Contacts of the helix formed by residues 1182 - 1192 (chain G) in PDB entry 4Z94
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 ASP1182 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1180G SER 3.3 4.2 + - - +
1181G THR* 1.3 72.9 - - - +
1183G VAL* 1.3 59.4 - - - +
1184G GLU* 3.4 15.0 - - - +
1185G GLU* 2.9 52.7 + - + +
1186G THR* 2.6 38.7 + - - -
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Residues in contact with VAL1183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181G THR* 4.6 5.2 - - - +
1182G ASP* 1.3 70.2 + - - +
1184G GLU* 1.3 62.7 - - + +
1186G THR* 3.2 1.3 + - - -
1187G LEU* 2.7 27.1 + - - +
1202G LEU* 4.8 2.2 - - + -
1205G ILE* 4.5 19.7 - - + -
1208G ILE* 4.3 38.6 - - + -
1212G THR* 4.6 8.7 - - + -
1216G TYR* 2.6 49.7 + - + +
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Residues in contact with GLU1184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182G ASP* 3.4 12.1 - - - +
1183G VAL* 1.3 77.1 - - + +
1185G GLU* 1.3 66.7 + - - +
1186G THR 3.1 0.3 + - - -
1187G LEU* 3.2 9.7 + - - +
1188G GLU* 2.9 27.8 + - - +
1209G PRO* 6.0 2.8 - - - +
1212G THR* 4.7 15.3 - - - +
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Residues in contact with GLU1185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1182G ASP* 2.9 40.8 + - + +
1184G GLU* 1.3 73.0 - - - +
1186G THR* 1.3 58.3 + - - +
1188G GLU* 3.2 14.4 - - - +
1189G ARG* 3.0 45.0 + - - +
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Residues in contact with THR1186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181G THR* 3.1 19.7 - - + +
1182G ASP 2.6 24.2 + - - -
1185G GLU* 1.3 74.4 - - - +
1187G LEU* 1.3 67.0 + - - +
1189G ARG* 2.9 26.4 + - - +
1190G ILE* 3.0 16.2 + - + +
1197G LEU* 4.1 25.4 - - + -
1200G VAL* 4.0 27.6 - - + -
1216G TYR* 3.5 10.1 - - - +
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Residues in contact with LEU1187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1183G VAL 2.7 21.4 + - - +
1184G GLU* 3.5 11.4 - - - +
1186G THR* 1.3 68.6 - - - +
1188G GLU* 1.3 69.9 + - - +
1190G ILE* 3.1 17.3 + - + +
1191G LYS* 3.3 28.5 + - - +
1212G THR* 3.8 27.6 - - + -
1215G ALA* 4.0 13.7 - - + -
1216G TYR* 3.5 32.4 + - + +
1219G ALA* 3.7 24.5 - - + -
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Residues in contact with GLU1188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184G GLU 2.9 14.4 + - - +
1185G GLU* 3.2 17.4 - - - +
1187G LEU* 1.3 75.7 - - - +
1189G ARG* 1.3 56.1 + - + +
1190G ILE 2.8 12.5 + - - -
1191G LYS* 2.8 27.9 + - + +
1192G ASN* 3.3 22.0 + - - +
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Residues in contact with ARG1189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1185G GLU* 3.0 32.1 + - + +
1186G THR* 2.9 19.7 + - - +
1188G GLU* 1.3 80.2 - - + +
1190G ILE* 1.3 58.8 + - - +
1192G ASN* 3.7 8.6 + - - +
1193G ASN 3.7 2.1 + - - -
1194G ASP* 3.2 58.2 + - + +
1196G LYS* 4.3 18.6 + - - +
1197G LEU* 3.9 30.8 - - + +
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Residues in contact with ILE1190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186G THR* 3.0 25.7 + - + +
1187G LEU* 3.5 9.4 - - + +
1188G GLU 2.8 1.4 + - - -
1189G ARG* 1.3 74.1 - - - +
1191G LYS* 1.3 69.2 + - - +
1193G ASN* 3.1 13.9 + - - +
1197G LEU* 3.4 19.3 - - + -
1200G VAL* 4.5 4.9 - - + -
1216G TYR* 3.6 35.9 - - + -
1219G ALA* 3.5 31.5 - - + +
1220G LEU* 3.6 24.9 - - + -
1223G ASN* 3.5 25.5 + - - +
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Residues in contact with LYS1191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187G LEU* 3.3 36.0 + - + +
1188G GLU* 2.8 12.9 + - + +
1190G ILE* 1.3 81.3 - - - +
1192G ASN* 1.3 65.9 + - - +
1193G ASN* 3.2 6.1 + - - +
1215G ALA* 5.4 5.6 + - - +
1219G ALA* 4.2 19.7 - - + +
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Residues in contact with ASN1192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188G GLU* 3.3 29.0 + - - +
1189G ARG* 3.7 8.4 + - - +
1190G ILE 3.2 1.0 - - - -
1191G LYS* 1.3 84.8 + - - +
1193G ASN* 1.3 69.2 + - - +
1194G ASP* 3.5 4.7 + - + +
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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