Contacts of the helix formed by residues 170 - 188 (chain A) in PDB entry 3VAS
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 170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A MET* 3.6 32.1 - - + +
13A GLY* 3.6 28.7 - - - -
14A ASN* 4.2 2.0 - - - +
66A THR* 4.0 0.9 - - - +
144A LEU* 4.7 1.1 - - + -
166A ILE* 3.6 12.6 - - + -
167A ALA 3.4 14.6 - - - +
168A GLY 3.0 1.0 + - - -
169A PHE* 1.3 72.8 - - - +
171A ILE* 1.3 65.7 + - - +
172A ASN 3.1 2.0 - - - -
173A THR* 3.1 15.7 + - - +
174A CYS* 2.9 31.7 + - + +
178A MET* 3.5 14.6 - - - -
402A CL 3.8 12.6 - - + -
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Residues in contact with ILE 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 GLY* 2.9 19.4 + - - +
170A VAL* 1.3 78.5 - - - +
172A ASN* 1.3 59.9 + - - +
173A THR 3.5 0.2 + - - -
175A TYR* 3.7 23.5 + - + +
178A MET* 3.4 21.2 - - + -
194A PHE* 4.3 12.1 - - + -
201A LEU* 4.4 8.1 - - + -
205A ASN* 3.9 25.1 - - + +
208A GLU* 3.6 44.4 - - + +
209A VAL* 3.9 29.2 - - + +
212A MET* 4.8 0.2 - - + -
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Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.5 19.5 - - + +
138A LEU* 4.1 18.8 - - + +
142A CYS* 5.1 4.7 - - - +
169A PHE* 3.4 13.1 + - - +
170A VAL 3.1 1.0 - - - -
171A ILE* 1.3 78.1 - - - +
173A THR* 1.3 59.7 + - - +
200A PHE* 3.4 24.8 - - - -
201A LEU* 3.7 9.4 - - - +
205A ASN* 3.7 29.1 + - - +
401A ADN 5.2 0.5 + - - -
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Residues in contact with THR 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 2.6 40.2 + - - +
138A LEU* 3.7 27.1 - - + -
141A ALA 3.4 27.4 - - - +
142A CYS* 3.3 24.4 - - - +
144A LEU* 3.7 5.9 - - - +
170A VAL* 3.1 14.3 + - - +
172A ASN* 1.3 81.7 - - + +
174A CYS* 1.3 64.8 + - - +
175A TYR 4.1 0.4 - - - -
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Residues in contact with CYS 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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12A MET* 3.9 5.1 - - + +
144A LEU* 3.3 44.2 - - + +
145A SER 4.1 4.9 - - - -
149A ILE* 4.0 15.0 - - - -
170A VAL* 2.9 10.0 + - + +
173A THR* 1.3 82.3 + - - +
175A TYR* 1.3 66.2 + - - +
176A GLU* 3.2 15.3 - - - -
177A GLY* 3.6 21.3 - - - -
178A MET* 3.2 16.1 + - - +
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Residues in contact with TYR 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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170A VAL 3.7 1.4 + - - -
171A ILE* 3.7 20.9 + - + +
174A CYS* 1.3 75.1 - - - +
176A GLU* 1.3 58.8 + - - +
178A MET* 3.3 19.4 - - + +
179A LEU* 2.8 48.1 + - + +
207A LYS* 5.2 5.4 - - - -
208A GLU* 3.6 40.8 + - + +
211A GLU* 2.4 49.6 + - - +
212A MET* 3.8 25.8 - - + -
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Residues in contact with GLU 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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144A LEU 4.9 0.3 - - - +
145A SER* 4.1 7.3 - - - -
146A LEU* 3.2 48.2 + - + +
174A CYS* 4.0 12.4 - - - -
175A TYR* 1.3 81.1 - - - +
177A GLY* 1.3 58.9 + - - +
179A LEU* 3.8 6.7 - - - +
180A LYS* 3.0 28.4 + - - +
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Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 3.9 6.5 - - - -
146A LEU* 3.8 12.8 - - - -
149A ILE* 3.8 24.9 - - - -
174A CYS* 3.2 8.3 + - - -
176A GLU* 1.3 80.4 - - - +
178A MET* 1.3 64.9 + - - +
180A LYS* 3.2 2.4 + - - +
181A ILE* 3.0 28.2 + - - +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A MET* 3.8 11.9 - - + -
166A ILE* 3.7 38.8 - - + +
167A ALA 3.8 11.0 - - - +
170A VAL* 3.5 12.8 - - - +
171A ILE* 3.4 34.3 - - + -
174A CYS 3.2 7.6 + - - +
175A TYR* 3.3 23.3 - - + +
177A GLY* 1.3 76.5 - - - +
179A LEU* 1.3 57.0 + - - +
181A ILE* 3.5 2.4 + - - +
182A ALA* 2.9 29.3 + - - +
194A PHE* 4.0 13.7 - - + -
212A MET* 3.6 30.3 - - + +
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Residues in contact with LEU 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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175A TYR* 2.8 36.1 + - + +
176A GLU* 3.8 6.5 - - - +
178A MET* 1.3 76.4 - - - +
180A LYS* 1.3 64.3 + - - +
182A ALA* 3.3 2.7 + - + +
183A LYS* 3.0 60.4 + - - +
211A GLU* 3.9 31.6 - - + +
