Contacts of the helix formed by residues 175 - 187 (chain B) in PDB entry 2C1H
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A HIS 5.5 2.7 + - - -
149B VAL* 4.5 1.5 - - - +
173B MET 3.6 1.2 + - - -
174B ASP* 1.3 71.2 - - - +
176B ARG* 1.3 62.4 + - - +
177B ILE 3.4 2.0 - - - -
178B GLY* 4.5 0.3 - - - -
179B ALA* 3.6 20.1 + - - +
242B ASP* 5.6 2.4 + - - -
245B GLU* 3.4 27.8 + - - +
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Residues in contact with ARG 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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149B VAL* 3.7 28.4 - - + +
152B LEU* 4.5 2.0 - - + -
169B PRO* 3.0 23.1 + - + -
171B ASP* 3.0 31.7 + - - +
172B MET* 3.3 26.9 - - - +
173B MET 3.2 15.7 + - - +
174B ASP 3.0 1.8 + - - -
175B GLY* 1.3 76.7 - - - +
177B ILE* 1.3 79.6 + - + +
179B ALA* 3.4 3.1 + - - +
180B ILE* 2.8 44.2 + - + +
196B SER* 3.8 5.8 + - - -
197B TYR* 2.9 28.9 + - - +
242B ASP* 3.4 16.3 + - - -
245B GLU* 3.9 0.2 + - - -
1329B MG 3.3 23.8 - - - -
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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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169B PRO* 3.8 23.1 - - + -
176B ARG* 1.3 98.8 - - + +
178B GLY* 1.3 56.9 + - - +
180B ILE* 3.2 4.3 + - - +
181B ARG* 2.8 30.0 + - - +
194B ILE* 3.8 22.1 - - + +
196B SER* 3.3 32.5 - - - +
242B ASP* 3.9 21.1 - - - +
245B GLU* 3.3 12.4 + - + +
246B GLY 4.6 1.8 - - - -
247B ALA* 4.0 23.8 - - + +
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Residues in contact with GLY 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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175B GLY 4.5 0.4 - - - -
176B ARG 3.4 0.2 - - - -
177B ILE* 1.3 71.5 - - - +
179B ALA* 1.3 56.7 + - - +
181B ARG* 3.3 4.0 + - - +
182B GLU* 2.8 29.0 + - - +
245B GLU* 2.8 46.3 + - - +
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Residues in contact with ALA 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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149B VAL* 3.7 21.5 - - + -
153B GLN* 3.1 26.7 - - - +
175B GLY 3.6 10.3 + - - +
176B ARG 3.4 7.4 + - - +
177B ILE 3.3 0.4 - - - -
178B GLY* 1.3 73.6 - - - +
180B ILE* 1.3 54.2 + - - +
182B GLU* 3.3 11.0 + - - +
183B ALA* 2.8 29.8 + - - +
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Residues in contact with ILE 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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124B VAL* 4.7 5.4 - - + -
149B VAL* 5.3 0.9 - - + -
152B LEU* 4.6 15.5 - - + +
153B GLN* 4.5 20.2 - - + +
156B ALA* 3.7 22.2 - - + -
167B VAL* 4.4 4.0 - - + -
169B PRO* 3.8 27.4 - - + -
176B ARG* 2.8 41.8 + - + +
177B ILE* 3.7 4.3 - - - +
179B ALA* 1.3 68.3 - - - +
181B ARG* 1.3 56.8 + - - +
183B ALA* 3.2 6.3 + - - +
184B LEU* 2.7 48.1 + - + +
194B ILE* 3.9 12.3 - - + -
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Residues in contact with ARG 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 ILE* 2.8 17.5 + - + +
178B GLY 3.4 6.3 - - - +
180B ILE* 1.3 76.4 - - - +
182B GLU* 1.3 56.3 + - - +
184B LEU* 3.8 12.7 - - - +
185B ASP* 2.9 72.5 + - - +
190B SER* 3.9 16.5 + - - +
192B VAL 2.8 29.1 + - - -
193B GLY* 3.8 7.3 - - - -
194B ILE* 3.4 33.5 - - + +
245B GLU 4.1 16.4 - - - +
246B GLY* 4.4 12.2 + - - +
248B ASP* 3.8 8.5 + - - -
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Residues in contact with GLU 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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153B GLN* 4.0 13.3 - - - +
178B GLY 2.8 17.9 + - - +
179B ALA* 3.4 10.5 - - - +
181B ARG* 1.3 73.2 - - - +
183B ALA* 1.3 58.7 + - - +
185B ASP* 3.4 6.6 + - - +
186B GLU* 3.0 52.9 + - + +
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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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153B GLN* 3.8 32.3 - - + +
157B VAL* 3.6 17.7 - - + +
179B ALA 2.8 20.6 + - - +
180B ILE* 3.6 4.7 - - - +
182B GLU* 1.3 74.0 - - - +
184B LEU* 1.3 59.6 + - + +
186B GLU* 3.7 11.8 + - - +
187B THR* 2.9 27.9 + - - +
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Residues in contact with LEU 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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156B ALA* 3.8 18.6 - - + +
157B VAL* 4.2 6.7 - - + -
160B ALA* 3.8 29.6 - - + -
167B VAL* 3.9 19.3 - - + -
180B ILE* 2.7 40.1 + - + +
181B ARG* 3.9 12.6 - - - +
183B ALA* 1.3 70.0 - - - +
185B ASP* 1.3 64.4 + - - +
187B THR* 3.3 8.0 + - - -
189B HIS* 2.9 39.7 + - + +
192B VAL* 4.2 18.2 - - + +
194B ILE* 4.1 12.6 - - + -
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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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181B ARG* 2.9 63.9 + - - +
182B GLU* 3.7 6.4 - - - +
184B LEU* 1.3 76.2 - - - +
186B GLU* 1.3 61.7 + - + +
187B THR 3.4 0.5 + - - -
188B ASP* 3.5 12.6 + - - +
190B SER* 3.4 26.9 + - - +
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Residues in contact with GLU 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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182B GLU* 3.0 39.3 + - + +
183B ALA* 3.8 12.0 - - - +
184B LEU 3.3 0.2 - - - -
185B ASP* 1.3 76.7 - - + +
187B THR* 1.3 63.1 + - + +
188B ASP* 3.3 8.6 + - - +
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Residues in contact with THR 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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157B VAL* 3.6 27.6 - - + +
161B GLU* 4.8 4.2 - - - +
183B ALA 2.9 18.6 + - - +
184B LEU* 3.3 6.2 + - - -
185B ASP 3.3 0.6 - - - -
186B GLU* 1.3 81.0 - - + +
188B ASP* 1.3 66.0 + - - +
189B HIS* 3.0 34.9 + - - -
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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