Contacts of the helix formed by residues 1125 - 1134 (chain E) in PDB entry 5B2G
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 ARG1125 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119E ARG* 3.8 24.5 + - - +
1120E MET* 2.8 75.2 + - - +
1121E LEU 4.5 0.4 + - - -
1123E GLN* 4.3 22.0 - - + +
1124E LYS* 1.3 70.2 - - - +
1126E TRP* 1.3 63.9 + - - +
1127E ASP 3.5 2.5 - - - -
1128E GLU* 3.4 41.9 + - + +
1129E ALA* 3.3 12.2 + - - +
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Residues in contact with TRP1126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091E LEU* 4.0 11.4 - - + -
1095E ARG* 3.9 34.0 - - - +
1121E LEU* 4.5 18.2 - - + -
1124E LYS* 3.5 42.9 + - + +
1125E ARG* 1.3 72.9 - - - +
1127E ASP* 1.3 65.5 + - - +
1129E ALA* 3.9 4.2 - - + +
1130E ALA* 2.9 32.7 + - - +
1153E PHE* 3.4 53.8 - + - -
1154E ARG* 3.3 37.0 + - + +
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Residues in contact with ASP1127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125E ARG 3.5 0.4 - - - -
1126E TRP* 1.3 80.7 - - - +
1128E GLU* 1.3 61.8 + - + +
1130E ALA* 3.6 4.9 - - - +
1131E VAL* 3.0 35.1 + - + +
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Residues in contact with GLU1128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120E MET* 4.1 23.3 - - - +
1125E ARG* 3.4 47.0 + - + +
1126E TRP 3.4 0.2 - - - -
1127E ASP* 1.3 76.0 - - + +
1129E ALA* 1.3 61.2 + - - +
1131E VAL* 3.2 10.4 + - - +
1132E ASN* 3.0 27.5 + - - +
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Residues in contact with ALA1129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117E SER* 4.3 7.9 + - - +
1120E MET* 3.5 19.6 + - - +
1121E LEU* 3.9 21.1 - - + -
1125E ARG 3.3 17.8 + - - +
1126E TRP* 3.9 8.1 - - + +
1128E GLU* 1.3 78.0 - - - +
1130E ALA* 1.3 58.0 + - - +
1132E ASN* 3.2 7.1 + - - +
1133E LEU* 2.9 36.7 + - + +
1153E PHE* 5.9 2.0 - - + -
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Residues in contact with ALA1130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126E TRP 2.9 20.2 + - - +
1127E ASP* 3.6 6.3 - - - +
1129E ALA* 1.3 75.8 - - - +
1131E VAL* 1.3 62.1 + - + +
1133E LEU* 3.2 15.3 + - + +
1134E ALA* 3.2 19.8 + - - +
1150E ILE* 4.7 19.2 - - + +
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Residues in contact with VAL1131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B SER 5.3 3.6 - - - +
309B ASN* 5.0 9.4 - - - +
1127E ASP* 3.0 21.0 + - + +
1128E GLU* 3.5 11.9 - - - +
1130E ALA* 1.3 77.7 - - + +
1132E ASN* 1.3 60.7 + - - +
1134E ALA* 3.3 19.1 - - + +
1135E LYS* 3.2 26.3 - - - +
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Residues in contact with ASN1132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B PRO* 5.7 2.8 - - - +
236B GLN* 5.3 3.6 + - - -
1114E PHE* 5.1 5.4 - - - +
1116E ASN* 3.4 29.6 + - - +
1117E SER* 2.7 34.6 + - - +
1120E MET* 5.0 8.6 - - - +
1128E GLU 3.0 13.2 + - - +
1129E ALA* 3.2 10.7 + - - +
1131E VAL* 1.3 72.9 - - - +
1133E LEU* 1.3 61.6 + - - +
1134E ALA 3.1 1.8 - - - -
1135E LYS* 2.9 53.3 + - - +
1136E SER* 4.7 0.5 + - - -
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Residues in contact with LEU1133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102E MET* 5.0 12.3 - - + -
1114E PHE* 6.2 3.1 - - + -
1117E SER* 4.1 20.9 - - - +
1121E LEU* 6.2 2.7 - - + -
1129E ALA* 2.9 21.5 + - + +
1130E ALA* 3.2 15.9 + - - +
1132E ASN* 1.3 72.4 - - - +
1134E ALA* 1.3 60.7 + - - +
1135E LYS 3.0 1.8 - - - -
1136E SER* 2.5 28.6 + - - +
1138E TRP* 3.6 26.9 - - + -
1139E TYR* 3.6 12.5 - - - +
1150E ILE* 3.8 36.3 - - + -
1153E PHE* 5.2 14.8 - - + -
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Residues in contact with ALA1134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B ALA* 4.8 2.6 - - - +
230B ASN* 3.9 28.3 + - + +
232B TYR* 4.9 4.7 + - + -
1130E ALA 3.2 9.9 + - - +
1131E VAL* 3.3 16.8 - - + +
1132E ASN 3.1 0.4 - - - -
1133E LEU* 1.3 76.6 - - - +
1135E LYS* 1.3 56.9 + - + +
1136E SER 3.2 10.4 + - - +
1139E TYR* 4.1 23.6 - - + -
1140E ASN* 4.7 5.5 + - - +
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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