Contacts of the helix formed by residues 516 - 539 (chain A) in PDB entry 6R7X
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 PRO 516 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A MET 4.8 2.9 - - - +
226A ALA* 5.2 0.9 - - - -
229A GLY* 3.4 27.7 - - - +
232A TYR* 4.5 6.1 - - + -
233A TYR* 3.7 24.9 - - + +
238A GLU* 5.8 2.7 - - - +
246A PHE* 3.6 26.5 - - + -
512A SER* 3.5 22.2 - - - +
513A CYS 4.3 4.0 - - - +
514A VAL 4.1 3.6 - - - +
515A TYR* 1.3 83.9 - - - +
517A LEU* 1.3 59.4 + - - +
518A ALA 3.1 2.9 - - - -
519A ALA* 3.0 30.8 + - + +
520A ALA 4.1 0.9 + - - -
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY 4.7 4.7 - - - -
230A LEU* 3.7 29.4 - - + +
233A TYR* 3.7 35.4 - - + +
234A LEU* 5.9 1.6 - - + -
515A TYR* 3.3 27.8 - - + +
516A PRO* 1.3 80.9 - - - +
518A ALA* 1.3 56.2 + - - +
520A ALA* 2.9 36.8 + - + +
521A PHE* 3.3 27.0 + - + -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A LEU* 4.6 6.7 - - + +
437A LEU* 3.6 22.0 - - + +
507A TYR 4.3 14.6 - - - +
508A VAL* 3.8 6.0 - - - +
515A TYR* 3.7 32.5 + - + +
516A PRO 3.1 0.8 - - - -
517A LEU* 1.3 77.0 - - - +
519A ALA* 1.3 57.7 + - - +
521A PHE* 3.0 30.6 + - + +
522A ALA 3.1 9.2 + - - -
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 4.8 3.2 - - + +
225A MET* 4.2 23.1 - - + +
226A ALA* 4.1 10.3 - - + +
508A VAL* 3.7 31.8 + - + +
512A SER* 6.3 1.3 - - - -
515A TYR 4.9 0.2 + - - -
516A PRO* 3.0 16.7 + - + +
518A ALA* 1.3 78.0 - - - +
520A ALA* 1.3 61.5 + - - +
522A ALA* 3.0 15.1 + - - +
523A VAL* 3.3 14.7 + - - +
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Residues in contact with ALA 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA* 3.8 24.2 - - + +
230A LEU* 5.5 7.4 - - + -
516A PRO 4.1 0.8 + - - -
517A LEU* 2.9 26.6 + - + +
519A ALA* 1.3 77.2 - - - +
521A PHE* 1.3 61.3 + - + +
523A VAL* 3.0 19.2 + - - +
524A LEU* 3.0 23.9 + - + +
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Residues in contact with PHE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA* 4.2 9.2 - - + -
437A LEU* 3.8 15.7 - - + -
438A ILE* 3.8 37.7 - - + -
441A GLN* 2.9 25.5 - - - +
515A TYR* 3.8 21.8 - + - -
517A LEU* 3.3 28.7 + - + -
518A ALA* 3.0 25.8 + - + +
520A ALA* 1.3 79.8 - - + +
522A ALA* 1.3 58.6 + - - +
524A LEU* 4.7 14.7 - - + +
525A ASN* 3.7 7.6 + - - +
713A UMQ 5.4 4.9 - - - -
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Residues in contact with ALA 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.7 16.2 - - + -
437A LEU* 4.8 0.6 - - + +
441A GLN* 4.0 9.6 - - - +
504A GLN* 3.7 15.9 - - + +
508A VAL* 3.7 24.2 - - + -
518A ALA 3.1 3.6 + - - -
519A ALA 3.0 11.5 + - - +
521A PHE* 1.3 78.6 - - - +
523A VAL* 1.3 59.2 + - - +
525A ASN* 3.0 5.2 + - - +
526A ASN* 2.8 31.4 + - - +
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A THR* 4.5 7.2 - - + +
222A LEU* 3.8 37.5 - - + +
223A ILE* 4.1 15.9 - - + +
226A ALA* 4.2 8.5 - - + -
519A ALA 3.5 13.7 - - - +
520A ALA* 3.0 8.1 + - - +
522A ALA* 1.3 74.7 - - - +
524A LEU* 1.3 59.0 + - + +
526A ASN* 3.0 9.3 + - - +
527A PHE* 3.0 59.3 + - + -
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ALA* 3.0 22.3 + - + +
521A PHE* 5.0 15.0 - - + +
523A VAL* 1.3 74.8 - - + +
525A ASN* 1.3 58.8 + - - +
