Contacts of the helix formed by residues 631 - 650 (chain S) in PDB entry 5IJ7
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 GLN 631 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A TRP* 3.4 42.0 - - + +
625S GLY 4.8 0.7 + - - +
626S PHE* 3.5 27.7 - - + +
627S ILE* 2.7 41.4 - - - +
628S ALA* 2.9 21.1 - - + +
629S ASP 3.1 1.0 - - - -
630S ASN* 1.3 88.0 - - - +
632S MET* 1.3 59.4 + - - +
633S ASN 3.4 1.6 - - - -
634S HIS* 3.6 11.4 + - + +
635S ALA* 3.0 29.0 + - - +
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Residues in contact with MET 632 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A PHE* 3.6 51.8 - - + -
617S TRP* 3.3 31.6 - - + -
626S PHE* 5.0 6.3 - - - -
628S ALA 4.2 2.9 - - - +
629S ASP 3.0 18.4 + - - +
631S GLN* 1.3 76.5 - - - +
633S ASN* 1.4 64.5 + - - +
635S ALA* 3.3 13.0 + - - +
636S CYS* 3.2 26.5 + - - -
663S MET* 3.7 21.3 - - + -
668S LEU* 3.3 28.7 - - + +
669S ILE* 3.7 4.9 - - + -
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Residues in contact with ASN 633 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629S ASP 5.0 2.2 + - - -
630S ASN* 4.3 13.1 + - - +
631S GLN 3.4 0.4 - - - -
632S MET* 1.4 74.7 - - - +
634S HIS* 1.3 61.7 + - - +
636S CYS* 3.3 13.9 + - - +
637S MET* 3.3 19.0 + - + +
668S LEU 4.1 7.9 + - - -
669S ILE* 3.4 10.5 - - - +
670S SER* 3.0 28.2 + - - +
673S SER* 2.8 28.1 + - - +
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Residues in contact with HIS 634 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626S PHE* 4.2 19.3 - + - -
630S ASN 5.0 2.2 + - - +
631S GLN* 3.6 12.9 + - + +
632S MET 3.4 0.4 - - - -
633S ASN* 1.3 76.5 - - - +
635S ALA* 1.4 53.7 + - - +
637S MET* 3.3 11.3 + - + +
638S LEU* 2.9 60.0 + - + +
641S GLU* 5.9 2.9 - - - -
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Residues in contact with ALA 635 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617S TRP* 3.9 15.0 - - + -
620S HIS* 2.8 23.5 + - - -
626S PHE* 3.6 39.7 - - + -
631S GLN 3.0 19.5 + - - +
632S MET* 3.4 13.9 - - - +
633S ASN 3.3 0.2 - - - -
634S HIS* 1.4 74.4 - - - +
636S CYS* 1.3 55.5 + - - +
638S LEU* 3.6 0.8 + - - -
639S PHE* 2.9 13.9 + - - +
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Residues in contact with CYS 636 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617S TRP* 3.9 5.4 - - - -
632S MET 3.2 16.6 + - - -
633S ASN* 3.3 8.0 + - - +
635S ALA* 1.3 73.2 - - - +
637S MET* 1.3 67.1 + - - +
639S PHE* 3.2 10.6 + - - +
640S VAL* 3.1 27.9 + - - +
656S PHE* 4.8 1.8 - - + -
659S HIS* 4.8 0.9 - - - -
660S LEU* 4.1 26.2 - - + -
663S MET* 3.5 32.1 - - - -
669S ILE* 3.6 17.0 - - + -
673S SER* 5.4 4.0 - - - -
677S ALA* 4.8 3.7 - - + +
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Residues in contact with MET 637 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633S ASN* 3.3 13.4 + - + +
634S HIS* 3.3 13.8 + - - +
636S CYS* 1.3 77.2 - - - +
638S LEU* 1.3 56.4 + - - +
640S VAL* 3.1 19.6 + - - +
641S GLU* 3.2 26.2 + - - +
673S SER* 4.3 9.0 - - - +
676S LYS* 3.8 36.8 - - + +
677S ALA* 3.8 25.1 - - - +
680S LYS* 3.7 34.8 + - + +
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Residues in contact with LEU 638 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620S HIS* 3.6 5.6 - - + -
624S HIS* 3.6 37.2 - - + +
626S PHE* 4.0 7.6 - - + -
634S HIS* 2.9 43.4 + - + +
635S ALA 3.9 3.6 - - - +
637S MET* 1.3 72.7 - - - +
639S PHE* 1.4 59.9 + - - +
641S GLU* 3.5 24.4 + - - +
642S ASN* 3.0 57.8 + - - +
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Residues in contact with PHE 639 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613S VAL* 4.5 6.5 - - + -
616S LEU* 3.4 43.3 - - + -
617S TRP* 3.7 30.3 - + + -
620S HIS* 3.6 24.2 - + - +
635S ALA 2.9 19.0 + - - +
636S CYS 3.3 7.0 - - - +
637S MET 3.2 0.4 - - - -
638S LEU* 1.4 76.9 - - - +
640S VAL* 1.4 54.5 + - - +
643S TYR* 2.7 55.6 + + + +
644S GLY 3.6 0.5 + - - -
647S ILE* 4.2 18.6 - - + -
656S PHE* 3.5 37.7 - + - -
659S HIS* 5.2 1.6 - - - -
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Residues in contact with VAL 640 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636S CYS 3.1 15.7 + - - +
