Contacts of the helix formed by residues 655 - 661 (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 GLY 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654A THR* 1.3 71.3 - - - +
656A ARG* 1.3 55.8 - - - +
658A PHE* 3.4 4.5 + - - +
659A ASP* 3.0 35.0 + - - -
677A ALA 3.0 13.1 + - - -
678A ARG 3.4 12.2 + - - -
679A VAL* 3.8 11.6 - - - +
683A HIS* 3.7 23.9 + - - -
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Residues in contact with ARG 656 (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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654A THR* 3.0 9.0 + - - +
655A GLY* 1.3 72.9 - - - +
657A GLU* 1.3 67.2 + - + +
658A PHE 3.1 1.7 + - - -
659A ASP* 3.1 6.6 + - + +
660A ASP* 3.0 49.6 + - - +
678A ARG 4.8 1.0 + - - -
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Residues in contact with GLU 657 (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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629A LYS* 2.9 29.8 + - - -
653A TYR* 3.4 17.7 - - + -
654A THR* 2.5 54.2 + - - +
656A ARG* 1.3 73.5 - - + +
658A PHE* 1.3 60.9 + - - +
660A ASP* 3.4 19.6 + - - +
661A LEU* 3.4 18.8 - - - +
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Residues in contact with PHE 658 (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* 4.5 8.9 - - + -
654A THR 2.9 15.7 + - - +
655A GLY* 3.5 7.4 - - - +
657A GLU* 1.3 73.5 - - - +
659A ASP* 1.3 72.2 + - - +
660A ASP 3.0 5.1 + - - -
661A LEU* 3.1 16.3 + - + +
666A GLN* 2.8 56.3 + - + +
669A ALA* 4.1 9.9 - - + -
670A CYS* 4.3 0.9 - - - -
676A PHE* 3.5 28.7 - + + -
679A VAL* 5.5 0.4 - - + -
683A HIS* 4.2 11.7 - + - -
686A LYS* 4.2 10.5 - - + -
687A ILE* 3.6 24.0 - - + -
690A TYR* 3.4 35.4 - + - -
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Residues in contact with ASP 659 (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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655A GLY 3.0 12.4 + - - +
656A ARG* 3.1 6.6 + - + +
658A PHE* 1.3 76.6 - - - +
660A ASP* 1.3 63.1 + - - +
661A LEU 3.3 2.3 - - - +
666A GLN* 3.1 13.8 + - - +
683A HIS* 2.9 41.5 + - - -
686A LYS* 3.9 15.8 + - - -
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Residues in contact with ASP 660 (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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656A ARG* 3.0 41.0 + - - +
657A GLU* 3.5 15.5 - - - +
658A PHE 3.0 0.6 - - - -
659A ASP* 1.3 81.5 - - - +
661A LEU* 1.3 65.3 + - + +
662A PRO* 3.8 4.2 - - - +
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Residues in contact with LEU 661 (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* 4.0 29.4 - - + +
657A GLU 3.4 15.7 - - - +
658A PHE* 3.1 14.7 + - + +
659A ASP 3.7 2.3 - - - +
660A ASP* 1.3 80.2 - - + +
662A PRO* 1.3 73.3 - - + +
663A LEU* 3.6 0.9 + - - +
665A GLU* 3.6 34.5 - - + +
666A GLN* 3.2 21.4 + - + +
669A ALA* 4.3 11.2 - - + -
672A ARG* 5.2 2.2 - - - +
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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