - - + +
327A THR* 3.8 32.1 - - + +
328A ILE* 4.0 19.6 - - + +
331A LEU* 4.9 3.6 - - + -
393A LEU* 4.0 14.8 - - + -
551A GLU* 2.9 40.6 + - + +
552A LEU* 4.2 2.7 - - - +
554A VAL* 1.3 72.7 - - - +
556A VAL* 1.3 66.9 + - - +
558A LEU* 3.2 6.2 + - + +
559A ALA* 2.9 24.8 + - - +
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Residues in contact with VAL 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.8 25.5 - - + +
335A THR* 3.8 21.7 + - - +
338A LEU* 4.0 22.0 - - + -
339A GLN* 3.6 30.7 - - + +
342A LEU* 4.2 13.0 - - + -
552A LEU* 2.8 29.0 + - + +
553A ASP* 4.1 2.5 - - - +
555A LEU* 1.3 71.8 - - - +
557A ASN* 1.3 63.2 + - - +
559A ALA* 3.2 9.0 + - - +
560A GLU* 3.1 18.2 + - - +
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Residues in contact with ASN 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU 2.9 20.3 + - - +
297A CYS* 2.9 46.5 + - - +
298A THR* 3.8 17.7 - - + +
307A LEU* 3.9 12.5 - - - +
339A GLN* 4.0 10.5 + - - +
553A ASP 3.0 19.3 + - - +
554A VAL 3.4 4.4 - - - +
556A VAL* 1.3 77.9 - - - +
558A LEU* 1.3 62.4 + - - +
560A GLU* 3.2 5.7 + - - +
561A ARG* 3.0 31.7 + - - +
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Residues in contact with LEU 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.8 20.4 - - + +
307A LEU* 4.3 13.0 - - + -
310A TRP* 4.4 12.6 - - + -
328A ILE* 3.9 27.8 - - + +
554A VAL* 2.8 40.5 + - + +
555A LEU* 3.2 5.6 + - + +
557A ASN* 1.3 82.3 - - - +
559A ALA* 1.3 56.4 + - - +
561A ARG* 3.5 5.1 + - + +
562A ALA* 3.0 29.8 + - - +
636A ILE* 4.4 13.0 - - + +
638A SER* 4.0 29.2 + - - +
639A TYR 5.7 0.9 + - - +
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Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.3 36.9 - - + +
331A LEU* 4.5 5.2 - - + -
332A GLN* 3.2 43.3 + - - +
335A THR* 4.5 1.8 - - - +
555A LEU 2.9 13.1 + - - +
556A VAL* 3.4 12.8 - - - +
557A ASN 3.2 0.2 - - - -
558A LEU* 1.3 76.0 - - - +
560A GLU* 1.3 63.2 + - - +
562A ALA 3.5 0.2 + - - -
563A TYR 3.2 5.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A CYS* 4.4 4.7 - - - +
332A GLN* 5.6 0.7 - - - -
335A THR* 3.7 34.7 + - + +
339A GLN* 4.8 10.0 + - - +
556A VAL 3.1 9.5 + - - +
557A ASN* 3.2 13.2 + - - +
559A ALA* 1.3 73.8 - - - +
561A ARG* 1.3 102.0 + - - +
563A TYR* 3.4 6.9 + - + +
564A THR* 2.6 60.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 3.2 27.0 + - - +
295A LEU* 3.6 33.9 - - + +
297A CYS* 3.8 18.7 - - - -
557A ASN* 3.0 28.7 + - - +
558A LEU* 3.8 7.6 - - + +
560A GLU* 1.3 115.6 + - - +
562A ALA* 1.3 56.0 + - - +
564A THR* 4.3 8.9 - - - +
565A LEU* 2.7 74.3 + - + +
567A TYR* 4.6 3.4 - - + -
590A GLN* 5.9 0.4 - - - -
----------------------------------------------------------
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Residues in contact with ALA 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 4.5 1.1 - - + -
332A GLN* 3.6 17.3 - - - +
558A LEU 3.0 18.0 + - - +
559A ALA* 3.7 2.0 - - - +
561A ARG* 1.3 77.3 - - - +
563A TYR* 1.3 60.3 + - - +
566A ASN* 3.3 1.7 + - - -
567A TYR* 2.7 44.5 + - + +
638A SER* 6.1 0.2 - - - +
639A TYR* 3.6 34.5 - - + -
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Residues in contact with TYR 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A GLN* 3.5 30.2 - - + +
559A ALA 3.2 13.8 + - - +
560A GLU* 3.7 5.8 - - + +
561A ARG 3.2 0.4 - - - -
562A ALA* 1.3 77.3 - - - +
564A THR* 1.3 78.1 + - - +
566A ASN* 3.3 11.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLU* 2.6 42.8 + - - +
561A ARG* 4.0 7.2 - - - +
563A TYR* 1.3 89.8 - - - +
565A LEU* 1.3 75.3 + - + +
566A ASN* 3.2 2.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 3.8 16.8 - - + +
295A LEU* 4.8 0.9 - - + -
561A ARG* 2.7 66.8 + - + +
564A THR* 1.3 84.3 - - + +
566A ASN* 1.3 61.6 + - - +
567A TYR* 3.5 33.1 - - + +
584A ARG* 2.9 24.1 + - - -
589A GLU* 4.3 2.0 - - - +
590A GLN* 3.6 26.6 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il