Contacts of the helix formed by residues 1136 - 1145 (chain E) in PDB entry 1AWV
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 MET1136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1095E PRO* 4.5 11.2 - - + +
1096E GLY* 3.4 29.2 - - - +
1114E ILE* 4.5 0.7 - - + -
1115E CYS 3.8 18.8 - - - +
1116E THR* 4.0 9.9 - - + -
1132E VAL* 3.7 20.7 - - + +
1134E GLU* 3.7 1.4 - - - -
1135E GLY* 1.3 77.3 - - - +
1137E ASN* 1.3 51.9 + - - +
1139E VAL* 3.0 42.6 + - + +
1140E GLU* 2.8 52.0 + - - +
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Residues in contact with ASN1137 (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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1135E GLY* 3.6 14.0 - - - +
1136E MET* 1.3 85.5 - - - +
1138E ILE* 1.3 93.0 + - + +
1140E GLU* 3.3 11.9 + - - +
1141E ALA* 3.3 21.3 + - - +
1144E ARG* 4.8 2.1 + - - -
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Residues in contact with ILE1138 (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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1010E ILE* 3.9 34.8 - - + -
1017E LEU* 3.9 18.8 - - + +
1018E GLY* 3.7 30.1 - - - +
1019E ARG 3.7 15.7 - - - +
1020E VAL* 4.7 4.9 - - + -
1135E GLY 2.8 9.9 + - - +
1137E ASN* 1.3 104.8 - - + +
1139E VAL* 1.3 60.9 + - - +
1141E ALA* 3.5 4.8 + - - +
1142E MET* 2.8 28.4 + - + +
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Residues in contact with VAL1139 (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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1020E VAL* 4.0 22.9 - - + -
1062E CYS* 4.3 4.3 - - - -
1114E ILE* 4.1 20.6 - - + -
1116E THR* 3.9 12.4 - - + +
1135E GLY 3.5 12.1 - - - +
1136E MET* 3.2 39.5 - - + +
1138E ILE* 1.3 78.4 - - + +
1140E GLU* 1.3 58.1 + - - +
1142E MET* 3.2 26.2 - - + +
1143E GLU* 3.0 26.7 + - - +
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Residues in contact with GLU1140 (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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1095E PRO* 5.9 1.7 - - - +
1116E THR* 4.9 5.0 - - - +
1136E MET* 2.8 38.1 + - - +
1137E ASN* 3.4 15.1 - - - +
1138E ILE 3.2 0.2 - - - -
1139E VAL* 1.3 75.3 - - - +
1141E ALA* 1.3 60.3 + - - +
1142E MET 3.0 4.3 - - - -
1143E GLU* 3.4 19.8 + - - +
1144E ARG* 3.3 36.7 + - - +
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Residues in contact with ALA1141 (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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1017E LEU* 4.3 20.1 - - + +
1137E ASN 3.3 8.4 + - - +
1138E ILE* 3.7 7.6 - - - +
1140E GLU* 1.3 78.7 - - - +
1142E MET* 1.3 62.8 + - - +
1144E ARG* 3.3 36.8 + - - +
1145E PHE* 3.6 24.9 - - + -
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Residues in contact with MET1142 (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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1010E ILE* 3.3 50.3 - - + -
1012E VAL* 6.3 0.2 - - - -
1017E LEU* 5.1 4.5 - - + -
1020E VAL* 5.2 2.0 - - + -
1053E PHE* 4.2 20.4 - - + -
1056E ILE* 3.8 10.9 - - + +
1062E CYS* 3.9 27.8 - - - -
1114E ILE* 4.9 2.9 - - + -
1138E ILE* 2.8 23.5 + - + +
1139E VAL* 3.2 23.3 - - + +
1141E ALA* 1.3 78.2 - - - +
1143E GLU* 1.3 57.6 + - - +
1145E PHE* 3.1 28.3 + - - +
1156E ILE* 4.2 17.1 - - + +
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Residues in contact with GLU1143 (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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1056E ILE* 3.6 12.6 - - + -
1057E ILE 4.0 1.7 - - - +
1058E PRO* 3.0 37.6 - - + +
1059E GLY* 2.6 35.0 + - - -
1062E CYS* 4.0 13.2 - - - -
1116E THR* 2.6 32.3 + - + +
1139E VAL 3.0 15.5 + - - +
1140E GLU* 3.5 22.3 - - - +
1142E MET* 1.3 72.5 - - - +
1144E ARG* 1.3 59.7 + - + +
1145E PHE 2.9 6.3 + - - -
1146E GLY 3.3 2.2 + - - -
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Residues in contact with ARG1144 (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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1058E PRO* 5.2 2.0 - - - +
1137E ASN 4.8 1.8 + - - -
1140E GLU* 3.3 19.6 + - - +
1141E ALA* 3.3 44.0 - - - +
1142E MET 3.2 1.2 - - - -
1143E GLU* 1.3 79.5 - - + +
1145E PHE* 1.3 71.0 + - + +
1146E GLY 3.3 3.3 + - - -
1153E SER* 5.1 0.9 + - - -
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Residues in contact with PHE1145 (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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1012E VAL* 3.7 39.3 - - + -
1017E LEU* 5.4 5.2 - - + -
1056E ILE* 4.1 3.5 - - - +
1141E ALA* 3.6 19.1 - - + -
1142E MET* 3.1 12.9 + - - +
1143E GLU 2.9 1.0 - - - -
1144E ARG* 1.3 89.4 - - + +
1146E GLY* 1.3 58.7 + - - +
1152E THR* 3.5 24.1 - - - +
1153E SER* 4.0 18.0 + - - +
1154E LYS* 3.9 31.9 - - + +
1156E ILE* 3.9 17.9 - - + -
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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