Contacts of the helix formed by residues 647 - 669 (chain A) in PDB entry 6T2C
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 SER 647 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ARG* 4.4 7.4 - - - -
645A TYR 3.5 1.4 + - - -
646A ALA* 1.3 75.2 - - - +
648A ALA* 1.3 65.0 + - - +
649A GLN* 3.8 16.7 + - - +
650A LEU* 3.5 15.5 + - - +
651A GLU* 3.3 20.2 + - - +
692A ASP* 2.8 29.5 + - - -
27B ASP 5.5 3.6 - - - -
29B PRO* 4.7 3.8 - - - -
5V G 4.8 15.3 - - - -
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Residues in contact with ALA 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A SER* 1.3 75.6 - - - +
649A GLN* 1.3 61.0 + - + +
651A GLU* 3.2 6.7 + - - +
652A GLY* 3.0 24.6 + - - -
29B PRO* 3.7 31.6 - - + +
235B LYS 4.3 2.0 - - - +
236B LEU* 3.9 33.8 - - + +
238B ARG* 4.1 3.4 - - - +
5V G 5.4 8.4 + - - +
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Residues in contact with GLN 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A PRO* 5.4 3.6 - - - +
647A SER* 3.3 9.5 + - - +
648A ALA* 1.3 77.2 - - + +
650A LEU* 1.3 56.4 + - - +
652A GLY 3.9 0.8 - - - +
653A PHE* 2.9 30.8 + - - +
688A CYS* 3.4 19.5 - - - +
689A ILE* 4.5 0.2 - - - -
690A ILE* 3.1 39.0 + - + +
691A ASN* 3.2 28.7 + - - -
692A ASP* 3.8 15.4 + - - +
695A VAL* 3.9 11.2 - - + +
236B LEU* 4.1 19.1 - - + -
5V G 4.8 13.7 - - - +
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ASN* 3.7 29.2 - - - +
645A TYR 4.5 8.1 - - - +
646A ALA* 4.5 4.5 - - + -
647A SER* 3.5 15.7 + - - +
648A ALA 3.2 0.6 - - - -
649A GLN* 1.3 76.4 - - - +
651A GLU* 1.3 61.3 + - + +
653A PHE* 4.5 7.9 - - + -
654A SER* 3.0 47.5 + - - +
694A TRP* 3.6 35.2 - - + +
695A VAL* 3.5 19.0 - - + +
698A ASN* 4.8 11.0 - - - +
23B PRO* 4.1 16.2 - - + -
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Residues in contact with GLU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A ALA* 5.4 4.5 - - - +
647A SER 3.3 20.2 + - - +
648A ALA* 3.2 11.4 + - - +
650A LEU* 1.3 79.0 - - - +
652A GLY* 1.3 62.1 + - - +
654A SER* 4.1 0.5 - - - -
655A ALA* 3.0 28.9 + - - +
23B PRO* 3.7 20.8 - - - +
24B TYR* 4.2 6.4 - - - -
27B ASP 4.7 7.3 - - - +
29B PRO* 4.3 13.7 - - + +
233B ARG* 3.0 43.9 + - - -
234B GLY* 3.8 21.6 + - - +
235B LYS 4.5 4.9 - - - +
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Residues in contact with GLY 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ALA 3.0 13.3 + - - -
649A GLN 3.9 0.9 - - - -
651A GLU* 1.3 78.4 - - - +
653A PHE* 1.3 54.2 + - - +
655A ALA* 3.9 2.8 - - - -
656A GLU* 3.0 37.3 + - - +
688A CYS* 3.9 22.8 - - - -
234B GLY 4.8 5.3 - - - -
236B LEU* 4.6 11.6 - - - +
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Residues in contact with PHE 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.1 7.6 - - + -
649A GLN 2.9 18.8 + - - +
650A LEU* 3.9 6.7 - - + +
652A GLY* 1.3 76.5 - - - +
654A SER* 1.3 67.4 + - - +
656A GLU* 3.4 2.3 + - - +
657A SER* 2.9 45.8 + - - -
685A ILE* 3.7 27.8 - - + +
688A CYS* 3.9 9.7 - - + +
689A ILE* 4.4 11.0 - - + -
695A VAL* 4.1 16.2 - - + -
698A ASN* 3.6 34.1 - - + -
699A ALA* 3.7 32.5 - - + -
702A PHE* 4.5 8.7 - - + -
6B MET* 4.7 6.7 - - + -
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LEU* 3.0 28.1 + - - +
651A GLU 4.2 1.1 - - - -
653A PHE* 1.3 81.1 - - - +
655A ALA* 1.3 63.3 + - - +
657A SER* 3.3 6.9 + - - -
658A ARG* 3.1 31.3 + - - +
698A ASN* 5.4 1.6 + - - -
21B THR* 3.9 13.9 - - - +
23B PRO* 3.7 31.5 - - - +
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Residues in contact with ALA 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A GLU 3.0 20.6 + - - +
