Contacts of the helix formed by residues 214 - 221 (chain X) in PDB entry 2QVY
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 VAL 214 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185X MET* 5.5 0.7 - - + -
199X VAL* 3.4 26.9 - - + +
200X LEU 4.0 12.8 - - - +
201X GLY* 4.2 3.8 - - - -
202X LEU 5.2 0.7 - - - +
203X MET* 4.5 8.3 - - + +
209X VAL* 2.9 21.6 + - + +
210X GLY* 3.6 13.0 - - - +
213X ALA* 1.3 80.1 - - - +
215X LEU* 1.3 72.5 + - - +
217X ALA 3.6 0.5 + - - -
218X ALA* 3.0 23.6 + - - +
225X TYR* 3.8 14.8 - - + -
249X PHE* 3.7 31.0 - - + +
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Residues in contact with LEU 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X LEU* 4.7 1.1 - - + -
68X VAL* 3.8 35.9 - - + -
71X ILE* 6.0 1.3 - - + -
72X LEU* 4.7 9.9 - - + -
205X LEU* 4.0 14.4 - - + -
210X GLY 3.2 13.5 + - - +
211X PHE* 3.3 37.0 + - + +
214X VAL* 1.3 79.1 - - - +
216X VAL* 1.3 68.5 + - + +
218X ALA* 3.0 9.9 + - - +
219X LEU* 3.1 25.6 + - + +
225X TYR* 3.6 39.7 - - + -
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Residues in contact with VAL 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X VAL* 4.2 15.5 - - + -
7X MET* 4.2 15.3 - - + -
8X LEU* 4.2 22.0 - - + -
72X LEU* 5.4 0.4 - - + -
182X VAL* 3.7 17.7 - - + -
211X PHE* 2.8 54.8 + - + +
212X PHE* 3.5 12.3 - - + +
215X LEU* 1.3 77.3 - - + +
217X ALA* 1.3 65.0 + - - +
219X LEU* 3.1 3.7 + - - +
220X ALA* 2.7 28.8 + - + +
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Residues in contact with ALA 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X VAL* 3.7 23.8 - - + +
185X MET* 4.6 10.5 - - + -
191X LEU* 5.3 3.8 - - + -
212X PHE 2.9 14.8 + - - +
213X ALA* 3.1 29.2 - - - +
216X VAL* 1.3 71.7 - - - +
218X ALA* 1.3 64.9 + - - +
221X LEU* 2.9 39.4 + - + +
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Residues in contact with ALA 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191X LEU* 6.4 0.2 - - - -
197X ASN* 5.0 1.5 - - - +
199X VAL* 3.4 37.4 - - + +
214X VAL 3.0 19.6 + - - +
215X LEU 3.0 3.6 + - - +
217X ALA* 1.3 76.3 - - - +
219X LEU* 1.3 58.6 + - - +
221X LEU* 3.7 5.7 + - - +
223X GLY* 2.8 31.9 + - - -
224X THR 4.0 14.6 - - - +
225X TYR* 4.2 8.7 - - + -
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Residues in contact with LEU 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X LEU* 3.5 35.4 - - + -
11X ALA* 3.7 3.2 - - - +
20X ALA* 3.7 45.8 - - + +
21X LEU* 4.8 2.5 - - + -
32X HIS* 3.3 19.8 - - + -
35X LEU* 3.8 22.0 - - + -
68X VAL* 5.4 0.9 - - + -
72X LEU* 4.3 8.5 - - + -
215X LEU* 3.1 29.1 + - + +
216X VAL 3.1 3.2 + - - +
218X ALA* 1.3 77.9 - - - +
220X ALA* 1.3 53.9 + - - +
222X ASP* 2.7 29.3 + - - -
223X GLY 4.4 2.0 - - - +
225X TYR* 4.4 7.9 - - + -
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Residues in contact with ALA 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X MET* 3.8 40.0 - - + +
8X LEU* 4.2 7.9 - - + -
11X ALA* 4.4 5.2 - - - -
14X ARG* 3.3 22.7 + - - -
182X VAL* 4.8 4.3 - - + -
193X HIS* 4.8 1.0 - - - -
216X VAL* 2.7 24.1 + - + +
217X ALA* 4.0 4.0 - - - +
219X LEU* 1.3 73.9 - - - +
221X LEU* 1.3 60.3 - - + +
222X ASP* 3.1 1.6 - - - -
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Residues in contact with LEU 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X VAL* 5.5 5.6 - - + -
183X LEU* 5.1 15.7 - - + -
185X MET* 5.8 1.3 - - + -
186X SER* 5.1 8.1 - - - -
191X LEU* 3.9 38.1 - - + +
192X ARG* 4.0 7.6 - - - +
193X HIS* 3.8 29.8 - - + +
194X GLY 2.9 27.6 + - - +
197X ASN* 4.2 15.0 - - - +
217X ALA* 2.9 27.5 + - + +
218X ALA* 4.3 4.0 - - - +
220X ALA* 1.3 78.0 - - - +
222X ASP* 1.3 66.5 + - - +
223X GLY 3.1 1.5 + - - -
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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