Contacts of the helix formed by residues 1086 - 1094 (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 ASP1086 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C 575 5.1 3.3 - - - -
1085C GLY* 1.3 74.7 - - - -
1087C LEU* 1.3 64.6 + - - +
1088C LYS* 3.5 12.5 - - - +
1089C SER* 2.8 44.1 + - - -
1090C TYR* 3.0 21.4 + - - +
1139C ARG* 3.6 28.0 - - - +
1141C CYS 3.2 7.6 - - - +
1142C MET* 4.1 9.4 - - + -
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Residues in contact with LEU1087 (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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1085C GLY 3.7 0.6 + - - -
1086C ASP* 1.3 71.4 - - - +
1088C LYS* 1.3 54.8 + - - +
1090C TYR* 4.2 3.8 - - + -
1091C LEU* 2.8 56.9 + - + +
1115C MET* 4.2 20.0 - - - -
1119C ILE* 4.0 22.0 - - + -
1138C ALA* 3.1 25.5 + - + +
1141C CYS* 2.8 33.6 + - + +
1142C MET* 4.4 0.2 - - - +
1143C VAL* 3.6 25.6 - - + -
1149C VAL* 4.1 8.3 - - + -
1201C VAL* 5.5 2.0 - - + -
1205C ILE* 4.7 10.8 - - + -
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Residues in contact with LYS1088 (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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1086C ASP* 3.2 10.2 + - - +
1087C LEU* 1.3 78.3 - - - +
1089C SER* 1.3 64.7 + - - +
1091C LEU* 3.1 4.0 + - - +
1092C ARG* 3.1 41.6 + - - +
1138C ALA* 3.2 13.3 + - + -
1139C ARG* 3.8 30.7 - - + +
1178C TRP* 4.9 16.1 - - + -
1204C GLU* 4.6 11.0 + - - +
1209C ALA* 3.9 23.3 + - + -
1210C GLU 5.5 4.8 + - - -
1211C GLN* 5.7 6.1 - - - +
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Residues in contact with SER1089 (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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1C 575 6.3 3.8 - - - -
1084C ARG 5.8 1.1 - - - -
1085C GLY* 6.1 0.2 - - - -
1086C ASP* 2.8 35.3 + - - -
1088C LYS* 1.3 76.4 - - - +
1090C TYR* 1.3 63.9 + - - +
1092C ARG* 3.2 10.3 + - - +
1093C SER* 3.1 21.9 + - - -
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Residues in contact with TYR1090 (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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1C 575 6.3 3.1 - - + -
1084C ARG* 3.7 32.0 + - + +
1086C ASP 3.0 17.7 + - - +
1087C LEU* 3.7 11.0 - - + +
1089C SER* 1.3 77.5 - - - +
1091C LEU* 1.3 68.9 - - + +
1093C SER* 2.8 27.6 + - - -
1094C LEU* 3.4 43.4 - - + +
1104C LEU* 4.9 9.8 - - + -
1105C ALA 5.4 0.3 + - - -
1115C MET* 5.0 10.3 - - + -
1143C VAL* 4.0 23.3 - - + -
1147C PHE* 3.3 39.5 - + - -
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Residues in contact with LEU1091 (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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1087C LEU* 2.8 46.2 + - + +
1088C LYS 3.1 4.2 + - - +
1090C TYR* 1.3 85.2 - - + +
1092C ARG* 1.3 61.5 + - - +
1094C LEU* 3.3 20.9 + - + +
1107C PRO* 4.6 7.0 - - + -
1115C MET* 4.7 7.6 - - - -
1138C ALA* 4.6 7.0 - - + -
1204C GLU 3.8 22.4 - - - +
1205C ILE* 3.9 21.3 - - + +
1208C LEU* 3.4 45.3 - - + +
1209C ALA* 4.0 12.3 - - + +
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Residues in contact with ARG1092 (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* 3.1 30.7 + - - +
1089C SER* 3.8 8.1 - - - +
1091C LEU* 1.3 77.0 - - - +
1093C SER* 1.3 61.9 + - - +
1095C ARG* 2.7 68.4 + - - +
1208C LEU 3.9 6.3 - - - +
1209C ALA* 3.4 21.7 + - + -
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Residues in contact with SER1093 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C 575 6.2 3.8 - - - -
1089C SER 3.1 12.5 + - - -
1090C TYR* 2.8 22.1 + - - -
1092C ARG* 1.3 76.6 - - - +
1094C LEU* 1.3 61.3 + - - +
1095C ARG 3.2 7.8 + - - +
1104C LEU* 3.6 33.1 - - - +
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Residues in contact with LEU1094 (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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1090C TYR* 3.4 49.1 - - + +
1091C LEU* 3.5 11.0 - - + +
1092C ARG 3.1 0.8 - - - -
1093C SER* 1.3 76.5 - - - +
1095C ARG* 1.3 63.9 + - - +
1096C PRO* 4.9 0.2 - - - +
1104C LEU* 3.7 21.8 - - + +
1105C ALA* 3.5 30.7 - - - +
1106C PRO* 3.1 33.9 - - + +
1107C PRO* 3.6 33.7 - - + -
1208C LEU* 4.1 11.0 - - + -
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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