527A PHE* 4.3 18.7 - - + +
528A THR* 3.5 19.1 + - - +
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Residues in contact with ASN 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN* 3.3 48.3 - - - +
445A GLN* 4.0 15.1 - - - +
500A GLU* 3.8 2.2 + - - +
504A GLN* 3.1 26.1 - - - +
521A PHE 3.7 3.3 + - - +
522A ALA 3.0 10.9 + - - +
524A LEU* 1.3 77.8 - - - +
526A ASN* 1.3 62.0 + - - +
527A PHE 3.3 0.2 - - - -
528A THR* 2.6 28.7 + - - -
529A GLU* 2.9 26.3 + - - +
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Residues in contact with ASN 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LEU* 4.1 15.4 - - + +
218A PHE* 4.0 23.2 + - - -
219A THR* 3.3 35.5 + - + +
222A LEU* 4.7 4.0 - - - +
501A LEU* 4.1 0.9 - - - +
504A GLN* 2.9 33.2 + - - +
522A ALA 2.8 17.9 + - - +
523A VAL* 3.0 5.0 + - - +
525A ASN* 1.3 77.1 + - - +
527A PHE* 1.3 60.1 + - - +
529A GLU* 3.0 6.8 + - - +
530A VAL* 2.9 36.9 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR* 5.0 4.2 + - - +
192A LEU* 4.4 23.3 - - + -
219A THR* 3.6 24.0 - - + -
220A PHE* 4.5 11.9 - + - -
223A ILE* 4.5 7.9 - - + -
523A VAL* 3.0 38.1 + - + +
524A LEU* 4.5 20.6 - - + +
525A ASN 3.3 0.2 - - - -
526A ASN* 1.3 75.7 - - - +
528A THR* 1.3 58.8 + - + +
530A VAL* 4.6 4.9 - - + +
531A ASN* 3.7 21.8 + - - +
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Residues in contact with THR 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A GLN* 2.6 31.0 + - - +
450A PHE* 6.2 0.2 - - - -
524A LEU 3.5 18.8 - - - +
525A ASN* 2.6 16.0 + - - -
527A PHE* 1.3 79.6 - - + +
529A GLU* 1.3 49.8 + - - +
530A VAL 3.3 0.4 - - - -
531A ASN* 3.0 9.2 + - - +
532A SER* 2.6 33.6 + - - -
707A UMQ 4.0 31.2 - - + +
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR* 4.6 1.3 - - - +
215A LEU* 4.2 12.8 - - + -
445A GLN* 2.6 24.8 - - - +
448A GLU* 2.6 16.6 - - - +
500A GLU* 2.5 24.9 - - - +
501A LEU* 6.0 1.6 - - + -
504A GLN* 5.5 0.9 - - - +
525A ASN* 2.9 19.8 + - - +
526A ASN* 3.0 12.7 + - - +
528A THR* 1.3 75.6 + - - +
530A VAL* 1.3 61.9 + - - +
532A SER* 4.0 1.3 - - - +
533A ASP* 2.8 51.8 + - - +
701A CA 2.5 9.0 - - - -
702A CA 2.5 23.6 - - - -
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Residues in contact with VAL 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TRP* 4.5 4.0 + - - +
188A THR* 4.7 15.0 - - + +
195A GLN* 3.4 35.8 + - + +
212A PHE* 4.1 1.8 - - - -
215A LEU* 3.7 31.4 - - + +
216A GLU* 5.0 2.7 - - - +
219A THR* 4.1 13.2 - - + +
526A ASN 2.9 19.6 + - - +
527A PHE* 4.8 6.1 - - + +
529A GLU* 1.3 76.3 - - - +
531A ASN* 1.3 67.0 + - - +
534A ALA* 3.3 18.7 + - - +
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Residues in contact with ASN 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TRP 4.8 0.4 - - - +
187A TYR* 3.9 13.4 - - + +
188A THR* 3.4 42.5 + - - -
189A ARG* 4.0 19.8 - - - +
527A PHE 3.7 16.2 + - - +
528A THR* 3.0 7.8 + - - +
530A VAL* 1.3 82.5 - - - +
532A SER* 1.3 58.8 + - - +
534A ALA* 3.0 9.3 + - - +
535A LEU* 2.9 25.8 + - - +
707A UMQ 4.0 30.7 - - + +
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Residues in contact with SER 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLN* 3.3 32.3 + - - -
448A GLU* 4.7 0.2 + - - -
449A SER* 2.7 29.1 + - - -
450A PHE* 4.4 12.3 - - - -
