Contacts of the helix formed by residues 176 - 183 (chain B) in PDB entry 3HAO
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 ASN 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.3 39.2 - - + +
172B LYS* 2.9 20.4 + - - +
173B VAL* 3.3 10.9 - - - +
175B ARG* 1.2 101.8 + - - +
177B VAL* 1.3 69.7 + - + +
179B VAL* 3.9 0.2 - - - +
180B VAL* 3.1 26.9 + - - +
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Residues in contact with VAL 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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173B VAL* 2.8 21.6 + - + +
174B LEU* 3.6 7.2 - - - +
176B ASN* 1.3 79.4 - - + +
178B THR* 1.3 57.7 + - - +
180B VAL* 4.0 3.3 - - - +
181B LEU* 3.0 53.0 + - + +
214B SER 4.5 8.3 - - - +
215B ALA* 5.1 0.4 - - - -
219B PHE* 4.7 18.6 - - + +
222B ILE* 3.8 26.7 - - + -
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Residues in contact with THR 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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97B LEU* 3.8 11.3 - - + +
149B LEU* 4.8 1.8 - - + -
152B LEU* 4.1 23.1 - - + -
174B LEU 3.2 12.2 + - - -
175B ARG* 3.7 9.4 - - - -
176B ASN 3.1 0.2 - - - -
177B VAL* 1.3 78.3 - - - +
179B VAL* 1.3 61.2 + - - +
181B LEU* 5.0 0.9 - - - -
182B TRP* 2.9 68.7 + - + +
215B ALA* 6.5 0.2 - - - -
219B PHE* 3.6 21.9 - - - -
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Residues in contact with VAL 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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190A LEU* 5.6 6.7 - - + -
191A ILE* 4.2 13.9 - - + -
196A ALA* 4.8 7.0 - - + -
198A ILE* 3.6 26.5 - - + -
149B LEU* 4.1 34.0 - - + +
152B LEU* 5.7 2.7 - - + -
153B PHE* 5.0 10.8 - - + +
175B ARG* 3.1 34.4 + - + +
176B ASN 3.4 0.4 + - - +
178B THR* 1.3 79.6 - - + +
180B VAL* 1.3 63.7 + - - +
182B TRP* 4.5 0.2 - - - +
183B SER* 3.4 26.2 + - - -
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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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187A VAL* 5.7 0.7 - - - +
191A ILE* 4.4 26.3 - - + +
198A ILE* 3.7 29.8 - - + -
199A VAL* 4.9 4.9 - - + -
176B ASN 3.1 18.0 + - - +
177B VAL* 4.0 3.8 - - - +
179B VAL* 1.3 77.3 - - - +
181B LEU* 1.3 68.9 + - + +
183B SER* 3.5 13.2 + - - -
184B ALA* 4.0 8.5 + - - +
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Residues in contact with LEU 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 VAL* 3.0 34.9 + - + +
178B THR* 4.3 1.1 - - - +
180B VAL* 1.3 82.5 - - + +
182B TRP* 1.3 71.4 + - + +
184B ALA* 3.0 11.1 + - - +
185B TYR* 3.2 5.6 - - + -
210B VAL* 6.1 1.1 - - + -
211B LEU* 3.2 40.1 - - + +
214B SER* 3.6 21.3 - - - +
215B ALA* 3.3 42.2 - - + +
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Residues in contact with TRP 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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90B THR* 3.7 35.7 - - - -
93B LEU* 4.4 14.3 - - + +
94B ALA* 5.3 7.0 - - + -
115B ASP* 4.5 2.5 - - - -
118B MET* 4.4 10.5 - - + -
145B MET* 4.0 5.9 - - + +
148B ILE* 4.1 31.4 - - + -
149B LEU* 4.2 23.3 - - + -
152B LEU* 5.8 1.8 - - + -
178B THR* 2.9 52.5 + - + +
181B LEU* 1.3 75.7 - - + +
183B SER* 1.3 61.8 + - - +
184B ALA 3.0 6.3 + - - -
185B TYR* 3.1 21.7 + + - +
186B PRO* 3.2 10.2 - - - +
215B ALA* 4.7 3.1 - - + +
301B RET 3.3 56.4 - - + +
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Residues in contact with SER 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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187A VAL* 3.5 37.5 - - - +
190A LEU* 4.4 20.0 - - - -
191A ILE* 4.2 4.8 - - - +
145B MET* 3.9 16.8 - - - -
146B LEU* 6.3 0.4 - - - -
149B LEU* 5.4 3.1 - - - +
179B VAL* 3.4 19.7 + - - -
180B VAL 3.5 8.1 + - - -
182B TRP* 1.3 77.0 - - - +
184B ALA* 1.3 62.2 + - - +
186B PRO* 3.4 13.6 - - - +
187B VAL* 4.2 2.6 - - - +
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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