Contacts of the helix formed by residues 976 - 982 (chain A) in PDB entry 6ZGI
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 VAL 976 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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974A SER* 3.4 4.1 - - - -
975A SER* 1.3 82.3 - - - +
977A LEU* 1.3 66.2 + - - +
978A ASN* 3.7 12.3 - - + +
979A ASP* 3.6 28.6 - - + +
980A ILE* 3.2 25.9 + - - +
996A LEU* 5.0 0.2 - - - -
546C LEU* 6.4 1.1 - - + -
567C ARG* 5.6 6.3 - - - +
571C ASP* 3.6 39.3 - - + +
572C THR* 4.7 11.4 - - - +
573C THR* 5.5 6.7 - - - +
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Residues in contact with LEU 977 (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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742A ILE 4.0 11.0 - - - +
743A CYS 3.6 24.7 - - - +
746A SER* 4.5 8.5 - - - -
749A CYS* 3.9 24.5 - - + -
975A SER 3.9 1.6 + - - -
976A VAL* 1.3 72.7 - - - +
978A ASN* 1.3 61.3 + - - +
980A ILE* 3.2 6.4 + - + +
981A LEU* 2.9 35.6 + - + +
993A ILE* 3.9 35.4 - - + -
996A LEU* 3.9 25.6 - - + -
997A ILE* 6.4 0.2 - - + -
1000A ARG* 4.2 9.6 - - - +
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Residues in contact with ASN 978 (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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746A SER* 5.3 5.7 - - - -
976A VAL* 3.3 10.2 - - + +
977A LEU* 1.3 80.2 - - - +
979A ASP* 1.3 60.0 + - - +
981A LEU* 4.2 12.1 - - - +
982A SER* 2.8 28.1 + - - -
541C PHE* 5.9 0.6 - - - -
546C LEU* 5.5 8.8 - - + +
547C THR* 3.3 30.5 + - - +
548C GLY* 4.1 13.5 - - - -
549C THR 5.1 1.2 - - - +
572C THR* 5.6 3.4 + - - -
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Residues in contact with ASP 979 (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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973A ILE* 5.4 0.9 - - - +
974A SER* 3.1 22.9 + - - +
976A VAL* 3.4 26.9 + - + +
977A LEU 3.2 0.8 - - - -
978A ASN* 1.3 80.1 - - - +
980A ILE* 1.3 52.1 + - - +
982A SER* 2.6 28.5 + - - +
983A ARG* 3.5 28.4 + - - +
518C LEU* 3.7 28.7 - - - +
519C HIS* 5.3 6.1 + - - -
546C LEU* 5.1 10.5 - - + +
567C ARG* 5.2 5.6 + - - -
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Residues in contact with ILE 980 (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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972A ALA* 4.8 0.9 - - + -
973A ILE* 4.0 13.7 - - + -
974A SER* 3.2 39.9 - - - +
976A VAL 3.3 9.6 - - - +
977A LEU* 3.2 9.5 + - + +
979A ASP* 1.3 72.8 - - - +
981A LEU* 1.3 59.7 + - - +
982A SER 2.7 15.7 - - - +
983A ARG* 5.0 0.4 - - - -
984A LEU* 3.3 32.8 - - + +
989A ALA* 4.3 14.2 - - + +
992A GLN* 3.9 34.5 - - + -
993A ILE* 4.7 7.0 - - + +
996A LEU* 3.9 16.2 - - + -
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Residues in contact with LEU 981 (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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746A SER* 3.4 28.5 - - - +
748A GLU* 3.1 33.9 - - + +
977A LEU* 2.9 24.1 + - + +
978A ASN* 4.2 10.8 - - - +
979A ASP 3.4 0.4 - - - -
980A ILE* 1.3 75.1 - - - +
982A SER* 1.3 58.2 + - - +
984A LEU 3.1 19.7 - - - +
989A ALA* 4.4 10.3 - - + -
993A ILE* 3.6 29.6 - - + -
386C LYS* 3.6 9.7 + - - -
547C THR* 5.4 2.5 - - - +
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Residues in contact with SER 982 (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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978A ASN 2.8 22.7 + - - -
979A ASP* 2.6 27.7 + - - +
980A ILE 2.7 10.4 - - - +
981A LEU* 1.3 76.9 - - - +
983A ARG* 1.3 59.7 + - - +
984A LEU 3.2 1.3 - - - -
386C LYS* 4.4 7.0 - - - +
390C LEU* 5.0 2.5 - - - -
518C LEU* 3.9 14.3 - - - +
545C GLY 3.7 21.1 + - - -
546C LEU* 4.6 1.4 - - - +
547C THR* 3.9 20.4 + - - -
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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