528A THR 2.6 18.9 + - - -
529A GLU* 3.0 2.4 + - - -
531A ASN* 1.3 72.3 - - - +
533A ASP* 1.3 59.9 + - - +
535A LEU* 3.0 11.7 + - - +
536A LYS* 2.9 24.1 + - - +
707A UMQ 4.9 4.7 - - - -
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Residues in contact with ASP 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A TYR* 2.3 33.2 + - + +
212A PHE* 3.7 19.5 - - + -
215A LEU* 4.2 0.8 - - + +
448A GLU* 2.7 30.0 - - - +
497A ASP* 4.1 0.4 - - - -
529A GLU* 2.8 28.7 + - - +
532A SER* 1.3 74.4 + - - +
534A ALA* 1.3 57.8 + - - +
536A LYS* 2.9 20.7 + - - +
537A MET* 2.9 30.9 + - + +
702A CA 2.5 10.6 - - - -
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Residues in contact with ALA 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TRP* 3.6 31.9 - - + +
187A TYR* 3.7 18.4 - - + -
212A PHE* 3.6 10.9 - - + -
530A VAL 3.3 15.3 + - - +
531A ASN 3.0 14.1 + - - +
533A ASP* 1.3 78.6 - - - +
535A LEU* 1.3 59.4 + - - +
537A MET* 3.0 11.4 + - - +
538A CYS* 3.0 19.6 + - - -
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A TYR* 3.4 18.5 + - - +
449A SER* 4.7 3.6 - - - +
450A PHE* 4.3 21.3 - - + -
453A TYR* 3.8 55.4 - - + -
531A ASN 2.9 11.1 + - - +
532A SER 3.0 8.5 + - - +
534A ALA* 1.3 73.7 - - - +
536A LYS* 1.3 59.2 + - - +
538A CYS 3.0 14.8 + - - +
539A ARG* 3.0 24.2 + - + -
540A VAL* 3.5 7.5 - - + +
707A UMQ 3.9 34.5 - - + +
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Residues in contact with LYS 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A GLU* 2.5 46.8 + - + +
449A SER* 4.1 6.1 - - - -
491A TYR* 4.3 13.2 - - - -
497A ASP* 2.4 40.3 + - - -
532A SER 2.9 12.7 + - - +
533A ASP* 2.9 21.7 + - - +
535A LEU* 1.3 76.5 - - - +
537A MET* 1.3 62.2 + - - +
540A VAL* 3.9 14.1 - - + -
541A PHE* 3.5 50.8 + - + +
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 4.0 9.7 + - - -
186A TRP* 4.3 2.9 - - + -
204A PHE* 3.3 36.1 - - + -
208A ILE* 3.9 22.9 - - + -
212A PHE* 3.9 22.7 - - + -
491A TYR* 3.6 37.5 - - + -
533A ASP* 2.9 18.1 + - + +
534A ALA 3.0 7.1 + - - +
536A LYS* 1.3 85.5 - - - +
538A CYS* 1.3 60.0 + - - +
540A VAL 5.0 0.2 - - - -
541A PHE* 4.8 5.7 - - + +
542A LYS 5.0 3.6 - - - +
544A PRO* 3.8 33.9 - - + -
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Residues in contact with CYS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A HIS* 4.4 7.3 + - - -
179A LEU* 3.5 35.3 - - - +
183A GLU* 3.4 36.8 - - - +
186A TRP* 3.5 27.1 - - - -
187A TYR* 3.6 11.2 - - - +
204A PHE* 4.8 0.7 - - - -
488A MET* 5.7 1.9 - - - +
534A ALA 3.0 18.4 + - - +
535A LEU 3.0 2.3 + - - +
537A MET* 1.3 82.5 - - - +
539A ARG* 1.3 67.4 + - + +
540A VAL 3.7 0.9 - - - -
541A PHE 4.9 2.6 - - - +
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Residues in contact with ARG 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A SER* 5.2 7.7 + - - +
179A LEU* 4.0 25.2 - - - +
180A LYS* 4.6 8.5 - - - +
183A GLU* 2.8 33.0 + - - +
453A TYR* 3.8 22.4 - - + -
456A GLN* 3.3 21.7 - - - +
488A MET* 4.5 9.8 - - - +
535A LEU* 3.0 16.9 + - + -
538A CYS* 1.3 80.0 + - + +
540A VAL* 1.3 62.1 + - - +
541A PHE 5.1 0.2 - - - -
707A UMQ 3.4 76.7 + - - +
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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