Contacts of the helix formed by residues 673 - 693 (chain A) in PDB entry 5W6V
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 673 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A GLN* 5.0 6.9 + - - -
635A GLU* 3.2 34.2 - - - +
636A ILE* 5.8 4.0 - - - +
670A PRO* 4.0 16.4 - - + +
671A GLU 3.3 5.2 + - - +
672A GLY* 1.3 75.6 - - - +
674A LEU* 1.3 63.0 + - - +
675A PRO* 3.5 2.5 - - - -
676A GLN* 3.3 27.1 + - + +
677A ILE* 3.0 35.3 + - + +
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Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A VAL* 4.4 22.4 - - + -
670A PRO 3.8 4.3 + - - +
671A GLU* 4.7 7.9 - - + -
672A GLY 3.3 9.1 - - - +
673A GLN* 1.3 77.7 - - - +
675A PRO* 1.3 76.4 - - + +
677A ILE* 3.2 6.3 + - + +
678A LEU* 3.0 24.8 + - + +
704A VAL* 4.5 17.7 - - + -
764A TYR* 5.0 11.4 - - + -
766A LEU* 3.6 37.9 - - + +
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Residues in contact with PRO 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A GLY* 4.0 12.8 - - - +
673A GLN 3.6 3.1 - - - -
674A LEU* 1.3 100.6 - - + +
676A GLN* 1.3 60.2 + - + +
678A LEU* 4.1 4.7 - - + +
679A HIS* 3.0 31.2 + - - +
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Residues in contact with GLN 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 4.4 12.6 - - + +
672A GLY 5.2 3.6 - - - +
673A GLN* 3.3 34.7 + - + +
674A LEU 3.3 0.8 - - - -
675A PRO* 1.3 80.6 - - + +
677A ILE* 1.3 62.6 + - + +
679A HIS* 4.0 6.5 - - - +
680A TYR* 3.4 22.0 + - - +
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Residues in contact with ILE 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A GLU* 3.8 24.5 - - + -
636A ILE* 3.9 22.4 - - + -
666A ARG* 3.7 13.7 - - - +
669A VAL* 4.2 15.9 - - + -
670A PRO* 4.1 19.3 - - + -
673A GLN* 3.0 27.3 + - + +
674A LEU* 3.8 4.5 - - - +
676A GLN* 1.3 76.1 - - + +
678A LEU* 1.3 61.3 + - - +
680A TYR* 3.4 2.4 + - - +
681A GLU* 2.9 61.4 + - - +
702A TYR* 3.9 7.4 - - + +
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Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 4.5 22.0 - - + +
23A ALA* 6.0 1.6 - - + +
674A LEU* 3.0 18.3 + - + +
675A PRO* 4.1 5.2 - - + +
677A ILE* 1.3 79.3 - - - +
679A HIS* 1.3 59.0 + - - +
681A GLU 4.5 0.2 - - - +
682A LEU* 2.7 53.9 + - + +
702A TYR* 3.5 46.7 - - + -
766A LEU* 3.6 46.7 - - + +
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Residues in contact with HIS 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.7 28.7 + + + -
675A PRO 3.0 19.5 + - - +
676A GLN* 4.0 7.0 - - - +
677A ILE 3.3 0.2 - - - -
678A LEU* 1.3 78.9 - - - +
680A TYR* 1.3 67.6 + - + +
683A LEU* 3.3 50.1 + - + +
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Residues in contact with TYR 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.4 35.9 - - + -
637A ILE 3.7 17.7 - - - -
638A GLU* 2.8 36.2 + - + +
676A GLN 3.4 15.3 + - - +
677A ILE 3.8 0.2 - - - +
678A LEU 3.3 0.4 - - - -
679A HIS* 1.3 85.9 - - + +
681A GLU* 1.3 64.8 + - + +
683A LEU* 3.4 3.7 + - - +
684A ALA* 2.9 34.0 + - + +
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Residues in contact with GLU 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.9 14.4 - - + -
637A ILE* 3.1 20.4 + - - +
640A LEU* 3.5 23.0 - - + +
664A PHE* 4.3 2.9 - - - -
666A ARG* 2.7 40.9 + - - -
677A ILE* 2.9 24.5 + - - +
680A TYR* 1.3 76.5 - - + +
682A LEU* 1.3 61.7 + - - +
684A ALA* 3.1 5.0 + - - +
685A ILE* 2.9 35.5 + - - +
702A TYR* 2.4 36.9 + - + +
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Residues in contact with LEU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.5 37.5 - - + -
678A LEU* 2.7 34.5 + - + +
681A GLU* 1.3 73.6 - - - +
683A LEU* 1.3 60.9 + - - +
685A ILE* 3.5 6.3 + - + +
686A ARG* 3.1 23.1 + - + +
700A ILE* 3.7 35.2 - - + +
702A TYR* 4.5 11.7 - - + -
767A TRP* 3.5 43.7 - - + +
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Residues in contact with LEU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 3.6 24.0 - - + -
679A HIS* 3.3 48.2 + - + +
680A TYR* 3.4 4.4 + - - +
681A GLU 3.3 0.4 - - - -
682A LEU* 1.3 74.2 - - - +
684A ALA* 1.3 60.3 + - - +
686A ARG* 3.7 10.4 - - + +
687A ASP* 2.8 31.1 + - - +
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Residues in contact with ALA 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A LEU* 4.1 10.1 - - + -
641A SER* 3.4 38.8 + - - +
680A TYR* 2.9 29.1 + - + +
681A GLU* 3.1 11.6 + - - +
683A LEU* 1.3 74.5 - - - +
685A ILE* 1.3 64.3 + - - +
