Contacts of the helix formed by residues 170 - 176 (chain A) in PDB entry 1QVA
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 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ALA 6.0 0.4 - - - +
66A GLN* 4.8 4.3 - - - +
67A SER* 2.7 24.3 + - - +
71A LYS* 3.4 19.0 - - + +
97A PRO* 3.5 12.8 - - + +
101A LEU* 3.0 38.8 - - - +
169A ASP* 1.3 83.9 + - - +
171A ALA* 1.3 65.5 + - - +
172A ASP* 3.3 8.7 - - - +
173A GLU* 3.0 28.2 + - + +
174A MET* 3.1 9.2 + - - +
199A LEU 3.0 12.5 + - - -
200A SER* 4.5 3.1 - - - +
201A ALA 5.5 1.3 - - - +
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Residues in contact with ALA 171 (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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168A LEU* 4.4 9.6 - - + +
169A ASP 3.3 3.0 - - - -
170A GLU* 1.3 75.9 - - - +
172A ASP* 1.3 63.3 + - - +
174A MET* 3.2 11.9 + - + +
175A LEU* 3.0 33.8 + - + +
183A ILE* 6.1 0.9 - - + -
198A LEU* 3.6 41.3 - - + -
199A LEU 2.9 9.0 + - - +
200A SER* 4.1 2.2 - - - -
207A VAL* 4.3 5.4 - - + -
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Residues in contact with ASP 172 (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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170A GLU* 3.6 8.3 - - - +
171A ALA* 1.3 76.0 - - - +
173A GLU* 1.3 90.9 + - - +
175A LEU* 3.9 3.4 - - - +
176A SER* 2.8 35.6 + - - +
200A SER* 2.8 22.4 + - - +
201A ALA* 3.5 7.8 + - - +
202A THR* 2.7 41.6 + - - +
204A PRO* 4.2 8.7 - - + -
207A VAL* 3.9 15.0 - - + +
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Residues in contact with GLU 173 (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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97A PRO* 3.8 18.6 - - + +
170A GLU* 3.0 23.7 + - + +
172A ASP* 1.3 96.6 + - - +
174A MET* 1.3 60.7 + - - +
176A SER* 3.6 9.1 + - - -
177A SER* 2.7 34.5 + - - +
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Residues in contact with MET 174 (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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95A LEU* 3.6 23.1 - - + +
96A ALA 3.6 34.5 - - - +
97A PRO* 3.7 6.7 - - + +
146A PRO* 3.6 21.8 - - + -
168A LEU* 3.8 23.6 - - + -
169A ASP 3.7 14.6 - - - +
170A GLU 3.1 7.4 + - - +
171A ALA* 3.5 10.5 - - - +
173A GLU* 1.3 77.6 - - - +
175A LEU* 1.3 62.0 + - - +
177A SER* 3.2 6.5 + - - -
179A PHE* 3.1 36.1 + - + +
183A ILE* 3.5 26.9 - - + -
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Residues in contact with LEU 175 (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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171A ALA* 3.0 29.9 + - + +
172A ASP* 3.9 3.6 - - - +
174A MET* 1.3 72.9 - - - +
176A SER* 1.3 57.3 + - - +
177A SER 2.9 4.9 - - - -
178A GLY* 2.8 22.0 + - - -
179A PHE 4.0 2.0 + - - +
180A LYS* 3.7 39.6 + - + +
183A ILE* 3.9 19.1 - - + -
198A LEU* 5.9 0.7 - - + -
206A ASP* 4.0 50.5 - - + +
207A VAL* 4.2 8.3 - - + +
210A VAL* 4.1 16.6 - - + -
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Residues in contact with SER 176 (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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172A ASP* 2.8 24.1 + - - +
173A GLU* 4.1 11.5 + - - -
174A MET 3.4 0.2 - - - -
175A LEU* 1.3 75.7 - - - +
177A SER* 1.3 58.0 + - - +
178A GLY 3.3 0.4 + - - -
206A ASP* 5.9 0.7 - - - -
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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