Contacts of the helix formed by residues 1136 - 1142 (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 SER1136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B ALA 3.8 9.4 - - - -
205B ALA* 3.9 6.8 - - - +
206B THR 4.6 1.5 + - - -
1114E PHE* 3.5 25.6 - - - -
1132E ASN 4.8 1.1 - - - -
1133E LEU* 2.5 30.2 + - - +
1134E ALA 3.2 4.0 + - - +
1135E LYS* 1.3 77.2 - - - +
1137E ARG* 1.3 63.3 + - - +
1138E TRP* 4.0 11.2 + - - +
1139E TYR* 3.6 16.3 + - - +
1140E ASN* 3.9 18.2 + - - +
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Residues in contact with ARG1137 (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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203B ALA 4.5 15.1 - - - +
204B ALA* 3.9 19.3 + - - +
205B ALA 5.4 0.2 - - - -
206B THR* 3.0 33.2 - - - +
239B ASN* 5.0 13.6 - - - +
241B HIS* 6.4 0.2 - - - -
1114E PHE* 4.9 7.3 - - + -
1136E SER* 1.3 70.7 - - - +
1138E TRP* 1.3 64.5 + - - +
1139E TYR 3.1 2.7 - - - -
1140E ASN* 3.1 4.0 + - - +
1141E GLN* 3.0 40.3 + - + +
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Residues in contact with TRP1138 (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* 4.5 29.6 - - + +
1105E GLN* 4.1 23.5 + - - +
1106E MET* 4.0 34.6 - - + +
1114E PHE* 5.2 9.9 - - + -
1133E LEU* 3.6 32.1 - - + -
1136E SER* 3.3 12.0 - - - +
1137E ARG* 1.3 78.3 - - - +
1139E TYR* 1.3 62.6 + - + +
1141E GLN* 5.6 1.1 - - - -
1142E THR* 3.5 19.2 + - - +
1145E ARG* 5.1 4.6 - - + +
1146E ALA* 3.4 43.3 - - + +
1149E VAL* 4.7 16.2 - - + -
1150E ILE* 4.0 22.9 - - + -
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Residues in contact with TYR1139 (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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230B ASN* 5.8 3.8 - - - -
1133E LEU 3.6 19.1 - - - +
1134E ALA* 4.1 24.7 - - + -
1136E SER* 3.6 5.4 + - - +
1137E ARG 3.1 1.0 - - - -
1138E TRP* 1.3 83.5 - - + +
1140E ASN* 1.3 75.2 + - - +
1141E GLN 3.6 0.2 - - - -
1142E THR 4.7 0.4 - - - -
1143E PRO* 3.6 22.0 - - + +
1146E ALA* 3.7 17.9 - - + -
1147E LYS* 3.8 36.2 - - + +
1150E ILE* 4.5 11.2 - - + -
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Residues in contact with ASN1140 (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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206B THR* 2.3 38.3 + - + +
207B GLU* 4.5 7.1 - - - +
208B ARG* 5.9 1.4 + - - -
1134E ALA 4.7 5.7 + - - +
1136E SER 3.9 9.8 + - - +
1137E ARG* 3.1 8.3 + - - +
1139E TYR* 1.3 98.8 - - - +
1141E GLN* 1.3 62.2 + - - +
1142E THR 3.6 0.2 - - - -
1143E PRO* 4.0 11.6 - - - +
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Residues in contact with GLN1141 (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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1137E ARG* 3.0 24.4 + - + +
1138E TRP* 5.5 0.7 - - - -
1140E ASN* 1.3 79.1 - - - +
1142E THR* 1.3 69.7 + - + +
1143E PRO* 3.5 6.6 - - - +
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Residues in contact with THR1142 (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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1105E GLN* 4.6 15.0 + - - +
1138E TRP* 3.5 16.7 + - - -
1139E TYR 4.2 2.2 - - - -
1141E GLN* 1.3 87.3 - - + +
1143E PRO* 1.3 68.8 - - - +
1144E ASN 3.6 1.3 - - - -
1145E ARG* 3.9 11.3 + - - +
1146E ALA* 3.4 19.2 + - - +
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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