Contacts of the helix formed by residues 971 - 976 (chain A) in PDB entry 4YOC
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 GLU 971 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A TYR 3.3 0.8 - - - -
970A PRO* 1.3 79.2 - - - +
972A HIS* 1.3 65.0 + - - +
973A TYR* 3.1 8.5 + - - -
974A ARG* 3.0 56.9 + - - +
1436A TRP* 3.8 23.4 - - + +
1437A ARG* 3.6 18.7 + - - +
1439A LEU 5.4 0.8 + - - +
1457A TYR* 2.3 44.0 + - - +
1496A ILE* 4.1 19.5 - - + -
1501A PRO* 3.5 19.4 - - - +
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Residues in contact with HIS 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A VAL* 3.4 40.1 - - + +
966A GLU* 6.3 0.7 - - + -
969A TYR* 3.5 24.2 + - + +
971A GLU* 1.3 78.2 - - - +
973A TYR* 1.3 56.5 + - - +
974A ARG 3.0 0.4 - - - -
975A LYS* 2.9 55.0 + - + +
976A TYR* 3.8 29.7 + + - -
979A TYR* 4.3 8.6 + - - -
1437A ARG 3.2 16.8 + - - +
1438A ASP* 3.9 10.5 + - - -
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Residues in contact with TYR 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A GLU* 4.7 8.5 - - + +
969A TYR 5.0 0.6 + - - -
970A PRO 3.1 28.7 - - - -
971A GLU* 3.1 13.2 + - - -
972A HIS* 1.3 78.3 - - - +
974A ARG* 1.3 96.4 + - + +
975A LYS 3.0 4.8 + - - -
976A TYR* 3.2 35.8 + - + +
977A SER* 4.4 1.9 + - - -
1464A ASN* 3.8 24.0 + - + -
1473A ARG* 3.3 71.1 + - + +
1509A HIS* 5.4 1.3 - + - -
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Residues in contact with ARG 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A GLU* 3.0 37.8 + - - +
972A HIS 3.0 1.2 - - - -
973A TYR* 1.3 119.9 + - + +
975A LYS* 1.3 53.4 + - - +
976A TYR 3.5 0.4 - - - -
977A SER* 3.7 13.4 + - - -
1436A TRP* 3.9 18.0 - - - -
1437A ARG* 2.7 36.5 + - - -
1461A ASP* 5.1 0.4 + - - -
1464A ASN* 3.8 4.1 - - - +
1473A ARG 4.9 3.6 + - - -
1501A PRO* 3.8 22.6 + - - +
1504A GLY* 3.5 8.1 - - - -
1505A ASN* 3.1 43.7 + - - +
1509A HIS* 3.0 35.4 + - + +
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Residues in contact with LYS 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A HIS* 2.9 35.9 + - + +
974A ARG* 1.3 78.2 - - - +
976A TYR* 1.3 55.9 + - - +
977A SER 3.1 5.4 - - - -
978A ASP* 2.8 24.1 + - + +
979A TYR* 3.1 40.2 - - + +
1433A GLY 2.8 29.3 + - - -
1435A ASP* 4.3 6.5 + - - -
1437A ARG* 3.6 42.0 - - + +
1438A ASP* 3.1 28.1 + - - +
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Residues in contact with TYR 976 (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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962A GLU 4.7 6.2 + - - -
963A PRO* 5.1 1.9 - - - +
964A VAL* 4.1 13.8 + - + +
966A GLU* 5.4 6.5 - - - -
972A HIS* 3.8 28.9 + + - -
973A TYR* 3.2 29.3 + - + +
975A LYS* 1.3 78.8 - - - +
977A SER* 1.3 55.9 + - - +
978A ASP 3.2 1.3 - - - -
979A TYR* 3.4 41.2 + + - +
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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
------------------------------------------------------------
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