Contacts of the helix formed by residues 172 - 185 (chain B) in PDB entry 2C11
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 LEU 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B ALA* 4.1 21.1 - - + +
89B ALA* 4.1 21.1 - - + +
90B ARG 5.3 4.9 - - - -
91B PRO* 6.1 0.4 - - + -
95B CYS* 4.3 11.2 - - - -
97B PHE* 3.8 14.1 - - + -
129B PHE* 3.4 41.3 - - + -
166B TYR* 5.9 0.7 - - - +
169B ARG* 5.1 3.8 - - - +
170B PRO 3.4 1.8 + - - +
171B VAL* 1.3 77.3 - - - +
173B PHE* 1.3 66.2 - - - +
174B GLN 4.0 2.9 - - - +
175B GLU* 3.1 33.3 + - + +
176B TYR* 3.2 12.6 + - - -
418B GLU* 3.4 16.4 - - + +
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Residues in contact with PHE 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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86B ALA 5.5 0.2 - - - +
87B ALA* 4.3 15.0 - - - +
171B VAL 3.8 0.2 + - - -
172B LEU* 1.3 69.7 - - - +
174B GLN* 1.3 68.8 + - - +
176B TYR* 2.9 29.8 + - - +
177B LEU* 3.2 39.7 + - + +
418B GLU* 2.6 26.6 + - + +
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Residues in contact with GLN 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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86B ALA 4.4 3.5 + - - +
87B ALA 3.6 14.6 + - - +
88B GLN* 3.2 29.6 - - - +
89B ALA 3.0 30.1 - - - +
90B ARG* 2.9 37.9 - - - +
172B LEU* 4.0 2.4 - - + +
173B PHE* 1.3 85.5 - - - +
175B GLU* 1.3 61.3 - - - +
177B LEU* 3.0 33.5 + - - +
178B ASP* 3.3 19.2 + - - +
418B GLU* 4.5 0.4 + - - -
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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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89B ALA 4.8 1.1 + - - +
91B PRO* 4.7 5.7 - - + +
169B ARG* 2.8 26.8 + - - -
171B VAL* 3.7 13.0 - - + +
172B LEU* 3.1 29.2 + - + +
174B GLN* 1.3 79.9 - - - +
176B TYR* 1.3 61.5 + - - +
178B ASP* 3.6 12.6 + - - +
179B ILE* 3.2 25.4 + - + +
223B ARG* 2.5 41.5 + - - -
251B HIS* 3.5 13.8 + - - +
259B TRP* 3.9 21.5 - - + -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 3.4 37.4 + - + +
172B LEU 3.2 19.2 + - - -
173B PHE* 2.9 15.2 + - - +
175B GLU* 1.3 74.3 - - - +
177B LEU* 1.3 71.3 + - + +
179B ILE* 2.8 20.6 + - + +
180B ASP* 3.0 18.0 + - - +
212B THR* 3.7 34.8 - - + +
216B ARG* 3.0 25.2 + - - -
227B PHE* 4.6 14.4 - + - -
389B PHE* 4.2 10.8 - + - -
394B TYR* 5.3 7.4 - - - -
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Residues in contact with LEU 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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173B PHE* 3.2 43.3 - - + +
174B GLN* 3.0 28.2 + - - +
176B TYR* 1.3 79.1 - - + +
178B ASP* 1.3 52.3 + - - +
180B ASP* 2.8 18.2 + - - +
181B GLN* 2.5 38.1 + - - +
206B ARG* 5.1 4.3 + - - +
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Residues in contact with ASP 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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89B ALA 5.3 0.2 - - - +
90B ARG* 2.5 43.1 + - - +
91B PRO* 5.3 1.6 - - - +
174B GLN* 3.3 17.6 + - - +
175B GLU* 3.7 9.9 - - - +
176B TYR 3.2 0.8 - - - -
177B LEU* 1.3 76.1 - - - +
179B ILE* 1.3 57.1 + - - +
181B GLN* 3.0 14.0 - - + +
182B MET* 2.7 31.5 + - - +
