Contacts of the helix formed by residues 170 - 185 (chain B) in PDB entry 1VQ9
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B GLY* 1.3 76.3 - - - -
171B VAL* 1.3 67.2 + - - +
172B SER* 3.9 5.7 + - - -
173B ASP* 2.6 39.3 + - - +
174B ARG* 2.8 23.7 + - - +
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Residues in contact with VAL 171 (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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132B HIS* 2.9 46.0 - - + +
137B LEU* 4.8 14.4 - - + +
140B LEU* 4.1 5.0 - - + +
170B SER* 1.3 72.9 - - - +
172B SER* 1.3 57.2 + - - +
174B ARG* 3.6 29.1 - - - +
175B LEU* 2.6 40.2 + - - +
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Residues in contact with SER 172 (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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129B ARG* 6.0 1.3 - - - +
132B HIS* 2.8 31.3 + - - -
170B SER* 3.3 6.6 + - - -
171B VAL* 1.3 80.7 - - - +
173B ASP* 1.3 60.3 + - - +
175B LEU* 3.6 7.0 - - - +
176B ASP* 2.7 38.8 + - - +
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Residues in contact with ASP 173 (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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36B PRO* 3.9 12.5 - - + +
169B GLY* 5.1 0.7 - - - -
170B SER* 2.6 34.1 + - - +
172B SER* 1.3 81.8 - - - +
174B ARG* 1.3 56.8 + - - +
176B ASP* 3.4 8.9 + - - +
177B HIS* 2.9 24.6 + - - +
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Residues in contact with ARG 174 (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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32B ASP* 3.5 27.1 + - - -
36B PRO* 3.3 31.1 - - + +
139B ASP* 5.6 4.6 - - - +
140B LEU* 3.8 19.7 - - + +
165B ARG* 3.9 7.9 - - - +
166B VAL* 3.0 40.1 + - + +
167B GLY 3.8 2.7 - - - -
168B GLY 3.1 30.9 + - - +
169B GLY 3.2 12.3 + - - -
170B SER 2.8 17.2 + - - +
171B VAL* 3.6 26.1 - - - +
173B ASP* 1.3 69.7 - - - +
175B LEU* 1.3 59.9 + - - +
176B ASP 3.1 1.8 - - - -
177B HIS* 3.3 0.9 - - - +
178B ALA* 2.7 34.8 + - - +
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Residues in contact with LEU 175 (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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84B LEU* 4.8 8.5 - - + -
125B GLU* 5.5 1.1 - - + -
128B ILE* 3.9 28.5 - - + -
129B ARG* 4.4 27.6 - - + +
132B HIS* 4.8 17.7 - - + -
137B LEU* 4.8 5.4 - - + -
140B LEU* 3.3 23.6 - - + -
171B VAL 2.6 23.8 + - - +
172B SER* 3.6 4.9 - - - +
174B ARG* 1.3 74.4 - - - +
176B ASP* 1.3 62.3 + - - +
178B ALA* 3.3 2.4 + - - +
179B LEU* 3.1 46.5 + - + +
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Residues in contact with ASP 176 (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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129B ARG* 2.6 33.1 + - - -
172B SER* 2.7 24.5 + - - +
173B ASP* 3.5 8.2 - - - +
175B LEU* 1.3 75.8 - - - +
177B HIS* 1.3 66.6 + - - +
179B LEU* 3.4 6.5 + - - +
180B ASP* 2.9 31.2 + - - +
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Residues in contact with HIS 177 (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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36B PRO* 3.5 45.1 + - + +
37B GLY* 3.5 13.1 - - - -
166B VAL* 4.6 6.7 - - + -
173B ASP 2.9 16.5 + - - +
174B ARG 3.3 7.4 - - - +
176B ASP* 1.3 76.5 - - - +
178B ALA* 1.3 64.7 + - - +
180B ASP* 3.0 23.9 - - - +
181B ILE* 3.1 37.8 + - + +
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Residues in contact with ALA 178 (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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84B LEU* 3.6 28.9 - - + -
