Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 2VK2
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 THR 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLU* 3.6 30.5 - - + +
168A GLY 3.1 1.6 + - - -
169A ASP* 3.1 19.4 - - + +
170A PHE* 1.3 79.3 - - - +
172A ARG* 1.3 58.5 + - - +
173A SER* 3.5 10.8 + - - +
174A LYS* 3.1 30.3 + - - +
175A GLY* 2.9 23.6 + - - -
202A MET* 3.3 12.6 - - - +
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Residues in contact with ARG 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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13A GLU 4.8 1.4 + - - -
171A THR* 1.3 73.8 - - - +
173A SER* 1.3 57.9 + - - +
175A GLY* 3.4 0.3 + - - -
176A LYS* 3.0 26.3 + - - +
201A ASP* 3.3 43.6 + - + +
204A ILE* 3.5 39.9 - - - +
205A GLY* 3.4 23.4 - - - +
208A GLN* 3.9 14.1 - - - +
229A VAL* 5.4 0.8 - - - +
231A ASP* 3.0 29.7 + - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 3.5 11.0 + - - -
172A ARG* 1.3 78.9 - - - +
174A LYS* 1.3 60.5 + - - +
176A LYS* 3.4 8.1 + - - +
177A GLU* 3.1 26.8 + - - +
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Residues in contact with LYS 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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167A SER* 3.9 7.5 + - - -
168A GLY* 3.2 21.1 - - - +
169A ASP* 3.2 32.7 + - - +
171A THR* 3.1 18.1 + - - +
173A SER* 1.3 78.7 + - - +
175A GLY* 1.3 58.4 + - - +
177A GLU* 3.2 32.4 + - - +
178A VAL* 2.9 50.4 + - - +
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Residues in contact with GLY 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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134A LEU* 3.9 10.3 - - - +
168A GLY* 3.8 5.9 + - - -
171A THR 2.9 18.6 + - - -
172A ARG 3.8 0.2 - - - -
174A LYS* 1.3 76.6 - - - +
176A LYS* 1.3 55.2 + - - +
178A VAL* 4.0 0.3 - - - -
179A MET* 2.9 31.2 + - - +
202A MET* 3.7 29.6 - - - -
206A ALA 4.2 0.2 - - - -
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Residues in contact with LYS 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 ARG 3.0 16.9 + - - +
173A SER* 3.6 7.2 - - - +
175A GLY* 1.3 76.2 - - - +
177A GLU* 1.3 56.6 + - - +
179A MET* 3.3 2.2 + - - +
180A GLU* 2.9 50.0 + - - +
205A GLY* 3.3 24.3 - - - +
208A GLN* 3.3 37.2 + - + +
209A ALA* 3.8 6.2 - - + +
212A GLU* 2.9 40.8 + - - -
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Residues in contact with GLU 177 (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 SER 3.1 13.7 + - - +
174A LYS* 3.2 37.1 + - - +
176A LYS* 1.3 75.1 - - - +
178A VAL* 1.3 63.7 + - + +
180A GLU* 3.4 18.9 + - - +
181A SER* 3.2 20.1 + - - -
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Residues in contact with VAL 178 (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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134A LEU* 3.4 18.6 - - + -
166A GLN* 3.9 14.4 - - + +
167A SER 3.6 21.5 - - - +
168A GLY* 4.3 0.9 - - - -
174A LYS* 2.9 38.8 + - + +
177A GLU* 1.3 74.3 - - + +
179A MET* 1.3 65.2 + - - +
181A SER* 2.6 25.6 + - - +
182A PHE* 3.0 38.5 + - + -
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Residues in contact with MET 179 (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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132A VAL* 3.9 30.7 - - + -
134A LEU* 4.2 3.5 - - + +
175A GLY 2.9 19.8 + - - +
176A LYS 3.7 3.8 - - - +
