Contacts of the helix formed by residues 179 - 193 (chain B) in PDB entry 3ROU
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 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B LYS* 4.1 12.0 - - - +
173B GLY* 4.8 0.2 - - - -
178B CYS* 1.3 80.1 - - - +
180B ARG* 1.3 64.9 + - - +
181B GLU* 3.3 18.9 + - - +
182B THR* 3.0 27.0 + - - -
183B VAL* 3.0 23.3 + - - +
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Residues in contact with ARG 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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169B ARG* 4.0 25.0 - - + +
170B GLN* 3.4 55.3 + - - +
173B GLY* 5.2 0.6 - - - -
178B CYS 4.0 0.6 + - - -
179B SER* 1.3 73.4 - - - +
181B GLU* 1.3 73.9 + - - +
183B VAL* 3.4 9.3 + - - +
184B GLY* 2.9 24.6 + - - -
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Residues in contact with GLU 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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179B SER* 3.1 20.8 - - - +
180B ARG* 1.3 87.6 + - + +
182B THR* 1.3 65.3 - - - +
184B GLY* 3.1 4.4 + - - +
185B ARG* 3.1 29.6 + - + +
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Residues in contact with THR 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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139B VAL* 4.0 11.0 - - + -
178B CYS* 4.0 19.5 - - + +
179B SER* 3.0 23.6 + - - -
181B GLU* 1.3 74.5 - - - +
183B VAL* 1.3 64.4 + - - +
185B ARG* 3.2 11.7 + - + +
186B ILE* 3.1 43.5 + - + +
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Residues in contact with VAL 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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143B ILE* 4.0 9.6 - - + +
169B ARG* 3.5 20.2 - - - +
172B ILE* 3.7 25.4 - - + -
173B GLY* 3.4 27.4 - - - +
178B CYS* 3.5 13.7 - - - -
179B SER 3.0 19.6 + - - +
180B ARG 3.5 7.4 - - - +
181B GLU 3.2 0.2 - - - -
182B THR* 1.3 77.9 - - - +
184B GLY* 1.3 62.6 + - - +
186B ILE* 3.2 1.0 + - - +
187B LEU* 2.9 44.5 + - + +
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Residues in contact with GLY 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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169B ARG* 4.3 17.7 - - - +
180B ARG 2.9 15.8 + - - -
181B GLU* 3.1 4.2 + - - -
183B VAL* 1.3 75.3 - - - +
185B ARG* 1.3 63.6 + - - +
187B LEU* 3.5 2.9 + - - +
188B LYS* 3.1 23.0 + - - +
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Residues in contact with ARG 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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181B GLU* 3.1 20.3 + - + +
182B THR* 3.2 10.7 + - - +
184B GLY* 1.3 77.4 - - - +
186B ILE* 1.3 61.8 + - + +
188B LYS* 3.3 7.1 + - - +
189B MET* 2.9 26.5 + - - +
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Residues in contact with ILE 186 (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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139B VAL* 3.8 34.5 - - + -
140B THR* 3.9 24.7 - - + +
143B ILE* 3.8 24.2 - - + -
182B THR* 3.1 25.7 + - + +
183B VAL 4.0 1.8 - - - +
185B ARG* 1.3 78.8 - - + +
187B LEU* 1.3 60.8 + - - +
189B MET* 3.0 19.6 + - + +
190B LEU* 2.7 52.8 + - + +
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Residues in contact with LEU 187 (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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143B ILE* 4.1 14.1 - - + -
147B LEU* 3.8 28.9 - - + -
169B ARG* 3.6 39.7 - - - +
172B ILE* 4.1 6.1 - - + -
183B VAL* 2.9 26.9 + - + +
184B GLY* 4.0 4.5 - - - +
186B ILE* 1.3 76.9 - - - +
188B LYS* 1.3 55.9 + - - +
190B LEU* 3.3 2.1 + - + -
191B GLU* 2.9 31.8 + - - +
196B ILE* 3.6 18.5 - - + +
198B ALA* 4.8 9.9 - - + -
203B ILE* 4.0 23.1 - - + -
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Residues in contact with LYS 188 (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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184B GLY 3.1 13.8 + - - +
185B ARG* 3.4 11.9 - - - +
186B ILE 3.1 0.4 - - - -
187B LEU* 1.3 73.1 - - - +
189B MET* 1.3 61.5 + - - +
191B GLU* 3.2 29.3 + - - +
192B ASP* 2.8 61.8 + - - +
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Residues in contact with MET 189 (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 THR* 3.3 42.6 - - + +
185B ARG 2.9 13.6 + - - +
186B ILE* 3.0 21.3 + - + +
188B LYS* 1.3 78.0 - - - +
190B LEU* 1.3 60.6 + - + +
192B ASP* 3.2 9.8 + - + +
193B GLN* 2.9 59.0 + - + +
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Residues in contact with LEU 190 (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 THR* 4.5 10.8 - - + +
143B ILE* 4.2 8.5 - - + -
144B ALA* 4.6 16.8 - - + +
147B LEU* 4.0 26.7 - - + -
186B ILE* 2.7 35.8 + - + +
187B LEU* 3.7 6.3 - - + +
189B MET* 1.3 83.8 - - + +
191B GLU* 1.3 60.8 + - - +
193B GLN* 3.3 23.6 + - - +
195B LEU* 3.0 43.5 + - + +
196B ILE* 3.8 16.6 - - + -
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Residues in contact with GLU 191 (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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187B LEU 2.9 15.8 + - - +
188B LYS* 3.4 30.8 + - - +
190B LEU* 1.3 75.1 - - - +
192B ASP* 1.3 59.5 + - - +
194B ASN* 2.8 25.1 + - - +
196B ILE* 3.4 24.1 - - + +
197B SER* 3.8 8.8 + - - -
198B ALA* 3.3 39.9 + - - +
206B TYR* 5.7 0.2 - - - +
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Residues in contact with ASP 192 (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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188B LYS* 2.8 53.3 + - - +
189B MET* 3.2 9.2 + - + +
191B GLU* 1.3 71.8 - - - +
193B GLN* 1.3 58.0 + - + +
194B ASN* 3.1 15.0 + - - +
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Residues in contact with GLN 193 (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 THR* 5.8 0.6 - - - +
189B MET* 2.9 51.3 + - + +
190B LEU* 3.6 14.4 - - - +
191B GLU 3.1 0.4 - - - -
192B ASP* 1.3 75.8 - - + +
194B ASN* 1.3 74.2 + - - +
195B LEU* 3.2 31.8 + - + +
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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