Contacts of the helix formed by residues 1175 - 1179 (chain A) in PDB entry 2ZM3
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 PRO1175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135A ASP* 4.1 7.4 - - - +
1139A ARG* 3.4 39.7 - - - +
1173A LEU 3.8 5.6 - - - +
1174A LEU* 1.3 84.8 - - + +
1176A VAL* 1.3 65.0 + - - +
1177A ARG* 3.3 1.8 + - + +
1178A TRP* 3.4 33.6 + - + +
1179A MET* 3.4 12.7 + - - +
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Residues in contact with VAL1176 (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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1174A LEU 3.6 3.3 + - - +
1175A PRO* 1.3 72.5 - - - +
1177A ARG* 1.3 65.6 + - + +
1178A TRP 2.9 6.5 + - - -
1179A MET* 3.1 29.7 + - - +
1184A LEU* 4.2 22.9 - - + +
1218A ASN* 3.8 48.0 - - + +
1221A VAL* 4.4 11.5 - - + +
1222A LEU* 4.5 17.7 - - + +
1225A VAL* 5.8 0.9 - - - +
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Residues in contact with ARG1177 (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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1175A PRO* 3.3 2.2 - - + +
1176A VAL* 1.3 78.9 - - + +
1178A TRP* 1.3 82.4 + - + +
1179A MET 3.6 0.7 - - - -
1196A TRP* 5.6 0.6 + - - -
1200A VAL* 3.9 12.6 - - - +
1211A GLN* 3.4 36.4 + - - +
1212A PRO* 2.9 29.4 + - + +
1213A TYR* 3.1 46.3 + - + +
1214A GLN* 4.4 0.2 - - - +
1216A LEU 2.8 21.2 + - - -
1217A SER* 3.5 1.2 - - - +
1218A ASN* 3.0 36.3 + - - +
1221A VAL* 3.7 25.5 - - + +
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Residues in contact with TRP1178 (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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1088A LYS* 4.6 11.2 - - - -
1135A ASP* 5.9 2.5 - - - +
1136A LEU 3.4 24.2 - - - +
1137A ALA* 3.3 18.5 - - + +
1139A ARG* 4.3 10.5 - - + -
1175A PRO* 3.4 33.9 + - + +
1176A VAL 2.9 0.8 + - - -
1177A ARG* 1.3 100.0 - - + +
1179A MET* 1.3 62.7 + - + +
1196A TRP* 3.9 8.1 - - - -
1197A SER* 2.7 32.2 + - - +
1200A VAL* 3.5 28.9 - - + +
1201A VAL* 4.8 0.2 - - + -
1204A GLU* 3.1 42.8 + - - -
1211A GLN* 5.6 1.8 - - + -
1212A PRO* 3.8 21.3 - - + -
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Residues in contact with MET1179 (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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1134A ARG 5.8 1.1 - - - +
1174A LEU* 3.8 39.5 - - + +
1175A PRO 3.4 12.8 - - - +
1176A VAL* 3.1 16.5 + - - +
1177A ARG 3.6 0.5 - - - -
1178A TRP* 1.3 80.9 - - - +
1180A SER* 1.3 65.8 + - - +
1183A SER* 3.9 30.7 - - - +
1184A LEU* 3.8 37.1 - - + +
1189A PHE* 4.3 13.7 - - + -
1196A TRP* 3.3 11.9 + - - -
1197A SER* 5.0 0.2 - - - -
1225A VAL* 4.0 5.4 - - - +
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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