687A ASP* 3.4 4.9 + - - -
688A ALA* 3.1 17.5 + - - +
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Residues in contact with ILE 685 (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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592A LEU* 5.6 0.2 - - + -
640A LEU* 4.0 11.7 - - + -
644A VAL* 4.4 20.4 - - + +
662A ILE* 4.3 21.5 - - + -
664A PHE* 3.9 40.6 - - + -
681A GLU 2.9 17.6 + - - +
682A LEU* 3.8 5.8 - - - +
683A LEU 3.3 0.2 - - - -
684A ALA* 1.3 75.9 - - - +
686A ARG* 1.3 62.6 + - - +
688A ALA* 3.2 15.7 + - - +
689A CYS* 3.3 13.2 + - - -
700A ILE* 3.6 29.6 - - + -
702A TYR* 4.2 13.2 - - + -
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Residues in contact with ARG 686 (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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682A LEU* 3.1 16.3 + - + +
683A LEU* 3.8 12.8 - - + +
685A ILE* 1.3 78.1 - - - +
687A ASP* 1.3 62.4 + - - +
689A CYS* 3.1 10.7 + - - +
690A ILE* 3.0 40.5 + - + +
697A GLN* 3.0 40.6 + - - +
698A PRO* 3.0 26.9 + - - +
700A ILE* 3.6 25.0 - - + +
767A TRP* 4.8 3.4 - - - +
769A ASP* 3.0 28.7 + - - -
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Residues in contact with ASP 687 (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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641A SER* 3.1 16.1 + - - +
683A LEU 2.8 22.3 + - - +
684A ALA* 3.7 7.9 - - - +
685A ILE 3.2 0.2 - - - -
686A ARG* 1.3 73.1 - - - +
688A ALA* 1.3 61.6 + - - +
690A ILE* 3.3 15.9 + - - +
691A LYS* 2.2 59.4 + - - +
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Residues in contact with ALA 688 (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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641A SER* 3.2 30.9 + - - +
644A VAL* 3.9 19.5 - - + -
645A ARG* 4.1 12.1 + - + +
648A LEU* 4.7 2.7 - - + -
684A ALA 3.1 11.0 + - - +
685A ILE 3.2 9.6 + - - +
687A ASP* 1.3 77.0 - - - +
689A CYS* 1.3 61.6 + - - +
691A LYS* 3.4 6.6 + - - +
692A LEU* 3.3 26.7 + - - +
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Residues in contact with CYS 689 (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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648A LEU* 4.2 9.0 - - - -
662A ILE* 3.9 15.9 - - - -
685A ILE* 3.3 14.6 + - - -
686A ARG* 3.1 17.5 + - - +
688A ALA* 1.3 77.5 - - - +
690A ILE* 1.3 65.3 + - - +
692A LEU* 3.3 9.7 + - - -
693A GLU 3.5 11.6 + - - +
696A TYR* 3.7 44.0 - - + +
698A PRO* 3.6 28.0 - - + -
700A ILE* 5.4 0.9 - - - -
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Residues in contact with ILE 690 (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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686A ARG* 3.0 37.2 + - + +
687A ASP* 3.7 16.2 - - + +
688A ALA 3.3 0.2 - - - -
689A CYS* 1.3 76.2 - - - +
691A LYS* 1.3 62.8 + - + +
693A GLU 2.9 22.3 - - - +
694A LYS* 4.8 4.8 - - - +
696A TYR 5.0 0.2 - - - -
697A GLN* 3.9 21.8 - - - +
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Residues in contact with LYS 691 (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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641A SER* 4.4 3.8 + - - -
645A ARG* 3.4 21.1 + - - +
687A ASP* 2.2 52.4 + - - +
688A ALA* 3.4 5.8 + - - +
689A CYS 3.2 0.2 - - - -
690A ILE* 1.3 78.5 - - + +
692A LEU* 1.3 60.8 + - - +
693A GLU 5.2 0.2 - - - -
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Residues in contact with LEU 692 (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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645A ARG* 3.4 34.1 - - + +
648A LEU* 3.7 42.4 - - + -
649A ILE* 4.1 14.1 - - + -
688A ALA 3.3 13.6 + - - +
689A CYS* 3.3 5.6 + - - +
690A ILE 3.3 0.8 - - - -
691A LYS* 1.3 80.1 - - - +
693A GLU* 1.3 65.1 + - - +
696A TYR* 4.7 2.7 - - + -
836B PRO* 5.3 2.1 - - - +
838B TRP* 3.8 55.6 + - + +
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Residues in contact with GLU 693 (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 LYS* 2.2 42.7 + - - +
689A CYS 3.5 7.7 + - - +
690A ILE* 2.9 20.8 - - - +
692A LEU* 1.3 77.2 - - - +
694A LYS* 1.3 66.8 + - - +
695A ASP 3.3 4.8 + - - +
696A TYR* 3.5 29.5 + - + +
835B GLY* 4.9 0.7 - - - -
836B PRO* 3.7 30.2 - - + +
838B TRP* 3.3 17.1 + - - +
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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) + - + + + + + -
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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