652A GLY 4.1 1.8 - - - +
654A SER* 1.3 77.2 - - - +
656A GLU* 1.3 68.7 + - + +
658A ARG* 3.8 30.8 + - - +
659A LYS* 4.4 12.6 + - - +
234B GLY* 3.9 25.6 - - - +
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Residues in contact with GLU 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A GLY* 3.0 21.6 + - - +
653A PHE 4.3 0.2 - - - +
655A ALA* 1.3 87.3 - - + +
657A SER* 1.3 59.4 + - - +
658A ARG 3.4 1.3 - - - -
659A LYS* 4.1 13.9 + - - +
660A LEU 4.6 1.0 + - - -
681A LEU* 3.5 34.5 - - - +
684A ALA* 3.9 23.4 - - + +
685A ILE* 3.3 30.6 - - + +
688A CYS* 5.4 0.9 - - - -
234B GLY 5.5 2.9 - - - +
481B LYS* 3.4 40.3 + - - +
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Residues in contact with SER 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 5.8 0.2 - - - -
653A PHE* 2.9 40.6 + - - -
654A SER* 3.3 8.2 + - - -
656A GLU* 1.3 73.8 - - - +
658A ARG* 1.3 66.2 + - - +
659A LYS 3.1 2.9 - - - -
660A LEU* 3.1 6.2 + - - +
661A LEU* 3.1 28.6 + - - +
685A ILE* 3.8 16.6 - - - -
702A PHE* 4.8 14.8 - - - -
6B MET* 5.8 2.4 - - - +
21B THR* 6.1 0.9 - - - -
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Residues in contact with ARG 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A SER* 3.1 11.5 + - - +
655A ALA* 3.8 33.2 + - - +
656A GLU 3.4 0.6 - - - -
657A SER* 1.3 77.6 + - - +
659A LYS* 1.3 64.1 + - + +
661A LEU* 3.3 10.1 + - - +
662A LEU* 3.0 34.1 + - + +
18B ILE* 3.8 17.5 - - + -
21B THR* 3.2 36.8 + - - +
22B PHE* 3.6 33.0 - - - +
23B PRO* 5.5 1.2 - - - +
24B TYR* 4.9 4.6 + - - -
491B GLU* 5.8 3.2 + - - -
494B SER* 5.1 4.6 + - - -
496B PHE* 4.0 26.6 - - - -
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Residues in contact with LYS 659 (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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655A ALA 4.4 13.4 + - - +
656A GLU* 4.1 16.7 + - - +
657A SER 3.1 1.0 - - - -
658A ARG* 1.3 82.9 - - + +
660A LEU* 1.3 59.7 + - - +
662A LEU* 3.4 7.3 + - + +
663A LEU* 2.9 34.7 + - - +
681A LEU* 4.3 23.3 - - + -
303B THR* 6.2 0.8 - - - +
305B ASP* 4.8 9.6 + - - -
481B LYS* 3.9 46.8 + - - +
483B TYR* 4.0 26.2 - - + +
491B GLU* 4.6 13.3 + - - +
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Residues in contact with LEU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 5.0 8.2 - - + -
265A ILE* 4.7 11.7 - - + -
268A LEU* 5.8 0.2 - - + -
656A GLU 4.6 0.2 - - - +
657A SER* 3.1 12.2 + - - +
659A LYS* 1.3 75.2 - - - +
661A LEU* 1.3 65.9 + - - +
663A LEU* 3.4 8.8 + - + +
664A ILE* 3.0 31.7 + - + +
678A LEU* 5.2 4.7 - - + -
681A LEU* 3.7 29.8 - - + +
682A TYR* 4.1 31.2 - - + +
685A ILE* 3.7 24.5 - - + -
702A PHE* 3.6 34.5 - - + -
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Residues in contact with LEU 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A SER* 3.1 19.7 + - - +
658A ARG* 3.6 10.8 - - - +
659A LYS 3.3 0.2 - - - -
660A LEU* 1.3 76.2 - - - +
662A LEU* 1.3 58.1 + - - +
664A ILE* 3.4 5.1 + - - +
665A GLN* 3.0 27.0 + - - +
702A PHE* 3.6 27.6 - - + -
705A PHE* 3.6 26.9 - - + -
6B MET* 5.4 9.6 - - + -
9B PHE* 3.9 28.7 - - + -
14B VAL* 3.9 20.8 - - + +
18B ILE* 5.1 0.9 - - + -
21B THR* 3.9 19.5 - - + -
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Residues in contact with LEU 662 (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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658A ARG* 3.0 30.4 + - + +
659A LYS* 4.0 5.4 - - + +
660A LEU 3.3 0.2 - - - -
661A LEU* 1.3 73.3 - - - +
