Contacts of the helix formed by residues 831 - 836 (chain A) in PDB entry 5A7R
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 ARG 831 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A PHE* 4.2 9.1 - - - +
830A ARG* 1.3 85.5 - - + +
832A TYR* 1.3 67.4 + - - +
833A LEU* 3.3 3.4 - - + +
834A ASP* 3.1 38.6 + - - +
1978A GOL 3.5 3.4 + - - -
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Residues in contact with TYR 832 (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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829A PHE* 5.8 0.4 - - - -
830A ARG 4.3 0.2 - - - -
831A ARG* 1.3 72.0 - - - +
833A LEU* 1.3 74.1 + - + +
834A ASP 3.2 0.9 + - - -
835A GLN* 3.1 45.6 + - - +
836A PHE* 3.6 28.8 - + - -
876A GLY 5.8 4.3 - - - -
877A GLY 6.3 0.2 - - - -
878A ASP* 3.6 26.8 + - + -
935A TYR* 5.0 1.0 + - - -
946A PRO 4.3 10.3 + - - +
947A GLY* 4.7 3.1 - - - -
948A PRO* 3.6 27.5 - - + +
951A LYS* 3.2 26.8 + - - -
952A LEU 5.7 1.0 + - - -
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Residues in contact with LEU 833 (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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831A ARG* 3.3 3.3 - - + +
832A TYR* 1.3 84.0 - - + +
834A ASP* 1.3 65.4 + - - +
835A GLN 3.1 1.4 + - - -
836A PHE* 3.2 19.5 + - + +
837A VAL* 4.0 5.9 + - - +
936A TYR* 5.6 0.7 - - - -
940A CYS* 3.9 36.6 - - + +
943A CYS* 4.0 23.1 - - + +
945A THR 3.6 16.2 - - - +
946A PRO* 3.2 21.9 + - + +
948A PRO* 3.7 28.7 - - + -
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Residues in contact with ASP 834 (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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829A PHE* 3.9 3.8 - - + -
831A ARG* 3.1 37.1 + - - +
833A LEU* 1.3 79.5 - - - +
835A GLN* 1.3 60.9 + - - +
836A PHE 3.3 1.0 + - - -
837A VAL* 3.4 18.8 + - - +
840A LYS* 3.4 22.4 - - + +
1978A GOL 2.6 42.3 + - - -
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Residues in contact with GLN 835 (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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829A PHE* 3.5 37.9 - - + +
831A ARG 5.2 0.2 + - - -
832A TYR* 3.1 38.7 + - - +
834A ASP* 1.3 79.9 - - - +
836A PHE* 1.3 68.8 + - + +
837A VAL 3.4 1.0 + - - -
840A LYS* 4.4 1.7 - - - +
841A MET* 3.3 26.0 + - - +
844A GLU* 6.2 0.2 - - - +
876A GLY 4.4 3.4 + - - -
877A GLY* 3.4 12.6 - - - -
878A ASP* 2.8 46.2 + - - +
881A LEU* 3.8 17.9 - - + +
882A LYS* 5.0 2.9 + - - +
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Residues in contact with PHE 836 (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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832A TYR* 3.6 43.1 - + - -
833A LEU* 3.2 16.1 + - + +
835A GLN* 1.3 93.5 - - + +
837A VAL* 1.3 63.2 + - - +
838A PRO 3.4 1.9 - - - -
841A MET* 3.4 23.4 - - - +
878A ASP* 4.8 4.7 - - + -
881A LEU* 3.8 38.4 - - + -
932A LEU* 6.0 1.1 - - + +
935A TYR* 3.6 31.9 - + + -
936A TYR* 3.3 17.4 - - + +
940A CYS* 3.8 27.8 - - + -
952A LEU* 4.3 11.9 - - + -
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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