140B LEU* 5.0 2.2 - - + -
142B LEU* 4.0 12.3 - - + -
166B VAL* 4.7 11.2 - - + -
174B ARG 2.7 20.7 + - - +
175B LEU* 3.4 7.9 - - - +
177B HIS* 1.3 70.5 - - - +
179B LEU* 1.3 67.4 + - - +
180B ASP 2.9 1.4 + - - -
181B ILE* 3.0 18.0 + - - +
182B VAL* 3.1 19.0 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.4 8.7 - - + -
100B VAL* 3.7 41.1 - - + -
125B GLU* 3.5 29.2 - - + +
128B ILE* 6.0 0.2 - - + -
129B ARG* 3.5 15.9 - - - +
175B LEU* 3.1 37.3 + - + +
176B ASP* 3.8 6.5 - - - +
178B ALA* 1.3 78.2 - - - +
180B ASP* 1.3 57.6 + - - +
182B VAL* 3.5 6.5 + - + -
183B GLU* 2.7 45.5 + - + +
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Residues in contact with ASP 180 (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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176B ASP* 2.9 20.6 + - - +
177B HIS* 3.0 17.1 - - - +
178B ALA 2.9 0.6 + - - -
179B LEU* 1.3 78.8 - - - +
181B ILE* 1.3 66.8 + - + +
183B GLU* 3.3 12.5 + - - +
184B ASP* 2.7 18.1 - - - +
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Residues in contact with ILE 181 (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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38B VAL* 3.7 28.0 - - + -
81B ALA* 3.9 23.6 - - + -
142B LEU* 4.4 8.1 - - + -
166B VAL* 6.1 0.7 - - + -
177B HIS* 3.4 41.5 - - + +
178B ALA* 3.0 6.4 + - - +
180B ASP* 1.3 78.6 - - + +
182B VAL* 1.3 67.7 + - - +
184B ASP* 2.6 26.8 - - - +
186B GLY* 3.5 15.1 + - - +
187B GLU 5.2 2.0 - - - +
188B HIS* 5.0 11.2 - - + +
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Residues in contact with VAL 182 (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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81B ALA 3.8 11.4 - - - +
82B VAL 3.8 16.6 - - - +
83B ALA* 3.8 17.7 - - - +
84B LEU* 4.1 6.7 - - + -
100B VAL* 3.9 11.0 - - + +
101B TRP 4.7 1.1 - - - -
102B THR* 2.8 33.1 - - + +
142B LEU* 3.4 27.8 - - + -
178B ALA 3.1 16.3 + - - +
179B LEU* 3.8 7.6 - - + +
181B ILE* 1.3 77.2 - - - +
183B GLU* 1.3 70.2 + - - +
184B ASP 3.1 0.2 + - - -
186B GLY 3.2 11.1 + - - -
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Residues in contact with GLU 183 (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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100B VAL* 4.5 12.2 - - - +
101B TRP 4.5 12.0 - - - +
102B THR* 3.7 12.3 - - - +
103B ASP* 5.6 1.6 - - - +
121B PRO* 5.2 6.7 - - - +
125B GLU* 5.2 4.3 - - - +
179B LEU* 2.7 45.7 + - + +
180B ASP* 3.5 7.2 - - - +
182B VAL* 1.3 77.0 - - - +
184B ASP* 1.3 70.4 + - - +
185B GLY* 3.3 0.3 + - - -
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Residues in contact with ASP 184 (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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104B GLU* 3.8 19.8 - - - +
180B ASP* 2.7 15.7 - - - +
181B ILE* 2.6 27.5 - - - +
183B GLU* 1.3 79.3 - - - +
185B GLY* 1.3 60.3 + - - +
186B GLY* 4.0 2.0 - - - +
187B GLU* 5.3 3.8 - - + +
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Residues in contact with GLY 185 (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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80B ARG* 4.0 20.4 + - - +
81B ALA 4.1 3.4 - - - +
82B VAL* 5.1 2.6 - - - +
102B THR* 4.9 5.8 + - - -
104B GLU* 4.1 29.6 - - - +
182B VAL 3.3 6.9 + - - -
183B GLU 4.1 0.9 - - - -
184B ASP* 1.3 77.2 - - - +
186B GLY* 1.3 60.5 + - - +
187B GLU* 3.2 10.9 + - - -
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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