Contacts of the helix formed by residues 171 - 185 (chain A) in PDB entry 3VLN
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 SER 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LYS* 5.9 0.2 - - - -
101A LYS 5.8 0.2 - - - -
102A LEU* 3.3 22.4 - - - -
104A PRO* 5.7 0.4 - - - -
113A GLN* 2.9 25.6 + - - -
166A GLY* 4.0 7.9 - - - -
169A SER 4.2 4.4 + - - -
170A ILE* 1.3 74.8 - - - +
172A MET* 1.3 69.2 + - - +
173A ILE* 3.3 3.9 - - - +
174A ASP* 2.9 27.0 + - - +
175A TYR* 3.4 16.8 + - - -
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Residues in contact with MET 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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41A VAL* 3.7 26.9 - - + -
90A CYS* 3.3 40.8 - - + +
91A GLU 4.2 0.4 - - - +
94A ASP* 3.8 20.4 - - + -
102A LEU* 3.0 31.9 + - + +
103A LEU* 3.8 15.9 - - + -
113A GLN* 3.7 7.0 - - - +
171A SER* 1.3 77.3 - - - +
173A ILE* 1.3 62.8 + - - +
175A TYR* 3.1 9.8 + - - +
176A LEU* 2.9 30.6 + - + +
903A SO4 3.7 19.5 - - - +
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Residues in contact with ILE 173 (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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113A GLN* 3.1 55.8 + - + +
116A ILE* 3.7 22.9 - - + -
117A LEU* 3.6 30.1 - - + +
165A PHE* 3.7 25.1 - - + +
166A GLY 3.8 7.2 - - - +
171A SER* 3.8 9.0 - - - +
172A MET* 1.3 74.3 - - - +
174A ASP* 1.3 66.3 + - - +
176A LEU* 3.2 7.1 + - + +
177A ILE* 3.2 31.0 + - + +
903A SO4 4.8 3.4 - - - +
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Residues in contact with ASP 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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164A PHE* 3.5 20.9 - - - +
165A PHE* 2.9 23.5 + - - -
166A GLY 4.3 0.3 + - - -
170A ILE* 3.6 7.1 - - + -
171A SER* 2.9 35.9 + - - +
173A ILE* 1.3 78.7 - - - +
175A TYR* 1.3 57.7 + - - +
177A ILE* 3.3 4.1 + - - +
178A TRP* 2.9 31.4 + - - +
202A TRP* 2.9 29.6 + - - +
206A MET* 3.4 21.5 - - + +
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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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37A ARG* 4.2 5.5 - - - +
40A LEU* 3.7 38.7 - - + +
41A VAL* 4.8 9.6 - - + -
44A ALA* 4.0 23.6 - - + +
100A LYS* 5.2 1.2 + - - +
102A LEU* 4.1 24.7 - - + -
170A ILE* 3.6 32.9 - - + +
171A SER 3.4 20.8 + - - -
172A MET* 3.1 7.8 + - - +
174A ASP* 1.3 76.8 - - - +
176A LEU* 1.3 62.6 + - + +
178A TRP* 4.4 1.3 - - - -
179A PRO* 3.3 20.4 - - - +
206A MET* 4.6 1.3 - - + -
209A ASP* 2.9 29.0 + - - -
211A THR* 3.7 18.6 + - + -
212A VAL* 3.9 12.8 - - + -
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Residues in contact with LEU 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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37A ARG* 2.8 52.2 + - + +
41A VAL* 5.7 0.4 - - + -
87A ALA* 4.5 9.4 - - + -
90A CYS* 3.9 29.8 - - + -
117A LEU* 4.0 25.6 - - + -
172A MET* 2.9 23.2 + - + +
173A ILE* 3.2 9.8 + - + +
175A TYR* 1.3 78.4 - - - +
177A ILE* 1.3 60.2 + - - +
179A PRO* 3.8 0.5 - - - +
180A TRP* 3.4 7.4 - - - -
903A SO4 3.5 41.5 - - - +
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Residues in contact with ILE 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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116A ILE* 5.3 1.6 - - + +
117A LEU* 4.3 2.7 - - + -
120A PHE* 3.5 46.2 - - + -
153A LEU* 4.8 8.3 - - + -
165A PHE* 3.3 44.9 - - + -
173A ILE* 3.2 31.5 + - + +
174A ASP 3.6 4.9 - - - +
176A LEU* 1.3 81.5 - - - +
178A TRP* 1.3 67.7 + - - +
179A PRO 3.2 2.4 - - - -
180A TRP* 3.4 12.8 + - - -
181A PHE* 3.6 19.5 - - + -
202A TRP* 3.7 12.6 - - + -
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Residues in contact with TRP 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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36A GLU* 4.2 7.6 + - - -
40A LEU* 4.3 10.5 - - + -
174A ASP 2.9 18.2 + - - +
175A TYR* 4.1 4.3 - - - +