637S MET* 3.1 8.2 + - - +
639S PHE* 1.4 72.9 - - - +
641S GLU* 1.3 61.7 + - - +
644S GLY* 2.8 32.3 + - - +
656S PHE* 3.6 25.1 - - + -
677S ALA* 3.7 22.4 - - + +
680S LYS* 3.9 10.5 - - + -
681S LEU* 3.7 41.1 - - + +
684S MET* 3.5 15.3 - - + +
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Residues in contact with GLU 641 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634S HIS* 5.9 2.9 - - - -
637S MET* 3.2 20.4 + - - +
638S LEU* 3.5 27.2 + - - +
640S VAL* 1.3 79.2 - - - +
642S ASN* 1.3 67.1 + - - +
644S GLY 4.5 0.9 + - - -
645S GLN 5.5 0.7 + - - -
680S LYS* 2.9 33.3 + - - +
684S MET* 4.1 17.1 - - - +
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Residues in contact with ASN 642 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620S HIS* 4.4 0.4 - - - +
624S HIS* 3.8 17.3 + - - -
638S LEU* 3.0 40.0 + - - +
641S GLU* 1.3 88.9 + - - +
643S TYR* 1.3 78.3 + - + +
644S GLY 3.7 0.4 - - - -
645S GLN* 5.2 3.5 + - - +
646S LYS* 5.5 3.1 - - - +
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Residues in contact with TYR 643 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616S LEU* 3.7 40.6 - - + -
619S LEU* 3.9 15.2 + - + +
620S HIS* 3.6 37.0 + - + -
623S LYS* 5.2 7.8 - - - +
624S HIS* 5.8 1.1 - + - -
639S PHE* 2.7 49.4 + + + +
642S ASN* 1.3 87.0 - - + +
644S GLY* 1.3 61.3 + - - +
645S GLN 3.3 3.1 - - - -
646S LYS* 3.0 19.4 + - + +
647S ILE* 3.0 24.3 + - + +
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Residues in contact with GLY 644 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639S PHE 3.6 1.8 + - - -
640S VAL* 2.8 29.2 + - - -
642S ASN 3.7 1.0 - - - -
643S TYR* 1.3 70.5 - - - +
645S GLN* 1.3 55.8 + - - +
647S ILE* 3.3 4.6 + - - +
648S ILE* 3.0 39.7 + - - +
681S LEU* 3.7 20.0 - - - -
684S MET* 3.9 5.2 - - - -
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Residues in contact with GLN 645 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641S GLU 5.5 1.0 + - - -
642S ASN 5.2 4.4 + - - +
643S TYR 3.3 0.4 - - - -
644S GLY* 1.3 73.8 - - - +
646S LYS* 1.3 62.6 + - + +
648S ILE* 4.1 7.7 - - - +
649S LYS* 3.0 67.0 + - + +
684S MET* 4.3 17.6 - - - +
687S LYS* 5.8 3.6 - - - +
688S LEU* 4.4 16.3 - - + +
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Residues in contact with LYS 646 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616S LEU* 4.3 19.5 - - + -
642S ASN 5.5 2.2 - - - +
643S TYR* 3.0 23.7 + - + +
645S GLN* 1.3 78.3 - - + +
647S ILE* 1.4 55.6 + - - +
649S LYS* 4.7 9.6 - - + +
650S LYS* 2.8 59.1 + - + +
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Residues in contact with ILE 647 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613S VAL* 4.3 13.2 - - + -
616S LEU* 3.8 22.7 - - + -
639S PHE* 4.2 24.7 - - + -
643S TYR 3.0 21.7 + - - +
644S GLY* 3.3 9.4 + - - +
646S LYS* 1.4 74.7 - - - +
648S ILE* 1.3 61.7 + - - +
650S LYS 3.8 0.3 - - - -
651S ASN 3.1 4.7 + - - -
652S LEU* 2.9 62.5 + - + +
653S CYS* 3.9 2.2 - - - +
656S PHE* 4.2 10.3 - - + -
681S LEU* 3.9 29.2 - - + -
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Residues in contact with ILE 648 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644S GLY 3.0 23.3 + - - +
645S GLN* 4.1 3.8 - - - +
647S ILE* 1.3 74.2 - - - +
649S LYS* 1.4 64.8 + - + +
651S ASN* 3.1 16.8 + - - +
653S CYS* 4.0 18.0 - - - -
681S LEU* 3.4 37.7 - - + +
684S MET* 4.1 10.3 - - + -
685S GLN* 3.7 45.3 + - + +
688S LEU* 3.8 20.9 - - + -
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Residues in contact with LYS 649 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645S GLN* 3.0 49.1 + - + +
646S LYS* 4.1 10.8 - - + +
648S ILE* 1.4 79.7 - - + +
650S LYS* 1.4 62.8 + - + +
651S ASN* 3.4 2.6 + - - +
688S LEU* 3.5 26.2 - - + +
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Residues in contact with LYS 650 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612S GLU* 3.7 34.5 + - + -
616S LEU* 5.0 5.2 - - + -
646S LYS* 2.8 48.5 + - + +
649S LYS* 1.4 72.8 - - + +
651S ASN* 1.4 69.3 + - - +
652S LEU* 3.7 23.1 - - + +
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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