Contacts of the helix formed by residues 208 - 218 (chain B) in PDB entry 1RVA
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174B TRP* 3.5 19.5 - - - -
206B PHE* 3.3 3.3 + - - +
207B ASP* 1.3 82.0 - - - +
209B GLU* 1.3 64.2 + - - +
210B ASP* 3.4 10.8 + - - +
211B GLU* 3.1 23.8 + - - +
212B PHE* 3.1 18.0 + - - +
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Residues in contact with GLU 209 (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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125B PHE* 6.1 0.2 - - - -
129B ILE 5.1 7.7 - - - +
130B ALA* 5.7 0.9 - - - -
131B HIS* 4.4 20.6 + - - +
174B TRP* 3.6 51.4 + - + +
208B SER* 1.3 72.5 - - - +
210B ASP* 1.3 64.3 + - - +
212B PHE* 3.3 8.0 + - + +
213B LEU* 3.0 36.5 + - + +
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Residues in contact with ASP 210 (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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208B SER* 3.2 10.8 + - - +
209B GLU* 1.3 80.3 - - - +
211B GLU* 1.3 59.3 + - - +
213B LEU* 3.5 8.8 + - - +
214B ASP* 3.0 29.2 + - - +
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Residues in contact with GLU 211 (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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206B PHE* 3.6 11.4 - - + -
207B ASP* 2.9 36.2 + - + +
208B SER* 3.1 21.7 + - - +
210B ASP* 1.3 76.7 + - - +
212B PHE* 1.3 66.8 + - - +
214B ASP* 3.3 1.5 + - - +
215B TYR* 2.9 24.3 + - - +
233B ILE* 4.3 1.3 - - - -
236B TYR* 3.6 30.1 + - + +
237B ARG* 3.0 37.7 + - - +
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Residues in contact with PHE 212 (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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114B ILE* 5.9 2.9 - - + -
173B LYS* 3.8 28.7 - - + -
174B TRP* 3.5 27.6 - - + -
177B ALA* 3.3 35.4 - - + -
189B ILE* 4.1 17.9 - - + -
206B PHE* 3.7 21.7 - + + -
208B SER 3.1 13.0 + - - +
209B GLU* 3.5 13.9 - - + +
211B GLU* 1.3 76.9 - - - +
213B LEU* 1.3 91.5 + - + +
215B TYR* 3.5 0.9 + - - +
216B TRP* 3.2 49.4 + + + +
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Residues in contact with LEU 213 (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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114B ILE* 4.3 21.7 - - + +
125B PHE* 4.1 28.9 - - + -
209B GLU* 3.0 31.4 + - + +
210B ASP* 3.9 7.2 - - - +
212B PHE* 1.3 94.3 - - + +
214B ASP* 1.3 60.2 + - - +
216B TRP* 3.4 2.3 + - + +
217B ARG* 2.9 67.3 + - - +
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Residues in contact with ASP 214 (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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210B ASP* 3.0 20.1 + - - +
211B GLU* 3.9 1.1 - - - +
213B LEU* 1.3 76.2 - - - +
215B TYR* 1.3 64.2 + - - +
217B ARG* 4.5 5.6 - - - +
218B ASN* 3.0 36.4 + - - +
230B TYR* 3.9 0.2 + - - -
236B TYR* 2.5 31.8 + - - +
239B TRP* 4.4 0.3 - - - -
240B ILE* 3.8 0.3 - - - +
244B ARG* 2.8 44.1 + - - -
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Residues in contact with TYR 215 (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 ASP* 2.6 37.4 + - + -
206B PHE* 3.5 20.0 - + + -
211B GLU 2.9 18.4 + - - +
212B PHE 3.6 2.2 - - - +
214B ASP* 1.3 77.5 - - - +
216B TRP* 1.3 81.4 + + - +
219B TYR* 3.2 30.0 + + - +
230B TYR* 2.6 43.3 + + - -
231B ASN 3.7 3.1 + - - -
232B ASN* 3.3 28.9 + - - -
233B ILE* 4.0 4.0 - - + -
236B TYR* 3.5 40.5 - + + -
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Residues in contact with TRP 216 (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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110B TYR* 3.6 39.2 - + + +
114B ILE* 3.7 19.7 - - + -
115B ARG* 2.9 23.0 + - - -
178B GLY 3.2 28.3 + - - -
179B ASP 3.8 10.3 - - - -
180B LEU 3.7 27.6 - - - -
181B ALA* 3.7 5.8 - - - -
189B ILE* 3.7 26.9 - - + +
190B GLY 4.1 2.9 - - - -
206B PHE* 3.8 5.1 - + - -
212B PHE* 3.2 45.7 + + + +
213B LEU* 4.3 1.3 - - - +
215B TYR* 1.3 88.2 - + - +
217B ARG* 1.3 60.0 + - - +
218B ASN 3.2 0.2 - - - -
219B TYR* 3.5 41.5 + + - +
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Residues in contact with ARG 217 (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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114B ILE* 2.7 38.4 + - + +
115B ARG* 3.2 31.4 + - + +
125B PHE* 4.0 25.3 - - - -
213B LEU* 2.9 52.2 + - - +
214B ASP* 3.9 3.7 - - - +
215B TYR 3.3 0.4 - - - -
216B TRP* 1.3 77.2 - - - +
218B ASN* 1.3 72.8 + - - +
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Residues in contact with ASN 218 (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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115B ARG* 4.8 1.1 - - - +
214B ASP* 3.0 37.9 + - - +
216B TRP 3.2 0.4 - - - -
217B ARG* 1.3 90.3 - - - +
219B TYR* 1.3 61.3 + - - +
220B GLU* 3.6 1.1 + - - -
229B LYS* 2.8 37.9 + - - +
230B TYR* 3.0 18.1 + - - +
239B TRP* 4.0 25.0 - - + -
244B ARG* 3.5 8.6 + - - +
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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