Contacts of the helix formed by residues 204 - 212 (chain B) in PDB entry 3VAH
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 SER 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 4.1 6.9 - - - +
180B GLN* 3.9 18.0 + - - -
202B PHE* 3.3 3.3 + - - +
203B ARG* 1.3 85.3 - - - +
205B VAL* 1.3 55.4 + - - +
206B ASP 3.7 1.4 + - - -
207B GLU* 3.1 40.2 + - - +
208B THR* 2.6 33.6 + - - -
405B SO4 3.8 16.8 - - - -
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.9 27.1 - - + -
148B ALA* 3.9 25.9 - - + +
149B ARG* 4.1 10.5 - - + +
204B SER* 1.3 69.9 - - - +
206B ASP* 1.3 74.0 + - - +
208B THR* 3.3 3.8 + - - -
209B THR* 3.2 25.6 + - - +
405B SO4 3.1 30.5 + - - +
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Residues in contact with ASP 206 (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 GLN* 3.2 28.4 + - - +
204B SER* 3.5 1.4 + - - -
205B VAL* 1.3 83.8 - - - +
207B GLU* 1.3 58.5 + - - +
209B THR* 3.4 8.9 + - - -
210B GLN* 3.1 33.2 + - + +
405B SO4 4.4 3.1 + - - -
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Residues in contact with GLU 207 (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 MET* 3.8 20.2 - - + +
178B LEU 4.1 8.5 - - - +
179B THR* 3.4 6.6 - - - -
180B GLN* 3.0 37.6 + - + +
185B PRO* 3.6 14.5 - - + +
202B PHE* 4.4 4.5 - - + -
203B ARG* 2.9 46.2 + - - +
204B SER* 3.1 24.3 + - - +
206B ASP* 1.3 75.2 - - - +
208B THR* 1.3 66.4 + - - +
210B GLN* 3.2 9.1 + - + +
211B ALA* 3.1 23.4 + - - +
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Residues in contact with THR 208 (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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148B ALA 3.4 21.3 - - - +
149B ARG* 3.3 7.5 - - - -
150B ARG 3.6 28.3 - - - +
151B LEU* 3.7 22.0 - - + +
202B PHE* 3.2 26.5 - - + +
204B SER 2.6 24.5 + - - -
205B VAL 3.6 2.0 - - - -
206B ASP 3.3 0.2 - - - -
207B GLU* 1.3 75.7 - - - +
209B THR* 1.3 61.7 + - - +
211B ALA* 3.3 15.9 + - - +
212B MET* 3.6 4.5 + - - +
228B ARG* 3.8 7.9 - - - +
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Residues in contact with THR 209 (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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205B VAL* 3.2 14.2 + - - +
206B ASP* 3.5 11.2 - - - +
208B THR* 1.3 78.7 - - - +
210B GLN* 1.3 72.0 + - - +
212B MET* 3.1 21.8 - - + +
228B ARG* 3.1 29.6 + - - +
232B TYR* 5.1 0.3 + - - -
407B SO4 5.3 3.4 - - - +
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Residues in contact with GLN 210 (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 MET* 4.8 1.3 - - + -
178B LEU* 3.5 60.8 - - + +
206B ASP* 3.1 24.1 + - + +
207B GLU* 3.2 8.2 + - + +
209B THR* 1.3 82.8 - - - +
211B ALA* 1.3 61.6 + - - +
212B MET 3.1 1.6 + - - -
213B ALA* 3.2 21.0 + - - +
214B PHE* 5.3 0.2 - - - -
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Residues in contact with ALA 211 (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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151B LEU* 3.8 7.2 - - + -
169B PHE* 5.7 3.4 - - + -
173B MET* 4.1 8.9 - - - -
200B LEU* 5.7 0.2 - - + -
202B PHE* 3.5 35.0 - - + -
207B GLU 3.1 9.7 + - - +
208B THR 3.6 7.6 - - - +
209B THR 3.2 0.6 - - - -
210B GLN* 1.3 71.5 - - - +
212B MET* 1.3 64.3 + - - +
213B ALA 3.1 2.7 - - - -
214B PHE* 3.1 39.0 + - + +
226B ILE* 4.2 6.6 - - - +
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Residues in contact with MET 212 (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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151B LEU* 3.9 27.1 - - - +
208B THR 3.6 3.2 + - - +
209B THR* 3.1 18.5 + - - +
210B GLN 3.1 0.2 - - - -
211B ALA* 1.3 78.3 - - - +
213B ALA* 1.3 55.8 + - - +
214B PHE 3.1 4.9 + - - -
215B ASP* 3.3 19.3 + - - +
226B ILE* 4.2 13.7 - - - +
227B ARG* 3.7 15.0 - - - -
228B ARG* 3.5 32.3 - - + +
407B SO4 3.5 28.3 - - - +
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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