Contacts of the helix formed by residues 635 - 658 (chain A) in PDB entry 4EGA
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 THR 635 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A TYR* 1.3 76.4 - - - +
636A GLU* 1.3 59.6 + - - +
637A GLU* 3.5 9.0 + - - +
638A ASP* 2.7 42.0 + - - +
639A GLU* 2.9 28.4 + - - +
694A ARG* 3.5 15.6 + - - +
424B PRO* 3.7 20.6 - - + +
425B GLY* 3.6 33.9 - - - +
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Residues in contact with GLU 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A THR* 1.3 73.1 - - - +
637A GLU* 1.3 57.9 + - - +
639A GLU* 3.2 15.5 + - - +
640A SER* 2.8 29.6 + - - -
-1B SER* 4.9 4.2 - - - -
425B GLY* 5.8 0.8 - - - -
541B LYS* 4.4 16.9 - - - +
654B HIS* 2.8 42.5 + - - -
657B LEU* 3.8 37.9 - - + +
658B ILE* 4.1 22.3 - - + +
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Residues in contact with GLU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A THR* 3.2 8.7 + - - +
636A GLU* 1.3 73.6 - - - +
638A ASP* 1.3 68.6 + - - +
640A SER* 2.8 26.2 + - - +
641A LEU* 3.3 5.7 + - - +
678A TYR* 4.0 17.3 - - + -
681A ASP* 3.1 28.1 - - - +
682A MET* 3.4 31.5 - - + +
428B VAL* 5.7 3.3 - - - +
429B PRO* 6.0 0.2 - - - +
430B GLU* 5.0 6.8 + - - +
658B ILE* 4.0 27.3 - - + +
663B LYS* 4.2 13.9 + - - +
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Residues in contact with ASP 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A TYR* 3.5 11.2 - - + -
635A THR* 2.7 44.9 + - - +
637A GLU* 1.3 77.0 - - - +
639A GLU* 1.3 59.2 + - - +
641A LEU* 3.1 4.3 + - - +
642A ILE* 3.0 30.6 + - - +
678A TYR* 2.4 38.9 + - - -
694A ARG* 2.9 30.9 + - - -
697A THR* 3.8 2.9 - - - +
701A ILE* 3.7 17.3 - - + +
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Residues in contact with GLU 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A TYR* 3.9 34.0 - - + +
635A THR 2.9 14.6 + - - +
636A GLU* 3.5 23.9 + - - +
637A GLU 3.2 0.2 - - - -
638A ASP* 1.3 74.3 - - - +
640A SER* 1.3 65.2 + - - +
641A LEU 3.3 0.2 - - - -
642A ILE* 3.8 14.7 - - + +
643A GLN* 3.1 24.1 + - - +
654B HIS* 4.0 23.1 + - + +
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Residues in contact with SER 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU 2.8 13.5 + - - -
637A GLU* 2.8 21.8 + - - +
639A GLU* 1.3 77.1 - - - +
641A LEU* 1.3 63.4 + - - +
643A GLN* 3.5 4.6 + - - +
644A LEU* 3.3 25.5 + - - +
651B THR* 5.5 3.0 - - - +
654B HIS* 3.8 22.6 - - - +
655B TYR* 3.9 31.8 + - - -
658B ILE* 4.3 7.0 - - - +
663B LYS* 5.8 0.7 + - - -
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU 4.1 5.2 - - - +
638A ASP 3.1 9.4 + - - +
640A SER* 1.3 81.3 + - - +
642A ILE* 1.3 65.7 + - - +
644A LEU* 3.1 11.9 + - + +
645A ILE* 3.1 32.2 + - + +
671A VAL* 4.7 1.1 - - + +
674A ALA* 4.1 15.0 - - + +
675A ILE* 3.8 42.0 - - + +
678A TYR* 3.3 47.1 - - + -
701A ILE* 3.7 15.0 - - + -
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A TYR* 3.6 37.0 - - + -
638A ASP 3.0 19.3 + - - +
639A GLU* 3.8 12.8 - - + +
641A LEU* 1.3 76.1 - - - +
643A GLN* 1.3 56.8 + - - +
645A ILE* 3.2 10.4 + - - +
646A LYS* 2.8 52.3 + - + +
701A ILE* 3.4 32.3 - - + -
743A PHE* 3.8 27.4 - - + -
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Residues in contact with GLN 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLU 3.1 16.5 + - - +
