Contacts of the helix formed by residues 176 - 186 (chain B) in PDB entry 3J0O
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 GLU 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 4.2 8.0 - - + +
13B VAL* 4.4 0.2 - - - +
14B LYS* 3.8 23.3 - - + -
175B GLU* 1.3 74.8 - - - +
177B ASP* 1.3 61.3 + - + +
178B VAL* 3.0 2.4 - - - +
179B LEU* 2.7 21.3 + - - +
180B VAL* 3.0 15.4 + - - +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ARG* 5.0 6.0 - - - +
176B GLU* 1.3 80.3 - - - +
178B VAL* 1.3 50.8 + - + +
180B VAL* 4.6 1.5 - - - +
181B ASN* 2.3 39.4 + - + +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B VAL* 4.8 0.3 - - - +
175B GLU* 4.3 7.6 - - + +
176B GLU 3.0 4.6 - - - +
177B ASP* 1.3 77.1 - - + +
179B LEU* 1.3 52.1 - - - +
181B ASN* 3.6 9.9 - - + +
182B GLN* 2.2 37.0 - - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 3.6 18.8 - - + +
14B LYS 4.6 0.4 - - - +
169B VAL* 5.8 0.2 - - - -
175B GLU* 3.2 35.9 - - + +
176B GLU* 2.7 14.5 + - - +
178B VAL* 1.3 79.4 - - - +
180B VAL* 1.3 61.0 + - - +
182B GLN* 3.1 6.2 + - - +
183B ILE* 2.9 23.9 + - - +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.4 47.6 - - + +
10B ARG* 3.7 6.5 - - + +
13B VAL* 3.4 7.3 - - + +
176B GLU 3.0 5.3 + - - +
177B ASP 4.7 1.1 - - - +
179B LEU* 1.3 74.6 - - - +
181B ASN* 1.3 58.5 + - - +
182B GLN 2.9 4.3 - - - -
183B ILE* 3.0 10.6 + - - +
184B LEU* 2.9 27.0 + - - +
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Residues in contact with ASN 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASP 2.3 33.3 + - - +
178B VAL* 3.6 7.0 - - - +
180B VAL* 1.3 75.0 - - - +
182B GLN* 1.3 56.3 + - - +
184B LEU* 4.3 8.7 - - - +
185B MET* 3.4 21.7 + - - +
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Residues in contact with GLN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LYS 4.7 0.2 - - - +
168B ALA 4.4 5.1 - - - +
169B VAL* 3.4 30.0 - - + +
178B VAL 2.2 28.1 + - - +
179B LEU* 3.2 11.9 - - - +
180B VAL 2.9 0.6 - - - -
181B ASN* 1.3 80.1 - - - +
183B ILE* 1.3 52.4 + - - +
184B LEU 3.3 0.4 - - - -
185B MET* 3.4 8.0 - - - +
186B SER* 2.7 32.3 + - - -
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Residues in contact with ILE 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B VAL* 6.2 0.2 - - + -
33B GLU 5.0 1.6 - - - +
34B LEU* 3.3 32.6 - - + +
179B LEU 2.9 11.7 + - - +
180B VAL* 3.0 13.7 + - - +
182B GLN* 1.3 76.2 - - - +
184B LEU* 1.3 59.9 + - - +
186B SER* 3.0 28.3 + - - +
187B VAL* 3.8 3.1 - - - +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL 2.9 14.3 + - - +
181B ASN* 4.3 9.6 - - - +
183B ILE* 1.3 72.7 - - - +
185B MET* 1.3 54.5 + - - +
186B SER 2.9 1.3 - - - -
187B VAL* 2.7 44.3 + - - +
191B VAL* 5.3 0.2 - - - +
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Residues in contact with MET 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.0 15.4 - - - +
54B LYS 2.7 25.6 + - - +
181B ASN 3.4 19.1 + - - +
182B GLN* 3.4 10.9 + - - +
183B ILE 3.3 0.2 - - - -
184B LEU* 1.3 77.7 - - - +
186B SER* 1.3 53.8 + - - +
187B VAL 2.9 8.2 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU 4.8 3.1 - - - +
36B VAL* 6.1 1.4 - - - +
53B LEU* 4.1 2.5 - - - -
55B LEU* 3.1 23.6 - - - +
166B ALA 3.7 12.5 - - - +
167B VAL* 3.3 30.8 - - - +
168B ALA 3.9 4.9 - - - -
182B GLN 2.7 15.9 + - - -
183B ILE* 3.0 19.4 - - - +
184B LEU 2.9 0.6 - - - -
185B MET* 1.3 74.0 - - - +
187B VAL* 1.3 58.1 + - - +
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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