Contacts of the helix formed by residues 204 - 211 (chain A) in PDB entry 3VAG
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ARG* 3.8 8.5 - - - +
180A GLN* 4.7 1.0 + - - -
202A PHE* 3.3 3.3 - - - +
203A ARG* 1.3 80.4 - - - +
205A VAL* 1.3 60.6 + - - +
206A ASP* 3.9 2.7 + - - -
207A GLU* 2.9 40.4 + - - +
208A THR* 2.9 26.2 + - - -
403A DIO 3.7 20.4 + - - -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA* 4.0 29.4 - - + +
149A ARG* 3.9 18.8 - - + +
204A SER* 1.3 71.7 - - - +
206A ASP* 1.3 75.5 + - - +
208A THR* 3.4 6.9 + - - -
209A THR* 3.3 23.7 + - - +
402A DIO 5.3 8.5 - - - +
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLN* 3.5 28.0 + - - +
204A SER* 3.5 2.7 + - - +
205A VAL* 1.3 88.5 - - - +
207A GLU* 1.3 61.5 + - - +
209A THR* 3.3 9.8 + - - -
210A GLN* 3.1 31.9 + - + +
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A MET* 3.9 13.5 - - + +
178A LEU 4.2 7.4 - - - +
179A THR* 3.4 5.9 - - - +
180A GLN* 3.0 36.2 + - + +
185A PRO* 4.0 11.2 - - + +
202A PHE* 4.0 6.5 - - + -
203A ARG* 2.9 47.6 + - - +
204A SER* 2.9 26.6 + - - +
206A ASP* 1.3 73.9 - - - +
208A THR* 1.3 64.0 + - - +
210A GLN* 3.8 7.0 - - - +
211A ALA* 3.1 24.1 + - - +
403A DIO 3.2 10.6 - - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA 3.6 15.7 - - - +
149A ARG* 3.4 9.2 - - - -
150A ARG 3.8 16.2 - - - +
151A LEU* 3.6 37.3 - - + +
202A PHE* 3.2 26.1 - - + +
204A SER 2.9 19.9 + - - -
205A VAL 3.4 10.0 + - - -
206A ASP 3.3 0.4 - - - -
207A GLU* 1.3 78.1 - - - +
209A THR* 1.3 63.2 + - - +
211A ALA 3.5 6.2 + - - -
212A MET* 3.7 4.0 - - - +
228A ARG* 3.9 11.4 - - - +
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Residues in contact with THR 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.3 14.7 + - - +
206A ASP* 3.3 12.3 + - - -
207A GLU 3.3 0.6 - - - -
208A THR* 1.3 76.5 - - - +
210A GLN* 1.3 71.6 + - - +
212A MET* 3.3 20.5 + - - +
213A ALA 4.6 0.2 + - - -
228A ARG* 3.1 30.6 + - - +
407A SO4 4.7 6.5 - - - +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A MET* 5.0 0.4 - - + -
177A GLY 5.7 0.4 + - - -
178A LEU* 3.9 51.1 + - + +
180A GLN* 4.4 13.7 + - - +
206A ASP* 3.1 22.9 + - + +
207A GLU* 3.8 5.8 - - - +
209A THR* 1.3 82.6 - - - +
211A ALA* 1.3 60.8 + - - +
212A MET 3.1 1.8 + - - -
213A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.0 6.3 - - + -
169A PHE* 5.6 3.6 - - + -
173A MET* 4.0 13.7 - - - -
200A LEU* 5.9 0.4 - - + -
202A PHE* 3.6 30.1 - - + -
207A GLU 3.1 16.9 + - - +
208A THR 3.8 4.7 - - - +
209A THR 3.3 0.6 - - - -
210A GLN* 1.3 75.2 - - - +
212A MET* 1.3 60.9 + - - +
213A ALA 3.1 0.4 - - - -
214A PHE* 3.2 34.8 + - + +
226A ILE* 4.3 7.1 - - - +
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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