Contacts of the helix formed by residues 183 - 191 (chain B) in PDB entry 3IIV
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 ASP 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ARG* 2.8 41.1 + - - -
172B SER* 2.7 39.8 + - - +
174B ASP* 4.4 0.5 - - - +
175B ARG* 3.9 22.0 + - + +
181B GLY 3.8 1.2 + - - -
182B TYR* 1.3 69.9 - - - +
184B THR* 1.3 62.4 + - - +
185B GLU* 3.7 3.1 + - - +
186B MET* 3.1 24.7 + - + +
187B ILE* 3.0 28.4 + - + +
201B HIS 5.7 0.4 + - - -
202B ARG 4.3 2.0 + - - -
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Residues in contact with THR 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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175B ARG* 5.5 0.6 - - - +
182B TYR* 2.9 20.4 + - + +
183B ASP* 1.3 74.0 + - - +
185B GLU* 1.3 57.4 + - - +
187B ILE* 3.3 7.8 + - + +
188B ARG* 2.8 41.9 + - - +
212B GLU* 3.7 42.0 - - + +
213B ALA* 4.1 6.3 - - - +
216B ALA* 3.8 11.4 - - + +
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Residues in contact with GLU 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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133B ARG* 2.9 36.9 + - - +
138B PHE* 4.5 11.3 - - + -
183B ASP* 3.2 2.0 - - - +
184B THR* 1.3 81.3 + - - +
186B MET* 1.3 56.6 + - - +
188B ARG* 3.3 8.5 + - - +
189B PHE* 2.9 28.9 + - + +
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Residues in contact with MET 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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131B ALA* 3.4 35.4 - - + +
132B LYS* 4.4 0.9 - - - +
133B ARG* 4.5 2.2 - - - +
138B PHE* 3.8 33.1 - - + -
153B LEU* 4.0 14.4 - - + -
170B LEU* 3.7 33.2 - - + +
171B GLY 4.4 0.4 - - - +
172B SER* 3.6 20.6 - - - +
183B ASP* 3.1 36.8 + - - +
185B GLU* 1.3 73.8 - - - +
187B ILE* 1.3 66.4 + - - +
189B PHE* 3.2 4.1 + - - +
190B VAL* 3.0 22.3 + - - +
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Residues in contact with ILE 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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170B LEU* 3.9 18.8 - - + +
182B TYR* 4.2 11.7 - - + -
183B ASP 3.0 22.4 + - - +
184B THR* 3.6 13.2 - - - +
186B MET* 1.3 76.5 - - + +
188B ARG* 1.3 57.3 + - - +
190B VAL* 3.2 2.3 + - - +
191B ARG* 2.9 28.1 + - - +
198B ILE* 4.6 10.5 - - + +
200B ALA* 3.7 30.1 - - + -
213B ALA* 4.2 14.1 - - + +
216B ALA* 3.5 21.5 - - + +
217B GLY 4.2 1.8 - - - -
218B ALA* 3.7 23.3 - - + +
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Residues in contact with ARG 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 THR* 2.8 27.0 + - - +
185B GLU* 3.8 6.7 - - - +
187B ILE* 1.3 73.6 - - - +
189B PHE* 1.3 65.0 + - - +
191B ARG* 3.7 3.0 + - - +
192B PRO* 3.2 18.9 - - - +
212B GLU 5.0 0.8 + - - -
215B LEU* 3.5 34.2 + - - +
216B ALA* 3.6 30.0 + - + +
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Residues in contact with PHE 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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138B PHE* 3.6 39.0 - + + -
153B LEU* 4.0 7.2 - - + -
154B ARG* 3.4 70.2 - - + -
185B GLU* 2.9 14.8 + - + +
186B MET 3.3 8.3 - - - +
188B ARG* 1.3 77.8 - - - +
190B VAL* 1.3 72.3 - - + +
192B PRO* 3.4 12.5 - - - +
193B LEU* 3.6 18.8 - - + +
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Residues in contact with VAL 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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153B LEU* 3.6 35.7 - - + -
157B VAL* 3.9 21.8 - - + -
168B ILE* 5.4 4.5 - - + -
170B LEU* 3.7 23.1 - - + -
186B MET 3.0 16.1 + - - +
187B ILE 4.0 1.3 - - - +
189B PHE* 1.3 79.1 - - + +
191B ARG* 1.3 67.3 + - - +
193B LEU* 2.9 22.1 + - + +
194B THR* 3.7 12.8 + - + +
198B ILE* 3.8 19.3 - - + -
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Residues in contact with ARG 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 ILE 2.9 17.4 + - - +
188B ARG* 4.0 4.9 - - - +
190B VAL* 1.3 75.5 - - - +
192B PRO* 1.3 67.8 - - + +
194B THR 3.0 35.1 + - - +
195B THR* 3.9 4.9 + - - +
196B LEU 2.8 24.5 + - - -
198B ILE* 3.5 23.3 - - + +
216B ALA 4.2 11.9 - - - +
217B GLY* 3.0 30.0 + - - -
219B ASP* 2.7 31.5 + - - -
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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