256B PRO* 4.6 8.6 - - + +
259B TRP* 3.3 29.5 - - + -
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Residues in contact with ILE 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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171B VAL* 5.1 1.6 - - + -
175B GLU* 3.2 20.6 - - + +
176B TYR* 2.8 20.1 + - + +
178B ASP* 1.3 77.8 - - - +
180B ASP* 1.3 57.4 + - - +
182B MET* 3.5 5.9 + - - +
183B ILE* 2.8 51.7 + - + +
227B PHE* 3.8 37.9 - - + -
249B VAL* 4.0 15.0 - - + -
251B HIS* 3.9 28.5 - - + +
259B TRP* 3.9 17.3 - - + -
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Residues in contact with ASP 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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448A TYR* 4.9 8.8 + - - -
176B TYR* 3.4 17.8 - - - +
177B LEU* 2.8 21.6 + - - +
179B ILE* 1.3 75.4 - - - +
181B GLN* 1.3 61.7 + - - +
183B ILE* 4.1 6.3 - - - -
184B PHE* 2.5 35.3 + - + -
206B ARG* 3.1 39.0 + - - +
210B THR* 3.0 30.1 + - - +
227B PHE* 5.7 0.3 - - - -
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Residues in contact with GLN 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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177B LEU 2.5 16.9 + - - +
178B ASP* 3.0 21.5 - - + +
180B ASP* 1.3 72.3 - - - +
182B MET* 1.3 59.1 + - + +
185B ASN* 2.8 69.4 + - - +
186B ARG* 6.2 1.6 - - + +
206B ARG* 4.2 3.7 - - - +
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Residues in contact with MET 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 ASP 2.7 19.6 + - - +
179B ILE* 3.7 4.9 - - - +
181B GLN* 1.3 76.7 - - + +
183B ILE* 1.3 59.4 + - + +
186B ARG* 3.2 44.1 + - - +
187B GLU* 2.9 41.5 + - + +
249B VAL* 4.6 11.0 - - + -
256B PRO 5.8 0.7 - - - +
259B TRP* 3.6 29.4 - - + +
260B THR* 3.6 35.9 - - - +
261B ILE* 3.7 24.7 - - + -
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Residues in contact with ILE 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 ILE* 2.8 44.2 + - + +
180B ASP* 2.9 4.1 + - - +
182B MET* 1.3 79.7 - - + +
184B PHE* 1.3 71.5 + - + +
187B GLU* 3.3 7.3 + - + -
188B LEU* 2.6 59.8 + - + +
210B THR* 4.3 18.8 - - + -
227B PHE* 4.8 8.3 - - + -
229B LEU* 5.0 2.0 - - + -
247B LEU* 3.9 22.9 - - + -
249B VAL* 4.0 17.7 - - + -
261B ILE* 5.0 3.4 - - + -
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Residues in contact with PHE 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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180B ASP* 2.5 18.6 + - + +
183B ILE* 1.3 77.3 - - + +
185B ASN* 1.3 65.4 + - - +
188B LEU* 3.8 23.3 - - + -
189B PRO* 3.6 7.3 - - - +
201B TYR* 3.0 25.9 + + - +
205B GLY* 6.4 0.2 - - - -
206B ARG* 2.8 68.4 - - - +
208B LEU* 2.9 47.3 - - + -
209B VAL* 3.9 6.3 - - - -
210B THR* 3.6 25.8 - - + -
229B LEU* 5.3 1.3 - - + -
1735B NAG 5.8 0.7 - - + -
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Residues in contact with ASN 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 GLN* 2.8 54.3 + - - +
184B PHE* 1.3 90.7 + - - +
186B ARG* 1.3 63.9 + - + +
187B GLU 3.5 0.2 - - - -
189B PRO* 2.8 23.7 - - - +
206B ARG* 5.5 3.0 - - - +
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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