663A LEU* 1.3 60.9 + - - +
665A GLN* 3.5 3.7 + - - +
666A ALA* 2.9 28.1 + - - +
14B VAL* 4.3 14.6 - - + -
15B GLN* 3.5 38.2 + - + +
18B ILE* 4.6 8.3 - - + -
483B TYR* 3.4 31.9 - - + +
491B GLU* 4.7 4.3 - - + +
496B PHE* 3.6 29.6 - - + -
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.8 24.0 - - + -
659A LYS 2.9 25.1 + - - +
660A LEU* 3.8 7.6 - - + +
662A LEU* 1.3 75.6 - - - +
664A ILE* 1.3 60.0 + - - +
666A ALA* 3.2 5.8 + - + +
667A PHE* 2.9 26.7 + - - +
673A PRO* 3.9 25.9 - - + +
674A GLY 4.6 2.2 - - - +
675A THR* 3.7 26.5 - - + -
678A LEU* 4.6 7.4 - - + -
681A LEU* 4.4 15.0 - - + -
483B TYR* 3.7 37.2 - - + -
484B ILE 5.3 0.2 - - - +
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Residues in contact with ILE 664 (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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260A PHE* 4.0 20.6 - - + -
262A PRO* 4.4 11.0 - - + -
265A ILE* 5.0 2.5 - - + -
660A LEU* 3.0 20.8 + - + +
661A LEU* 3.4 4.7 + - - +
663A LEU* 1.3 75.0 - - - +
665A GLN* 1.3 64.0 + - - +
667A PHE* 3.1 5.8 + - - +
668A ARG* 3.0 38.1 + - + +
702A PHE* 4.6 10.3 - - + -
705A PHE* 4.3 26.2 - - + -
706A LEU* 3.8 28.9 - - + -
709A VAL* 4.3 17.5 - - + -
713A MET* 5.5 0.4 - - + -
14B VAL* 6.2 0.9 - - + -
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Residues in contact with GLN 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU 3.0 17.0 + - - +
662A LEU* 3.7 5.6 - - - +
663A LEU 3.3 0.2 - - - -
664A ILE* 1.3 78.1 - - - +
666A ALA* 1.3 61.5 + - - +
668A ARG* 3.3 23.5 + - - +
669A ASP* 2.6 61.9 + - - +
13B PRO* 3.4 11.1 - - - +
14B VAL* 3.0 40.8 + - + +
15B GLN* 3.4 24.7 - - - +
489B THR* 6.2 0.2 - - + -
498B ARG* 3.3 15.6 - - - +
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Residues in contact with ALA 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU 2.9 17.8 + - - +
663A LEU* 3.2 6.7 + - + +
665A GLN* 1.3 74.9 - - - +
667A PHE* 1.3 64.2 + - - +
669A ASP* 3.8 2.2 + - - -
671A LEU* 3.3 35.2 + - + +
673A PRO* 4.0 14.9 - - + +
483B TYR* 6.2 0.2 - - + -
485B ASN* 3.4 31.9 - - + +
489B THR* 4.6 6.7 - - - +
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Residues in contact with PHE 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 3.9 12.6 - - + -
261A ASP* 4.4 7.0 - - - -
262A PRO* 3.5 40.8 - - + -
263A ARG* 3.5 28.9 - - - -
663A LEU 2.9 13.3 + - - +
664A ILE* 3.1 9.2 + - - +
666A ALA* 1.3 78.4 - - - +
668A ARG* 1.3 64.1 + - - +
670A ASN* 3.2 17.2 + - - -
672A ASP* 5.3 1.9 + - - -
673A PRO* 3.8 24.6 - - + +
713A MET* 3.8 30.5 - - + -
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Residues in contact with ARG 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ILE* 3.0 27.1 + - + +
665A GLN* 3.3 25.7 + - - +
667A PHE* 1.3 78.5 - - + +
669A ASP* 1.3 66.2 + - - +
670A ASN* 3.3 7.2 + - - -
705A PHE* 5.9 2.4 - - - -
709A VAL* 5.0 9.6 - - - +
712A SER* 5.5 6.6 + - - -
713A MET* 3.7 31.4 - - + -
9B PHE 3.3 23.7 + - - -
10B LEU* 4.3 24.0 + - - +
12B VAL 4.0 6.9 + - - -
13B PRO* 4.9 1.0 - - - +
14B VAL* 5.2 1.8 - - - +
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Residues in contact with ASP 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A GLN* 2.6 34.3 + - - +
666A ALA* 3.8 0.6 + - - -
667A PHE 3.2 1.6 - - - -
668A ARG* 1.3 81.5 - - - +
670A ASN* 1.3 69.0 + - - +
671A LEU* 3.3 23.3 + - + +
489B THR* 4.5 5.7 - - - +
498B ARG* 2.6 41.7 + - - +
499B TYR* 4.1 12.9 + - - +
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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