640A SER 3.6 6.7 - - - +
641A LEU 3.2 0.2 - - - -
642A ILE* 1.3 76.4 - - - +
644A LEU* 1.3 58.7 + - - +
646A LYS* 3.2 17.7 + - - +
647A ASP* 2.8 62.9 + - - +
-4B GLY* 3.9 16.9 - - - -
-3B PRO* 3.4 18.9 + - - +
647B ASP 5.6 0.2 - - - +
650B GLY 4.6 4.6 + - - -
651B THR* 4.4 13.5 - - - +
654B HIS* 3.2 33.2 + - + -
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Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A SER 3.3 13.0 + - - +
641A LEU* 3.1 16.0 + - + +
643A GLN* 1.3 77.3 - - - +
645A ILE* 1.3 57.5 + - - +
647A ASP* 3.2 7.3 + - + +
648A LEU* 2.9 30.3 + - - +
670A ASP 5.6 0.2 - - - +
671A VAL* 4.0 20.5 - - + +
674A ALA* 3.7 30.3 - - + -
651B THR* 4.1 30.1 - - + +
655B TYR* 3.7 18.2 - - - +
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Residues in contact with ILE 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 3.1 35.5 + - + +
642A ILE* 3.5 8.7 - - - +
644A LEU* 1.3 76.3 - - - +
646A LYS* 1.3 63.2 + - - +
648A LEU* 3.3 8.9 + - + +
649A PRO* 3.2 18.9 - - - +
671A VAL* 4.2 18.2 - - + -
675A ILE* 4.8 0.9 - - + -
701A ILE* 4.1 14.1 - - + +
705A GLY* 3.7 36.3 - - - +
708A VAL* 4.2 22.7 - - + +
709A THR* 6.0 0.7 - - + -
741A PHE 5.4 0.2 - - - +
743A PHE* 4.0 22.9 - - + -
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Residues in contact with LYS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE* 2.8 40.1 + - + +
643A GLN* 3.5 18.8 + - - +
645A ILE* 1.3 74.2 - - - +
647A ASP* 1.3 62.1 + - - +
649A PRO* 3.1 17.8 - - - +
650A GLY 4.9 1.0 + - - -
741A PHE 5.4 1.2 - - - +
743A PHE* 3.8 32.3 - - + +
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Residues in contact with ASP 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN* 2.8 50.1 + - - +
644A LEU* 3.8 6.5 - - + +
646A LYS* 1.3 75.8 - - - +
648A LEU* 1.3 67.0 + - - +
649A PRO* 3.3 0.8 - - - -
650A GLY* 3.3 4.4 + - - +
651A THR* 3.3 20.8 + - - +
-4B GLY* 3.8 10.4 + - - -
643B GLN* 5.5 0.2 - - - +
647B ASP* 3.3 46.4 - - + +
651B THR* 4.0 5.4 + - - -
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LEU 2.9 13.4 + - - +
645A ILE* 3.5 10.3 - - + +
647A ASP* 1.3 77.0 - - - +
649A PRO* 1.3 65.6 - - + +
651A THR* 3.0 7.0 + - - -
652A ALA* 2.8 33.9 + - + +
667A ALA* 3.8 32.1 - - + +
668A VAL* 4.0 21.1 - - + -
671A VAL* 3.9 19.3 - - + -
708A VAL* 5.2 2.7 - - + -
709A THR* 3.7 35.2 - - + +
712A LEU* 4.0 11.7 - - + -
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Residues in contact with PRO 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ILE 3.2 9.6 - - - +
646A LYS 3.1 19.1 - - - +
647A ASP 3.3 1.1 - - - -
648A LEU* 1.3 91.9 - - + +
650A GLY* 1.3 55.9 + - - +
652A ALA* 4.1 0.3 - - - +
653A ASP* 2.8 32.5 + - - +
708A VAL* 4.1 6.5 - - + -
712A LEU* 3.5 26.6 - - + +
741A PHE* 3.5 50.9 - - + +
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Residues in contact with GLY 650 (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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646A LYS 4.9 0.8 + - - -
647A ASP 3.3 6.3 + - - -
648A LEU 3.3 0.6 - - - -
649A PRO* 1.3 80.2 - - - +
651A THR* 1.3 59.5 + - - +
653A ASP* 3.6 5.6 - - - +
654A HIS* 3.0 36.7 + - - -
643B GLN* 4.4 10.1 - - - -
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Residues in contact with THR 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ASP* 3.3 11.8 + - - +
648A LEU* 3.0 10.8 + - + -
