Contacts of the helix formed by residues 1086 - 1093 (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 ASP1086 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 575 5.2 1.0 - - - -
1085A GLY* 1.3 75.0 - - - -
1087A LEU* 1.3 63.9 - - - +
1088A LYS* 3.1 14.0 + - - +
1089A SER* 2.7 35.7 + - - -
1090A TYR* 3.2 17.3 + - - +
1139A ARG* 3.6 22.4 - - - +
1141A CYS 3.2 12.1 - - - +
1142A MET* 3.8 12.3 - - - +
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Residues in contact with LEU1087 (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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1085A GLY 3.7 1.4 + - - -
1086A ASP* 1.3 71.1 - - - +
1088A LYS* 1.3 56.1 + - - +
1090A TYR* 3.3 7.7 + - + +
1091A LEU* 2.9 51.5 + - + +
1115A MET* 4.2 17.0 - - + -
1119A ILE* 4.0 26.5 - - + -
1138A ALA* 3.2 29.1 + - + +
1141A CYS* 2.8 24.1 + - + +
1142A MET* 4.1 0.2 - - - +
1143A VAL* 3.8 25.6 - - + -
1149A VAL* 4.2 9.0 - - + -
1201A VAL* 5.4 1.6 - - + -
1205A ILE* 4.7 9.4 - - + -
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Residues in contact with LYS1088 (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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1086A ASP* 3.1 11.5 + - - +
1087A LEU* 1.3 78.5 - - - +
1089A SER* 1.3 64.2 + - - +
1091A LEU* 3.2 4.3 + - - +
1092A ARG* 3.2 54.6 + - - +
1138A ALA* 3.3 12.9 + - + -
1139A ARG* 3.6 30.7 - - + +
1178A TRP* 4.6 13.9 - - - -
1204A GLU* 4.0 16.6 + - - +
1209A ALA* 3.6 22.8 + - + +
1210A GLU 4.9 5.5 + - - -
1211A GLN* 5.5 2.6 - - - +
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Residues in contact with SER1089 (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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1084A ARG 5.6 0.7 + - - -
1085A GLY* 5.7 0.2 - - - -
1086A ASP* 2.7 30.7 + - - -
1088A LYS* 1.3 79.3 - - - +
1090A TYR* 1.3 64.4 + - - +
1092A ARG* 3.6 12.8 + - - +
1093A SER* 3.1 22.0 + - - -
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Residues in contact with TYR1090 (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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1A 575 6.4 1.3 - - + -
1084A ARG* 4.0 41.7 + - + +
1086A ASP 3.2 12.9 + - - +
1087A LEU* 3.5 17.9 - - + +
1088A LYS 3.1 0.6 - - - -
1089A SER* 1.3 76.6 + - - +
1091A LEU* 1.3 66.0 + - - +
1093A SER* 2.6 27.5 + - - -
1094A LEU* 3.3 32.8 - - + +
1104A LEU* 3.8 22.8 - - + +
1105A ALA 5.6 0.2 + - - -
1115A MET* 3.8 24.8 - - + +
1143A VAL* 3.9 18.4 - - + -
1147A PHE* 3.2 27.6 - + - -
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Residues in contact with LEU1091 (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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1087A LEU* 2.9 47.5 + - + +
1088A LYS 3.2 4.2 + - - +
1090A TYR* 1.3 76.9 - - + +
1092A ARG* 1.3 63.0 + - - +
1094A LEU* 3.1 31.7 + - + +
1095A ARG 3.9 0.2 + - - -
1107A PRO* 4.7 2.0 - - + -
1115A MET* 4.5 9.2 - - + -
1138A ALA* 4.5 6.3 - - + -
1204A GLU 3.9 8.3 - - - +
1205A ILE* 3.9 41.7 - - + +
1208A LEU* 3.6 36.1 - - + +
1209A ALA* 4.0 13.0 - - + -
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Residues in contact with ARG1092 (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* 3.2 43.2 + - - +
1089A SER* 3.9 10.8 - - - +
1090A TYR 3.3 0.4 - - - -
1091A LEU* 1.3 74.7 - - - +
1093A SER* 1.3 62.8 + - - +
1094A LEU 3.0 4.7 - - - -
1095A ARG* 3.1 46.9 + - - +
1208A LEU 3.6 13.5 - - - +
1209A ALA* 3.0 24.2 + - + +
1210A GLU* 4.7 0.8 - - - +
1211A GLN* 4.6 12.7 - - - +
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Residues in contact with SER1093 (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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1A 575 6.3 2.5 - - - -
1089A SER 3.1 14.1 + - - -
1090A TYR* 2.6 26.2 + - - -
1092A ARG* 1.3 76.0 - - - +
1094A LEU* 1.3 61.6 + - - +
1095A ARG 3.3 6.0 + - - +
1104A LEU* 3.6 32.8 - - - +
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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