Contacts of the helix formed by residues 688 - 696 (chain A) in PDB entry 2XR9
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 688 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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686A SER* 3.3 9.4 + - - -
687A SER* 1.3 82.8 + - - +
689A PRO* 1.3 74.4 - - - +
690A GLU* 3.0 23.3 + - - +
691A ALA* 3.0 24.5 + - - +
692A LYS* 3.0 18.2 + - - -
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Residues in contact with PRO 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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688A SER* 1.3 85.9 - - - +
690A GLU* 1.3 71.2 + - - +
692A LYS* 3.3 20.1 + - + +
693A TYR* 3.3 23.1 - - + -
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Residues in contact with GLU 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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578A LEU* 4.1 27.0 - - + +
579A GLU* 4.8 7.1 - - - +
688A SER* 3.0 23.1 + - - +
689A PRO* 1.3 87.1 - - - +
691A ALA* 1.3 62.4 + - - +
692A LYS 3.2 1.2 + - - -
693A TYR* 3.4 21.7 + - - +
694A ASP* 4.5 1.2 + - - -
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Residues in contact with ALA 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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615A THR* 4.4 16.4 - - + +
616A ASP* 3.4 28.2 - - - +
617A PHE* 5.8 0.2 - - - -
681A PHE* 5.8 1.0 - - - -
686A SER* 4.3 2.1 - - - -
687A SER* 3.6 11.2 - - - +
688A SER* 3.0 21.0 + - - +
690A GLU* 1.3 75.7 - - - +
692A LYS* 1.3 64.7 + - - +
693A TYR 3.1 0.2 - - - -
694A ASP* 3.1 29.2 + - - +
695A ALA* 3.9 2.1 + - - +
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Residues in contact with LYS 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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642A SER* 2.9 26.6 + - - -
643A SER 3.4 19.7 + - - +
644A ILE* 4.9 0.7 - - - -
645A PRO* 3.9 23.1 - - + -
648A LEU* 4.8 4.7 - - + -
683A PRO* 2.6 37.6 + - + +
684A TYR* 4.2 0.4 - - - +
686A SER* 3.2 22.2 + - - +
688A SER 3.0 8.3 + - - +
689A PRO* 3.5 17.5 - - + +
690A GLU 3.2 0.8 - - - -
691A ALA* 1.3 76.8 - - - +
693A TYR* 1.3 64.5 + - + +
695A ALA* 3.0 16.2 + - - +
696A PHE* 3.3 28.9 - - + -
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Residues in contact with TYR 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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568A CYS* 4.6 8.7 - - - -
569A ASP* 6.4 0.4 - - + -
579A GLU* 4.8 9.2 - - - +
647A HIS* 4.1 7.3 + - - -
648A LEU* 3.8 34.0 - - + +
651A CYS* 5.1 0.9 - - - -
653A ARG* 3.0 50.4 + - - +
689A PRO 3.3 26.9 - - - -
690A GLU* 3.7 13.5 - - - +
691A ALA 3.1 0.6 - - - -
692A LYS* 1.3 78.6 - - + +
694A ASP* 1.3 60.2 + - - +
696A PHE* 3.3 13.9 + - - +
1890A IOD 3.4 29.8 - - + +
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Residues in contact with ASP 694 (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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579A GLU* 3.5 16.8 - - - +
585A LEU* 5.0 3.9 - - - +
586A HIS* 3.2 28.4 + - - -
614A HIS* 3.7 20.0 - - + +
615A THR* 4.1 13.9 + - - -
616A ASP* 5.3 1.2 + - + -
617A PHE* 4.0 22.9 - - + -
653A ARG* 4.3 1.8 + - - +
690A GLU 5.3 0.2 - - - -
691A ALA* 3.1 21.6 + - - +
693A TYR* 1.3 71.5 - - - +
695A ALA* 1.3 66.5 + - - +
696A PHE 3.0 4.1 + - - -
697A LEU* 3.1 28.2 + - - +
700A ASN* 4.6 0.2 - - - +
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Residues in contact with ALA 695 (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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617A PHE* 4.4 6.0 - - - -
679A PHE* 3.2 11.8 - - - -
681A PHE* 4.0 17.7 - - + +
683A PRO* 3.6 37.9 - - + -
691A ALA 3.9 1.0 + - - +
692A LYS* 3.0 16.1 + - - +
694A ASP* 1.3 79.7 - - - +
696A PHE* 1.3 59.3 + - - +
697A LEU 3.3 0.7 + - - -
700A ASN* 2.7 28.0 + - - +
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Residues in contact with PHE 696 (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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644A ILE* 3.7 28.9 - - + -
648A LEU* 3.4 44.2 - - + -
649A THR 5.1 2.5 - - - -
651A CYS* 3.4 38.4 - - - +
652A VAL* 3.4 5.7 - - - +
653A ARG* 2.7 32.1 + - - -
679A PHE* 3.7 27.7 - + - -
683A PRO* 3.7 19.1 - - + -
692A LYS* 3.3 37.0 - - + -
693A TYR* 3.3 11.5 + - - +
694A ASP 3.0 1.6 - - - -
695A ALA* 1.3 75.9 - - - +
697A LEU* 1.3 57.8 + - - +
1864A SCN 5.7 0.2 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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