177A ILE* 1.3 76.9 - - - +
179A PRO* 1.3 72.5 - - + +
181A PHE* 2.8 28.0 + - + -
182A GLU* 2.9 54.1 + - + -
185A GLU* 5.7 0.9 - - - -
202A TRP* 3.9 14.6 - + - -
203A MET* 4.1 18.6 - - + -
206A MET* 3.6 37.5 - - + -
207A LYS* 3.7 31.6 - - + -
212A VAL* 3.5 23.2 - - + +
216A LEU* 3.6 20.6 - - + +
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Residues in contact with PRO 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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33A PRO* 3.5 35.7 - - + +
36A GLU* 3.4 30.5 - - + +
37A ARG* 4.2 3.8 - - + +
40A LEU* 4.1 5.4 - - + -
175A TYR 3.3 18.4 - - - +
176A LEU 3.8 5.4 - - - +
177A ILE 3.4 4.0 - - - -
178A TRP* 1.3 95.6 - - + +
180A TRP* 1.3 64.9 + - + +
182A GLU* 3.5 1.6 + - + -
183A ARG* 2.9 35.9 + - - +
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Residues in contact with TRP 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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33A PRO* 3.7 36.0 - - + +
34A PHE* 3.6 45.6 - + - -
37A ARG* 3.5 18.4 - - - -
120A PHE* 3.6 32.5 - + + -
123A VAL* 4.0 12.3 - - + -
124A PRO* 3.6 24.9 + - + +
127A VAL* 3.8 32.6 - - + +
176A LEU 3.4 19.7 - - - -
177A ILE 3.8 5.8 - - - +
178A TRP 3.1 0.6 - - - -
179A PRO* 1.3 85.1 - - + +
181A PHE* 1.3 66.2 + - + +
183A ARG* 3.5 8.7 + - - +
184A LEU* 3.2 27.3 + - - +
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Residues in contact with PHE 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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120A PHE* 4.0 22.4 - + - -
123A VAL* 5.5 1.1 - - + -
150A PHE* 3.7 33.9 - + - -
153A LEU* 3.9 21.5 - - + -
177A ILE* 3.6 19.3 - - + -
178A TRP* 2.8 24.7 + - + +
180A TRP* 1.3 77.1 - - + +
182A GLU* 1.3 64.6 + - - +
184A LEU* 3.0 25.9 + - + +
185A GLU* 2.9 17.7 - - - +
193A VAL* 4.5 2.2 - - + -
199A LEU* 4.0 24.7 - - + -
202A TRP* 3.7 18.4 - + + -
203A MET* 3.9 20.8 - - + +
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Residues in contact with GLU 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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36A GLU* 2.5 36.6 - - - +
178A TRP* 2.9 38.3 + - + +
179A PRO 3.6 8.1 - - - +
180A TRP 3.4 0.2 - - - -
181A PHE* 1.3 76.7 - - - +
183A ARG* 1.3 73.2 + - + +
185A GLU* 3.4 22.7 - - - +
186A ALA* 5.3 0.9 - - - +
216A LEU* 3.7 23.5 - - + +
217A THR* 3.2 37.7 + - - +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ARG 4.9 2.0 + - - -
31A PHE* 2.9 33.1 + - - +
32A SER 3.7 1.8 + - - -
33A PRO* 3.6 28.4 - - - +
36A GLU* 2.8 30.3 + - - +
127A VAL* 5.5 3.8 - - + -
179A PRO* 2.9 25.9 + - - +
180A TRP* 3.9 10.8 - - - +
181A PHE 3.2 0.4 - - - -
182A GLU* 1.3 91.0 + - + +
184A LEU* 1.3 64.7 + - - +
185A GLU 3.6 0.4 - - - -
186A ALA* 3.3 11.6 + - - +
187A MET* 3.1 35.0 + - - +
217A THR* 5.7 3.6 + - - -
222A TRP* 3.6 41.7 - - + +
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Residues in contact with LEU 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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123A VAL* 6.0 1.6 - - + -
127A VAL* 4.7 8.1 - - + -
146A PHE* 4.7 7.6 - - + -
150A PHE* 3.5 38.6 - - + -
180A TRP 3.2 23.6 + - - +
181A PHE* 3.0 31.7 + - + +
183A ARG* 1.3 74.2 - - - +
185A GLU* 1.3 67.6 + - - +
187A MET* 3.1 9.3 + - + +
189A LEU* 3.0 62.8 + - + +
190A ASN* 4.6 4.3 - - - +
193A VAL* 4.3 7.2 - - + -
203A MET* 5.0 4.5 - - + -
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Residues in contact with GLU 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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178A TRP* 5.7 0.9 - - - -
181A PHE 2.9 18.8 - - - +
182A GLU* 3.4 21.4 - - - +
184A LEU* 1.3 68.1 - - - +
186A ALA* 1.3 57.6 + - + +
188A LYS* 2.7 43.9 + - - +
189A LEU 4.9 1.1 - - - +
190A ASN* 4.8 17.4 - - + +
203A MET* 3.8 14.9 - - - +
207A LYS* 3.7 24.3 + - - -
219A GLU* 4.8 13.5 - - + +
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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