178A VAL* 1.3 77.6 - - - +
180A GLU* 1.3 55.7 + - - +
182A PHE* 3.1 10.0 + - - +
183A ILE* 2.9 50.9 + - + +
192A ILE* 4.1 5.4 - - + -
195A VAL* 4.0 19.3 - - + -
206A ALA* 3.6 31.4 - - + +
209A ALA* 3.9 6.7 - - + -
210A ILE* 3.9 24.9 - - + -
221A ILE* 4.1 13.0 - - + -
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Residues in contact with GLU 180 (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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176A LYS* 2.9 44.0 + - - +
177A GLU* 3.4 20.6 - - - +
178A VAL 3.3 0.2 - - - -
179A MET* 1.3 76.4 - - - +
181A SER* 1.3 61.0 + - - +
183A ILE* 3.4 7.4 + - + +
184A LYS* 3.1 44.8 + - - +
209A ALA* 3.7 17.2 - - + +
212A GLU* 3.8 8.5 - - + +
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Residues in contact with SER 181 (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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177A GLU 3.2 8.7 + - - -
178A VAL* 2.6 26.0 + - - +
180A GLU* 1.3 75.1 - - - +
182A PHE* 1.3 74.6 + - - +
184A LYS* 3.5 8.9 + - - +
185A ALA* 3.0 24.5 + - - +
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Residues in contact with PHE 182 (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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132A VAL* 3.6 26.7 - - + -
133A GLU 3.6 17.0 - - - -
134A LEU* 3.8 9.9 - - + -
164A ARG* 3.7 36.1 - - + -
165A SER 4.5 0.2 - - - -
166A GLN* 3.7 35.2 - - + -
178A VAL* 3.0 41.6 + - + -
179A MET* 3.5 11.4 - - - +
181A SER* 1.3 81.4 + - - +
183A ILE* 1.3 65.3 + - - +
185A ALA* 3.2 4.8 + - + -
186A GLU* 3.1 29.1 + - - +
192A ILE* 4.1 13.5 - - + -
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Residues in contact with ILE 183 (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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179A MET* 2.9 38.5 + - + +
180A GLU* 3.7 6.5 - - - +
182A PHE* 1.3 75.5 - - - +
184A LYS* 1.3 65.8 + - + +
186A GLU 3.2 7.6 + - - -
188A ASN* 3.2 17.0 + - - +
189A GLY* 2.9 46.0 + - - +
192A ILE* 4.1 1.6 - - + -
209A ALA* 3.5 39.5 - - + +
210A ILE* 3.9 12.8 - - + +
213A ALA* 3.8 16.6 - - + -
215A LEU* 5.2 0.7 - - + -
221A ILE* 4.9 2.7 - - + -
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Residues in contact with LYS 184 (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 GLU* 3.1 36.2 + - - +
181A SER* 3.9 7.6 - - - +
183A ILE* 1.3 80.6 - - + +
185A ALA* 1.3 60.2 + - - +
186A GLU 3.5 0.3 + - - -
187A ASN* 4.4 4.2 + - - -
188A ASN* 4.7 12.3 + - - +
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Residues in contact with ALA 185 (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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164A ARG* 3.7 34.2 + - - +
181A SER 3.0 18.6 + - - +
182A PHE* 3.2 6.5 + - + +
184A LYS* 1.3 75.5 - - - +
186A GLU* 1.3 67.7 + - - +
187A ASN 3.8 1.9 + - - -
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Residues in contact with GLU 186 (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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163A ILE* 3.4 28.4 - - + +
164A ARG* 2.9 36.8 + - + +
182A PHE 3.1 17.4 + - - +
183A ILE 3.2 3.0 + - - +
185A ALA* 1.3 84.4 - - - +
187A ASN* 1.3 71.3 + - - +
188A ASN 3.5 1.1 - - - -
189A GLY 3.1 8.3 + - - -
191A ASN* 2.8 44.1 + - + +
192A ILE* 3.8 20.2 - - + -
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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