Contacts of the helix formed by residues 179 - 184 (chain B) in PDB entry 2QVH
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 ASP 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B GLU* 3.0 21.4 - - + +
157B GLN* 2.9 9.3 - - - +
177B ALA 4.0 0.6 + - - -
178B ALA* 1.3 73.9 - - - +
180B GLU* 1.3 70.8 + - - +
181B SER 3.0 0.4 - - - -
182B ILE* 2.8 20.8 + - - +
183B ARG* 2.8 42.4 + - - +
201B VAL* 3.7 19.5 - - + +
203B LYS* 3.4 6.5 - - - +
400B MG 2.0 27.8 - - - -
5551B OSB 3.1 12.0 + - - +
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Residues in contact with GLU 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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132B ASN* 3.1 37.0 + - - +
133B GLY* 5.3 0.9 - - - -
157B GLN* 3.2 34.0 - - + +
160B ALA* 5.6 4.3 - - - +
179B ASP* 1.3 91.0 - - - +
181B SER* 1.3 58.2 + - - +
183B ARG* 3.3 30.3 + - - +
184B ARG* 2.9 41.4 + - + +
400B MG 3.9 2.6 - - - -
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLN* 2.8 30.9 + - - +
160B ALA 4.1 5.6 + - - -
162B VAL* 3.9 24.2 + - - +
165B LEU* 3.8 11.9 - - - +
178B ALA* 4.2 2.2 - - - -
179B ASP 3.0 1.0 - - - -
180B GLU* 1.3 76.6 - - - +
182B ILE* 1.3 58.2 + - - +
185B ALA* 3.2 23.9 - - - +
187B ASP 4.8 0.3 - - - +
188B PRO* 4.1 4.3 - - - +
191B VAL* 3.7 26.6 - - - +
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Residues in contact with ILE 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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49B ARG* 5.2 1.2 + - - -
178B ALA* 3.5 26.5 - - + +
179B ASP 2.8 8.0 + - - +
181B SER* 1.3 80.2 - - - +
183B ARG* 1.3 61.9 + - + +
184B ARG 3.6 0.6 + - - -
185B ALA 4.4 2.4 + - - -
188B PRO* 3.5 36.2 - - + +
191B VAL* 3.7 26.7 - - + -
200B VAL* 3.7 28.0 - - + -
201B VAL 3.7 17.0 - - - +
207B LEU* 4.2 11.9 - - + +
216B LEU* 3.7 24.5 - - + -
220B CYS* 4.5 7.6 - - - -
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 4.6 8.1 + - - -
46B GLU* 5.3 1.7 - - - +
49B ARG* 4.2 14.5 + - - -
50B TRP* 6.3 0.8 - - - -
132B ASN* 4.5 0.6 - - - +
179B ASP* 2.8 50.4 + - - +
180B GLU* 3.3 27.9 + - - +
182B ILE* 1.3 80.4 - - + +
184B ARG* 1.3 85.1 + - + +
185B ALA 3.6 1.6 + - - -
201B VAL 5.9 1.3 - - - +
203B LYS* 3.4 27.2 - - + +
206B PRO* 3.8 34.9 - - + +
207B LEU* 4.0 16.4 - - + -
5551B OSB 3.6 21.3 + - - -
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Residues in contact with ARG 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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41B GLU* 5.7 0.6 - - - +
42B TYR* 3.7 26.2 + - - -
46B GLU* 2.7 42.4 + - - +
180B GLU* 2.9 28.3 + - + +
183B ARG* 1.3 106.9 - - + +
185B ALA* 1.3 57.6 + - - +
206B PRO* 6.2 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