Contacts of the helix formed by residues 662 - 673 (chain A) in PDB entry 3AR2
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 PRO 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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660A ASP 4.1 4.0 - - - +
661A LEU* 1.3 84.8 - - + +
663A LEU* 1.3 57.4 + - + +
664A ALA* 3.3 4.3 - - + +
665A GLU* 2.8 47.4 + - + +
666A GLN 2.9 10.2 + - - -
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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
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661A LEU 5.0 0.4 - - - +
662A PRO* 1.3 71.5 - - + +
664A ALA* 1.3 58.0 + - - +
666A GLN* 2.9 42.8 + - - +
667A ARG* 3.0 14.6 + - - +
686A LYS* 4.5 8.5 - - - +
690A TYR* 3.8 16.0 + - + +
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Residues in contact with ALA 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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662A PRO* 3.3 3.7 - - + +
663A LEU* 1.3 77.8 - - - +
665A GLU* 1.3 65.2 + - + +
667A ARG* 3.7 11.1 - - - +
668A GLU* 3.4 21.8 + - - +
694A TYR* 5.2 0.3 + - - -
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Residues in contact with GLU 665 (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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661A LEU* 3.6 23.0 - - + +
662A PRO* 2.8 37.6 + - + +
664A ALA* 1.3 81.0 - - + +
666A GLN* 1.3 56.9 + - - +
667A ARG 3.1 1.8 - - - -
668A GLU* 3.3 12.7 + - - +
669A ALA* 2.9 29.3 + - - +
672A ARG* 4.6 8.3 + - - +
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Residues in contact with GLN 666 (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 PHE* 2.8 63.7 + - + +
659A ASP* 3.1 20.8 + - - +
661A LEU* 3.2 23.1 + - + +
662A PRO 2.9 5.9 + - - +
663A LEU* 2.9 16.3 + - - +
665A GLU* 1.3 75.8 - - - +
667A ARG* 1.3 63.5 + - - +
669A ALA* 3.5 2.1 + - - -
670A CYS* 3.4 13.9 + - - -
686A LYS* 3.0 23.9 + - - +
690A TYR* 2.7 38.2 + - + +
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Residues in contact with ARG 667 (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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663A LEU 3.0 14.0 + - - +
664A ALA* 3.7 10.3 - - - +
666A GLN* 1.3 77.5 - - - +
668A GLU* 1.3 61.8 - - - +
670A CYS* 3.0 20.8 + - - +
671A ARG 3.7 0.2 + - - -
690A TYR* 3.6 29.1 - - + -
693A SER* 3.1 35.2 + - - +
694A TYR* 3.1 58.6 - - + +
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Residues in contact with GLU 668 (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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664A ALA 3.4 12.4 + - - +
665A GLU* 3.3 18.0 + - - +
667A ARG* 1.3 78.7 - - - +
669A ALA* 1.3 60.6 - - - +
671A ARG* 3.0 58.4 + - - +
672A ARG* 3.4 26.5 + - - +
694A TYR* 3.5 14.9 + - - +
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Residues in contact with ALA 669 (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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653A TYR* 3.9 24.7 - - + -
658A PHE* 4.1 13.5 - - + -
661A LEU* 4.3 5.4 - - + -
665A GLU 2.9 18.1 + - - +
666A GLN 3.6 7.4 - - - +
667A ARG 3.2 0.4 - - - -
668A GLU* 1.3 76.0 - - - +
670A CYS* 1.3 56.0 + - - +
672A ARG* 3.9 16.8 - - - +
673A ALA* 2.7 38.6 + - - +
676A PHE* 4.3 0.9 - - - -
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Residues in contact with CYS 670 (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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620A ARG* 2.7 32.1 + - - -
622A ILE* 3.9 3.3 - - - +
658A PHE* 4.1 8.7 - - - -
666A GLN 3.4 6.1 - - - -
667A ARG 3.0 10.9 + - - +
669A ALA* 1.3 76.9 - - - +
671A ARG* 1.3 52.1 + - - +
673A ALA 3.7 3.5 - - - +
676A PHE* 4.3 7.9 - - - -
687A ILE* 3.8 23.1 - - - -
690A TYR* 3.4 41.1 - - + -
691A LEU* 3.6 23.3 - - + +
694A TYR* 5.5 0.9 - - + -
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Residues in contact with ARG 671 (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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620A ARG* 3.1 28.1 + - - +
668A GLU* 3.0 33.3 + - - +
670A CYS* 1.3 78.5 - - - +
672A ARG* 1.3 57.0 + - + +
691A LEU* 5.4 1.6 - - + -
694A TYR* 3.1 58.7 - - + -
696A GLU* 5.5 3.8 - - - +
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Residues in contact with ARG 672 (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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620A ARG* 4.2 0.6 + - - -
650A ASP* 3.0 40.7 + - - +
651A ARG* 3.5 36.6 + - + +
653A TYR* 2.9 20.8 + - - -
661A LEU* 5.2 3.6 - - - +
665A GLU* 4.6 9.7 + - - +
668A GLU* 3.5 34.7 + - - +
669A ALA* 3.4 17.7 + - - +
671A ARG* 1.3 79.0 - - - +
673A ALA* 1.3 68.2 + - - +
674A CYS* 4.0 4.0 - - - -
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Residues in contact with ALA 673 (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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620A ARG* 3.1 7.8 + - - -
622A ILE* 3.1 20.9 - - - +
651A ARG* 3.4 18.6 - - - +
653A TYR* 3.7 21.5 - - + -
669A ALA 2.7 23.5 + - - +
670A CYS 3.7 2.4 - - - +
672A ARG* 1.3 76.2 - - - +
674A CYS* 1.3 60.1 + - - +
675A CYS 3.6 0.4 - - - +
676A PHE* 3.5 24.5 - - + -
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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