650A GLY* 1.3 73.9 - - - +
652A ALA* 1.3 66.9 + - - +
654A HIS* 3.2 6.9 + - - +
655A TYR* 3.1 53.3 + - + -
667A ALA* 3.9 15.0 - - + -
640B SER 5.7 1.6 - - - +
643B GLN* 3.9 19.0 - - - +
644B LEU* 4.0 21.3 - - + +
647B ASP* 4.0 5.0 + - - -
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Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A LEU* 2.8 29.9 + - + +
651A THR* 1.3 74.2 - - - +
653A ASP* 1.3 63.6 + - - +
655A TYR* 3.2 10.5 + - - +
656A TYR* 3.0 36.1 + - + -
664A ALA* 4.6 7.2 - - + +
667A ALA* 5.1 0.7 - - + -
668A VAL* 4.4 9.9 - - + -
712A LEU* 3.7 29.2 - - + -
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 2.5 34.7 + - - +
276A LYS* 3.0 28.4 + - - +
649A PRO 2.8 21.7 + - - +
650A GLY* 3.6 8.2 - - - +
652A ALA* 1.3 78.0 - - - +
654A HIS* 1.3 68.9 + - - +
656A TYR* 3.3 2.3 + - - +
657A LEU* 3.0 44.0 + - - +
741A PHE* 5.5 3.1 - - + -
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Residues in contact with HIS 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLY* 3.0 22.6 + - - -
651A THR* 3.2 6.7 + - - +
653A ASP* 1.3 84.7 - - - +
655A TYR* 1.3 63.7 + - - +
657A LEU* 3.2 7.3 + - + +
658A ILE* 3.1 25.3 + - - +
636B GLU* 2.9 27.9 + - - +
639B GLU* 3.7 36.2 + - + +
640B SER* 3.7 19.3 - - - -
643B GLN* 3.2 32.4 + - + -
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Residues in contact with TYR 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A THR* 3.1 44.7 + - + -
652A ALA 3.6 5.6 - - - +
654A HIS* 1.3 75.7 - - - +
656A TYR* 1.3 57.8 + - - +
658A ILE* 3.0 20.4 + - + +
660A ASP 2.7 32.7 + - - +
663A LYS* 3.4 48.3 - - + +
664A ALA* 3.6 19.1 - - + +
667A ALA* 4.2 10.3 - - + -
637B GLU* 5.0 0.4 - - - -
640B SER* 3.4 27.1 + - - -
644B LEU* 3.5 26.0 - - + +
674B ALA* 5.5 1.0 - - - +
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Residues in contact with TYR 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.0 20.0 - - + -
269A ILE* 4.9 9.4 - - + +
272A TYR* 3.5 67.3 - + + -
273A HIS* 5.0 5.6 + - - -
652A ALA* 3.0 26.2 + - + -
653A ASP 3.6 2.5 - - - +
655A TYR* 1.3 75.8 - - - +
657A LEU* 1.3 59.9 + - - +
659A PRO* 3.1 22.0 - - - +
660A ASP 4.6 2.0 - - - +
661A ILE* 4.5 15.7 - - + -
664A ALA* 4.1 17.2 - - + +
712A LEU* 2.6 34.2 + - + -
715A PRO* 3.7 6.5 - - + +
716A ILE* 3.2 23.8 - - + +
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Residues in contact with LEU 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 5.7 0.7 - - + -
272A TYR* 5.1 1.3 - - + -
273A HIS* 3.6 32.3 - - + +
276A LYS* 4.2 11.2 - - - +
512A VAL* 5.8 1.2 - - - +
541A LYS* 3.4 17.7 - - - +
653A ASP* 3.0 44.0 + - - +
654A HIS* 3.6 4.3 - - + +
655A TYR 3.1 0.6 - - - -
656A TYR* 1.3 79.1 - - + +
658A ILE* 1.3 67.0 + - - +
659A PRO* 3.4 1.7 - - - +
636B GLU* 3.4 39.4 - - + +
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Residues in contact with ILE 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL* 3.4 25.6 - - + +
541A LYS* 2.6 27.9 + - - +
654A HIS 3.1 16.0 + - - +
655A TYR* 3.0 33.6 + - + +
657A LEU* 1.3 74.7 - - - +
659A PRO* 1.3 71.9 - - + +
660A ASP* 4.2 3.1 - - + -
663A LYS* 5.1 0.7 - - + -
636B GLU* 4.1 6.3 - - - -
637B GLU* 3.8 46.2 - - + +
640B SER* 4.0 3.8 - - - +
801B GOL 4.0 24.7 - - - +
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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