Contacts of the helix formed by residues 178 - 186 (chain B) in PDB entry 2VGO
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 LEU 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B GLY 3.5 2.8 + - - -
177B GLU* 1.3 72.6 - - - +
179B TYR* 1.3 59.7 + - - +
181B GLU* 3.0 5.7 + - - +
182B LEU* 2.9 26.5 + - + -
188B PHE* 4.1 12.9 - - + -
196B PHE* 4.0 30.5 - - + -
219B PRO* 4.0 17.3 - - + +
222B LEU* 3.1 47.6 + - + +
223B LEU 4.9 0.7 - - - +
224B MET* 4.0 23.1 - - + -
230B LEU* 4.5 4.9 - - + -
282B PHE* 3.4 30.5 - - + -
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Residues in contact with TYR 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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177B GLU* 3.2 38.2 + - + -
178B LEU* 1.3 78.6 - - - +
180B LYS* 1.3 80.9 + - + +
182B LEU* 3.4 6.0 + - - +
183B GLN* 3.0 60.9 + - + +
219B PRO* 3.8 34.7 + - + -
220B GLU* 3.9 33.7 - - + +
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Residues in contact with LYS 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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177B GLU* 3.3 35.2 + - + +
178B LEU 3.2 0.6 - - - -
179B TYR* 1.3 105.5 - - + +
181B GLU* 1.3 59.9 + - - +
183B GLN* 3.5 15.9 + - - +
184B LYS* 3.0 28.4 + - - +
1359B AD5 5.3 14.2 - - - -
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Residues in contact with GLU 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 GLU 3.5 2.6 + - - +
178B LEU 3.0 10.0 + - - +
180B LYS* 1.3 77.2 - - - +
182B LEU* 1.3 63.8 + - - +
184B LYS* 3.4 13.6 + - - +
185B HIS* 3.1 58.4 + - - +
188B PHE* 3.6 12.8 - - + -
192B ARG* 2.8 34.8 + - - +
224B MET* 3.7 23.3 - - + +
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Residues in contact with LEU 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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178B LEU* 2.9 12.5 + - + +
179B TYR* 3.6 9.2 - - - +
180B LYS 3.4 0.2 - - - -
181B GLU* 1.3 73.9 - - - +
183B GLN* 1.3 55.5 + - - +
185B HIS* 5.0 0.4 - - - -
186B GLY* 2.8 52.6 + - - +
187B ARG* 3.9 14.1 - - - -
188B PHE* 3.7 26.2 - - + +
219B PRO* 4.3 18.6 - - + -
281B GLU* 3.9 37.0 - - + +
282B PHE* 4.0 19.1 - - + +
285B GLY* 4.8 4.0 - - - +
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Residues in contact with GLN 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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179B TYR* 3.0 44.6 + - + +
180B LYS* 3.5 19.7 - - - +
182B LEU* 1.3 77.0 - - - +
184B LYS* 1.3 63.1 + - - +
186B GLY* 3.5 7.8 + - - -
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Residues in contact with LYS 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 LYS 3.0 18.0 + - - +
181B GLU* 3.6 17.4 + - - +
182B LEU 3.3 0.2 - - - -
183B GLN* 1.3 79.4 - - - +
185B HIS* 1.3 78.9 + - + +
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Residues in contact with HIS 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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181B GLU* 3.1 53.6 + - - +
182B LEU 4.2 1.1 - - - +
184B LYS* 1.3 97.5 - - + +
186B GLY* 1.3 55.8 + - - +
187B ARG* 3.0 29.1 + - - +
188B PHE* 4.7 9.9 - + + -
192B ARG* 4.4 11.4 + - - -
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Residues in contact with GLY 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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182B LEU* 2.8 20.9 + - - +
183B GLN 3.5 6.1 + - - -
184B LYS 3.5 2.6 - - - -
185B HIS* 1.3 73.8 - - - +
187B ARG* 1.3 62.5 + - - -
285B GLY* 3.2 25.5 - - - +
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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