Contacts of the helix formed by residues 203 - 208 (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 LYS 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B ASP* 3.4 28.7 - - - +
183B ARG* 3.4 27.3 - - - +
201B VAL* 4.3 1.0 + - + -
202B LEU* 1.3 74.1 - - - +
204B VAL* 1.3 67.0 + - - +
205B GLN 3.6 0.2 - - - -
206B PRO* 3.4 20.8 - - + +
207B LEU* 3.2 29.8 + - - +
227B SER* 2.9 41.2 + - - +
228B SER 2.7 29.5 + - - +
229B ALA* 5.0 4.0 - - + +
242B LEU* 5.2 0.4 - - - -
5551B OSB 3.1 33.1 + - + +
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Residues in contact with VAL 204 (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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53B ALA* 4.1 9.0 - - + +
56B GLU* 5.1 0.4 - - - +
62B TRP* 5.9 0.2 - - - +
202B LEU 4.2 0.2 - - - -
203B LYS* 1.3 70.7 - - - +
205B GLN* 1.3 65.1 + - + +
207B LEU* 3.3 3.1 + - - +
208B GLY 3.1 4.7 + - - -
209B GLY* 2.9 50.6 + - - -
210B VAL* 3.9 5.4 - - + +
213B ALA* 5.3 0.2 - - - -
226B VAL* 5.1 0.9 - - + -
227B SER 4.6 1.8 + - - -
231B GLU* 5.6 3.3 + - - +
238B ALA* 3.6 41.3 - - + +
239B GLY* 3.6 17.3 - - - +
242B LEU* 3.8 24.4 - - + +
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Residues in contact with GLN 205 (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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35B GLU* 3.1 23.7 + - - +
36B PHE* 3.4 2.8 - - - -
37B SER* 2.9 44.6 + - - -
49B ARG 3.2 14.7 - - - +
50B TRP* 3.1 39.8 - - + +
53B ALA* 3.6 17.3 - - + -
204B VAL* 1.3 77.6 - - + +
206B PRO* 1.3 73.3 - - + +
208B GLY 3.1 10.4 + - - -
231B GLU* 3.0 33.5 + - - +
235B GLY* 5.3 1.7 - - - -
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Residues in contact with PRO 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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49B ARG* 3.3 27.4 + - - +
50B TRP* 3.5 38.0 + - + +
183B ARG* 3.8 39.7 - - + +
184B ARG* 6.2 0.9 - - + -
203B LYS* 3.4 30.7 - - + +
204B VAL 4.2 0.2 - - - +
205B GLN* 1.3 95.7 - - + +
207B LEU* 1.3 58.2 + - - +
229B ALA* 4.9 4.9 - - + -
231B GLU* 5.4 0.2 - - - +
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Residues in contact with LEU 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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49B ARG* 4.3 16.2 - - - +
182B ILE* 4.2 6.7 - - + +
183B ARG* 4.0 29.8 - - + -
188B PRO* 6.0 0.7 - - + -
201B VAL 4.7 0.2 - - - +
202B LEU* 3.7 31.2 - - + -
203B LYS 3.2 33.2 + - - +
204B VAL 4.0 2.2 - - - +
205B GLN 3.1 0.8 - - - -
206B PRO* 1.3 77.6 - - - +
208B GLY* 1.3 58.6 + - - +
209B GLY 3.6 0.2 - - - -
212B ALA* 3.3 19.0 - - - +
213B ALA* 4.2 20.9 - - + -
216B LEU* 4.0 23.6 - - + -
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Residues in contact with GLY 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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49B ARG* 3.2 29.3 - - - +
52B ALA* 3.9 12.8 - - - +
53B ALA 3.8 12.2 + - - -
56B GLU* 5.1 2.4 - - - +
204B VAL 3.1 2.6 + - - -
205B GLN 3.1 5.1 + - - -
206B PRO 3.4 1.0 + - - -
207B LEU* 1.3 79.6 - - - +
209B GLY* 1.3 58.8 + - - +
212B ALA* 3.7 11.4 + - - +
310B TRP* 5.3 4.2 - - - -
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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