212A MET* 4.5 6.3 - - - -
215A TYR* 3.9 23.3 - - + -
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Residues in contact with LYS 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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146A LEU* 3.8 17.9 - - + -
149A ILE* 5.5 0.2 - - + -
150A GLU* 3.1 40.8 + - + +
155A TRP* 3.6 45.8 - - + +
176A GLU 3.0 18.1 + - - +
177A GLY 3.2 4.7 + - - +
179A LEU* 1.3 77.6 - - - +
181A ILE* 1.3 61.4 + - - +
183A LYS* 3.4 9.2 + - + +
184A HIS* 3.1 21.8 + - - +
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Residues in contact with ILE 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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10A PHE* 3.5 29.6 - - + -
12A MET* 3.5 27.6 - - + -
149A ILE* 4.5 7.0 - - + -
155A TRP* 4.1 20.0 - - + -
158A VAL* 4.0 11.0 - - + -
164A TYR* 3.8 35.7 - - + -
166A ILE* 4.4 4.7 - - + -
177A GLY 3.0 14.7 + - - +
178A MET 3.9 3.8 - - - +
180A LYS* 1.3 75.3 - - - +
182A ALA* 1.3 58.3 + - - +
184A HIS* 3.2 8.6 + - - +
185A SER* 2.9 26.5 + - - -
192A PHE* 4.3 8.5 - - + -
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Residues in contact with ALA 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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178A MET 2.9 19.7 + - - +
179A LEU* 3.3 6.9 + - - +
181A ILE* 1.3 77.6 - - - +
183A LYS* 1.3 61.3 + - - +
185A SER* 3.3 3.8 + - - -
186A LEU* 3.1 18.5 + - - +
192A PHE* 3.8 22.8 - - + -
212A MET* 4.0 12.3 - - + -
215A TYR* 3.7 36.1 - - + +
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Residues in contact with LYS 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 LEU* 3.0 49.0 + - + +
180A LYS* 3.7 7.6 - - - +
182A ALA* 1.3 72.6 - - - +
184A HIS* 1.3 66.4 + - - +
186A LEU* 3.5 1.0 + - - +
187A GLU* 3.0 33.3 + - - +
211A GLU* 5.3 2.0 + - - -
215A TYR* 3.4 39.9 - - + -
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Residues in contact with HIS 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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155A TRP* 3.9 23.6 - + + -
158A VAL* 3.8 11.6 + - + -
159A GLU* 4.1 23.3 - - + -
164A TYR* 3.0 22.8 + + - -
180A LYS 3.1 13.6 + - - +
181A ILE* 3.2 8.3 + - - +
183A LYS* 1.3 77.9 - - - +
185A SER* 1.3 61.1 + - - +
187A GLU* 3.2 15.0 + - - +
188A ASN* 3.0 51.8 + - - +
190A LYS* 2.9 26.2 + - - -
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Residues in contact with SER 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 TYR* 3.6 28.5 - - - -
181A ILE 2.9 10.8 + - - -
182A ALA 3.5 8.5 - - - -
184A HIS* 1.3 77.9 - - - +
186A LEU* 1.3 59.1 + - - +
188A ASN 3.1 2.1 + - - -
189A GLU 2.9 9.2 + - - -
190A LYS* 2.9 52.0 + - - +
192A PHE* 3.5 23.3 - - - +
215A TYR 5.1 0.2 + - - -
217A ASN* 4.4 0.9 + - - -
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Residues in contact with LEU 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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182A ALA 3.1 13.0 + - - +
183A LYS 3.5 2.4 + - - +
185A SER* 1.3 78.5 - - - +
187A GLU* 1.3 63.8 + - - +
189A GLU* 3.2 22.2 + - - +
190A LYS 5.1 1.8 - - - +
214A SER 4.3 1.1 - - - +
215A TYR* 3.8 39.2 + - + +
217A ASN* 5.0 5.4 - - - +
252A PHE* 4.0 13.5 - - + -
253A ALA* 4.2 7.6 - - + +
254A ASP* 3.8 42.8 - - + +
258A ARG* 3.5 33.0 + - - +
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Residues in contact with GLU 187 (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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183A LYS* 3.0 20.8 + - - +
184A HIS* 3.2 27.2 + - - +
186A LEU* 1.3 76.9 - - - +
188A ASN* 1.3 74.3 + - - +
189A GLU* 3.8 2.4 + - - +
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Residues in contact with ASN 188 (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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162A GLN* 5.6 0.9 + - - -
184A HIS* 3.0 47.9 + - - +
185A SER 4.0 0.7 - - - +
187A GLU* 1.3 92.7 + - - +
189A GLU* 1.3 71.2 + - - +
190A LYS* 3.3 24.7 + - - +
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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
------------------------------------------------------------
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