Contacts of the helix formed by residues 170 - 185 (chain A) in PDB entry 1V2E
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 GLY 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A VAL 3.3 5.1 + - - -
169A PHE* 1.3 69.6 - - - +
171A GLU* 1.3 63.2 + - - -
172A ARG 3.3 2.5 - - - -
173A GLU* 2.8 29.0 + - - +
174A LEU* 2.7 24.6 + - - +
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Residues in contact with GLU 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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169A PHE 4.1 0.4 + - - -
170A GLY* 1.3 68.9 - - - -
172A ARG* 1.3 74.0 + - + +
174A LEU* 3.1 11.3 + - - +
175A GLU* 3.0 41.5 + - - +
204A ARG* 2.5 54.7 + - + +
209A PHE* 3.7 13.4 - - + -
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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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142A LEU* 5.5 0.6 - - - +
170A GLY 3.3 0.8 - - - -
171A GLU* 1.3 84.9 + - + +
173A GLU* 1.3 63.8 + - + +
175A GLU* 3.4 21.0 + - - +
176A ALA* 3.2 21.1 + - - +
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Residues in contact with GLU 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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139A ARG* 6.0 3.9 - - - +
140A LEU* 3.9 34.1 + - + +
142A LEU* 4.6 13.1 - - + +
167A LEU* 5.5 3.2 - - - +
168A VAL 4.7 2.1 - - - +
169A PHE* 4.0 20.1 - - + -
170A GLY* 2.8 29.1 + - - +
172A ARG* 1.3 77.2 - - + +
174A LEU* 1.3 66.9 + - + +
176A ALA* 3.3 9.5 + - - +
177A ILE* 3.2 25.4 + - + +
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Residues in contact with LEU 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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158A LEU* 4.7 2.5 - - + -
160A THR* 5.1 5.6 - - + -
169A PHE* 3.3 42.0 - - + +
170A GLY 2.7 41.6 + - - +
171A GLU* 3.1 7.8 + - - +
173A GLU* 1.3 73.3 - - - +
175A GLU* 1.3 66.7 + - - +
177A ILE* 2.9 6.7 + - + +
178A ALA* 2.8 24.1 + - - +
204A ARG* 4.0 19.3 - - + +
205A ARG 4.4 0.2 - - - +
206A LEU* 3.4 38.9 - - + +
209A PHE* 3.9 18.8 - - + -
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Residues in contact with GLU 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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171A GLU* 3.0 34.1 + - - +
172A ARG* 3.4 17.8 - - - +
174A LEU* 1.3 74.9 - - - +
176A ALA* 1.3 55.5 + - - +
177A ILE 2.9 0.5 + - - -
178A ALA* 3.0 3.6 + - - +
179A ARG* 2.7 60.5 + - - +
209A PHE* 3.3 26.3 - - + -
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Residues in contact with ALA 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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142A LEU* 3.3 37.7 - - + -
172A ARG 3.2 8.5 + - - +
173A GLU 3.4 7.0 - - - +
175A GLU* 1.3 79.0 - - - +
177A ILE* 1.3 58.2 + - - +
179A ARG* 3.4 14.2 - - - +
180A LEU* 3.1 34.2 + - - +
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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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140A LEU* 4.2 17.9 - - + -
142A LEU* 4.6 2.9 - - + -
145A LEU* 4.2 19.1 - - + -
156A LEU* 3.8 23.6 - - + +
158A LEU* 3.6 41.3 - - + -
169A PHE* 4.7 6.7 - - + -
173A GLU* 3.2 14.8 + - + +
174A LEU* 2.9 10.5 + - - +
176A ALA* 1.3 75.0 - - - +
178A ALA* 1.3 62.0 + - - +
179A ARG 2.9 1.1 - - - -
180A LEU* 3.3 5.5 + - - +
181A ALA* 2.8 28.8 + - - +
188A LEU* 4.1 13.0 - - + -
206A LEU* 4.5 5.6 - - + -
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Residues in contact with ALA 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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174A LEU 2.8 14.2 + - - +
175A GLU 3.7 2.5 - - - +
177A ILE* 1.3 73.1 - - - +
179A ARG* 1.3 59.1 + - - +
181A ALA* 3.2 4.8 - - - +
182A ARG* 3.0 35.4 + - - +
188A LEU* 4.4 3.8 - - - -
206A LEU* 4.7 4.2 - - + +
209A PHE* 3.4 31.0 - - + +
210A ALA* 3.3 28.8 - - + +
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Residues in contact with ARG 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 GLU* 2.7 45.7 + - - +
176A ALA* 3.4 12.9 - - - +
177A ILE 2.9 0.2 - - - -
178A ALA* 1.3 73.4 - - - +
180A LEU* 1.3 72.7 + - + +
181A ALA 3.0 0.7 - - - -
182A ARG* 2.9 22.1 + - - +
183A ALA* 3.0 14.0 + - + +
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Residues in contact with LEU 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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142A LEU* 4.9 6.3 - - + +
145A LEU* 4.1 35.2 - - + -
146A GLU* 3.9 44.6 - - + +
149A LEU* 4.5 17.2 - - + +
156A LEU* 5.8 5.4 - - + -
176A ALA* 3.1 19.1 + - + +
177A ILE* 3.3 4.5 + - - +
179A ARG* 1.3 82.3 - - + +
181A ALA* 1.3 67.2 + - - +
183A ALA* 3.2 15.5 + - + +
184A HIS* 3.2 22.9 + - + +
186A LEU* 4.8 0.6 - - + +
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Residues in contact with ALA 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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156A LEU* 5.8 2.1 - - - +
177A ILE 2.8 18.1 + - - +
178A ALA 3.2 8.5 - - - +
180A LEU* 1.3 78.9 - - - +
182A ARG* 1.3 52.4 + - - +
185A ASP 2.7 30.7 + - - -
186A LEU* 2.8 23.8 + - - +
188A LEU* 3.7 23.1 - - + -
213A ARG* 3.3 22.2 - - - -
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Residues in contact with ARG 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 ALA* 3.0 18.9 + - - +
179A ARG* 2.9 9.5 + - - +
181A ALA* 1.3 74.4 - - - +
183A ALA* 1.3 64.6 + - - +
185A ASP* 3.0 14.0 + - - +
209A PHE 2.5 30.8 + - - -
210A ALA* 4.1 4.6 - - - +
211A PRO* 4.5 3.2 - - - +
212A GLU* 3.5 16.7 + - - -
213A ARG* 3.2 33.8 + - - +
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Residues in contact with ALA 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 ARG* 3.0 14.1 + - + +
180A LEU* 3.2 11.4 + - + +
182A ARG* 1.3 77.3 - - - +
184A HIS* 1.3 79.2 + - + +
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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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146A GLU* 5.8 4.0 - - + +
149A LEU* 3.7 36.1 - - + +
150A THR 5.0 10.8 - - - +
180A LEU* 3.2 18.2 + - + +
183A ALA* 1.3 94.8 - - + +
185A ASP* 1.3 71.1 + - - +
186A LEU* 3.2 27.2 + - + +
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Residues in contact with ASP 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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154A ARG* 5.3 0.3 - - - +
181A ALA 2.7 10.2 + - - -
182A ARG 3.0 11.1 + - - +
184A HIS* 1.3 80.9 - - - +
186A LEU* 1.3 58.7 + - - +
187A PHE* 3.9 0.9 + - - -
213A ARG* 3.6 21.8 + - - +
1B MET* 3.0 51.3 + - - +
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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