Contacts of the helix formed by residues 170 - 185 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B VAL 3.5 3.5 + - - -
169B PHE* 1.3 73.8 - - - +
171B GLU* 1.3 65.6 + - - -
172B ARG 3.5 2.0 - - - -
173B GLU* 3.3 22.4 + - - -
174B LEU* 2.8 27.2 + - - +
204B ARG* 6.0 0.7 - - - -
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Residues in contact with GLU 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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170B GLY* 1.3 71.2 - - - -
172B ARG* 1.3 66.3 + - + +
173B GLU 3.1 0.2 + - - -
174B LEU* 3.2 7.2 + - - +
175B GLU* 3.0 27.1 + - + +
204B ARG* 2.7 48.0 + - + +
209B PHE* 3.6 21.8 - - + -
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Residues in contact with ARG 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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142B LEU* 5.8 0.4 - - - -
170B GLY 3.5 0.6 - - - -
171B GLU* 1.3 80.8 - - + +
173B GLU* 1.3 60.0 - - + +
175B GLU* 3.7 19.2 - - - +
176B ALA* 2.8 29.4 + - - +
179B ARG* 4.3 1.4 + - - -
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Residues in contact with GLU 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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140B LEU* 3.8 35.6 - - + +
142B LEU* 4.9 9.4 - - + -
167B LEU* 6.1 0.9 - - - +
169B PHE* 4.8 11.3 - - + -
170B GLY* 3.3 28.6 + - - +
171B GLU 3.1 0.8 - - - -
172B ARG* 1.3 78.8 - - + +
174B LEU* 1.3 61.3 + - - +
176B ALA* 3.2 6.9 + - - +
177B ILE* 2.8 38.1 + - + +
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Residues in contact with LEU 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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158B LEU* 4.9 13.7 - - + -
160B THR* 5.0 6.7 - - + -
169B PHE* 3.3 38.8 - - + +
170B GLY 2.8 29.2 + - - +
171B GLU* 3.6 7.0 - - - +
173B GLU* 1.3 73.9 - - - +
175B GLU* 1.3 52.7 + - - +
177B ILE* 2.8 13.4 + - + +
178B ALA* 2.6 32.6 + - - +
204B ARG* 4.7 10.5 - - + +
206B LEU* 3.4 50.0 - - + +
209B PHE* 4.0 17.7 - - + -
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Residues in contact with GLU 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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171B GLU* 3.0 15.4 + - - +
172B ARG* 3.7 18.4 - - - +
174B LEU* 1.3 79.9 - - - +
176B ALA* 1.3 61.7 + - - +
178B ALA* 3.0 11.3 + - - +
179B ARG* 2.9 55.2 + - - +
209B PHE* 3.8 27.8 - - + -
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Residues in contact with ALA 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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142B LEU* 3.5 33.2 - - + -
172B ARG 2.8 23.7 + - - +
173B GLU 3.4 6.1 - - - +
174B LEU 3.2 0.2 - - - -
175B GLU* 1.3 71.3 - - - +
177B ILE* 1.3 63.1 + - - +
179B ARG* 3.2 39.4 + - - +
180B LEU* 3.3 12.1 + - - +
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Residues in contact with ILE 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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108B LEU* 6.2 0.2 - - + -
140B LEU* 4.4 15.0 - - + -
142B LEU* 4.3 4.0 - - + -
145B LEU* 3.7 22.2 - - + -
156B LEU* 3.5 30.0 - - + +
158B LEU* 4.0 29.8 - - + -
169B PHE* 4.5 6.5 - - + -
173B GLU 2.8 24.5 + - - +
174B LEU* 2.8 13.8 + - + +
176B ALA* 1.3 74.1 - - - +
178B ALA* 1.3 62.9 + - - +
180B LEU* 3.6 9.8 + - - +
181B ALA* 3.2 20.3 + - - +
188B LEU* 4.3 11.7 - - + -
206B LEU* 4.9 7.4 - - + -
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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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174B LEU 2.6 12.7 + - - +
175B GLU* 3.1 10.3 - - + +
177B ILE* 1.3 71.9 - - - +
179B ARG* 1.3 59.0 + - - +
181B ALA* 3.3 3.8 + - - +
182B ARG* 2.7 37.9 + - - +
188B LEU* 4.4 11.7 - - - -
206B LEU* 4.6 2.7 - - + +
209B PHE* 3.5 41.5 - - + +
210B ALA* 4.4 4.2 - - + +
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Residues in contact with ARG 179 (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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172B ARG 4.3 1.0 + - - -
175B GLU* 2.9 47.6 + - - +
176B ALA* 3.3 34.9 - - - +
178B ALA* 1.3 76.1 - - - +
180B LEU* 1.3 66.8 + - + +
182B ARG* 3.0 12.5 + - - +
183B ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 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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142B LEU* 5.0 3.1 - - + +
145B LEU* 3.2 50.3 - - + -
146B GLU* 3.8 28.0 - - + +
149B LEU* 3.9 25.8 - - + -
156B LEU* 5.4 2.9 - - + -
176B ALA 3.3 12.5 + - - +
177B ILE* 3.7 7.2 - - + +
178B ALA 3.4 0.2 - - - -
179B ARG* 1.3 79.5 - - + +
181B ALA* 1.3 65.3 + - - +
183B ALA* 3.0 6.1 + - + +
184B HIS* 2.9 32.9 + - + +
186B LEU* 5.1 2.5 - - + -
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Residues in contact with ALA 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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156B LEU* 5.9 0.6 - - + +
177B ILE 3.2 7.8 + - - +
178B ALA 3.5 8.5 - - - +
179B ARG 3.2 0.4 - - - -
180B LEU* 1.3 79.1 - - - +
182B ARG* 1.3 56.5 + - - +
185B ASP* 2.9 8.5 + - - -
186B LEU* 2.7 45.8 + - + +
188B LEU* 3.6 38.6 - - + -
210B ALA* 5.5 0.2 - - + -
213B ARG* 4.0 11.4 - - - -
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Residues in contact with ARG 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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178B ALA* 2.7 31.4 - - - +
179B ARG* 3.0 8.0 + - - +
181B ALA* 1.3 72.0 - - - +
183B ALA* 1.3 68.0 + - - +
185B ASP* 3.3 10.9 + - - +
209B PHE 2.8 26.8 + - - -
210B ALA* 4.0 5.5 - - + +
211B PRO* 4.4 4.8 - - - +
212B GLU* 2.7 39.1 + - - +
213B ARG* 3.7 22.7 + - - +
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Residues in contact with ALA 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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179B ARG 2.9 12.4 + - - +
180B LEU* 3.4 10.8 - - - +
182B ARG* 1.3 80.8 - - - +
184B HIS* 1.3 74.6 + - + +
185B ASP* 3.4 1.7 + - - +
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Residues in contact with HIS 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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146B GLU* 4.8 10.1 + - - -
149B LEU* 3.5 43.8 + - + +
150B THR 5.0 9.0 - - - -
180B LEU* 2.9 21.1 + - + +
183B ALA* 1.3 83.2 - - + +
185B ASP* 1.3 70.1 + - - +
186B LEU* 3.5 23.4 + - + +
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Residues in contact with ASP 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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1A MET* 3.0 42.3 + - - +
154B ARG 4.7 1.4 - - - +
181B ALA 2.9 7.8 + - - -
182B ARG 3.3 6.9 + - - +
183B ALA 3.2 5.3 - - - +
184B HIS* 1.3 82.4 - - - +
186B LEU* 1.3 61.7 + - - +
187B PHE* 5.9 0.2 - - - -
213B ARG* 3.1 22.0 + - - +
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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