Contacts of the helix formed by residues 1175 - 1179 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1135C ASP* 4.4 3.8 - - - +
1139C ARG* 3.0 36.1 - - - +
1173C LEU 3.7 4.7 - - - +
1174C LEU* 1.3 88.5 - - + +
1176C VAL* 1.3 65.5 + - - +
1177C ARG* 3.3 0.8 + - + +
1178C TRP* 3.4 35.6 + - + +
1179C MET* 3.4 13.3 + - - +
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Residues in contact with VAL1176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1174C LEU 3.4 3.8 + - - +
1175C PRO* 1.3 72.1 - - - +
1177C ARG* 1.3 62.7 + - + +
1178C TRP 2.9 6.3 + - - -
1179C MET* 3.1 28.2 + - - +
1184C LEU* 4.0 25.3 - - + +
1218C ASN* 3.6 50.0 - - + +
1221C VAL* 4.5 10.7 - - + +
1222C LEU* 4.5 16.6 - - + +
1225C VAL* 5.8 1.0 - - - +
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Residues in contact with ARG1177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175C PRO* 3.3 2.0 - - + -
1176C VAL* 1.3 80.2 - - + +
1178C TRP* 1.3 81.4 + - + +
1179C MET 3.7 0.7 - - - -
1196C TRP* 5.4 1.0 + - - -
1200C VAL* 3.9 14.0 - - - +
1211C GLN* 3.1 36.6 + - - +
1212C PRO* 3.0 22.7 + - + +
1213C TYR* 2.9 58.2 + - + -
1216C LEU 3.0 20.0 + - - -
1217C SER* 3.7 1.6 - - - +
1218C ASN* 3.2 33.4 + - - +
1221C VAL* 3.5 24.8 - - + +
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Residues in contact with TRP1178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C LYS* 4.9 14.1 - - + -
1135C ASP* 6.1 0.7 - - - +
1136C LEU 3.6 12.8 - - - +
1137C ALA* 3.4 28.8 - - + +
1139C ARG* 5.1 8.5 - - - +
1175C PRO* 3.4 36.8 + - + +
1176C VAL 3.0 0.8 - - - -
1177C ARG* 1.3 102.0 - - + +
1179C MET* 1.3 62.6 + - - +
1196C TRP* 3.7 8.1 - - - -
1197C SER* 2.6 32.8 + - - +
1200C VAL* 3.5 28.1 - - + +
1204C GLU* 3.0 42.4 + - - -
1211C GLN* 5.5 2.9 - - + -
1212C PRO* 3.8 22.7 - - + -
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Residues in contact with MET1179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1134C ARG 5.9 0.9 - - - +
1174C LEU* 3.9 37.2 - - + +
1175C PRO 3.4 12.8 - - - +
1176C VAL* 3.1 15.9 + - - +
1177C ARG 5.3 0.3 - - - -
1178C TRP* 1.3 81.3 - - + +
1180C SER* 1.3 64.8 + - - +
1181C PRO 4.0 0.2 - - - -
1183C SER* 3.7 31.6 - - - +
1184C LEU* 3.8 37.1 - - + +
1187C GLY* 5.9 0.2 - - - -
1189C PHE* 4.2 15.0 - - + -
1196C TRP* 3.3 13.1 + - - -
1197C SER* 4.8 0.4 - - - -
1225C VAL* 4.1 3.6 - - - +
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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