Contacts of the helix formed by residues 174 - 185 (chain B) in PDB entry 2C6E
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 GLU 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B PHE* 3.8 26.2 - - - -
168B LEU* 3.6 29.0 + - + +
169B GLU* 4.5 0.2 - - - +
171B ALA* 4.5 5.2 - - - +
172B GLY* 2.4 38.8 - - - +
173B VAL* 1.3 67.5 - - - +
175B HIS* 1.3 60.5 - - - +
176B GLN* 2.8 35.2 + - + +
177B LEU* 3.5 29.2 + - + +
178B ARG* 4.0 9.0 + - - +
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Residues in contact with HIS 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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173B VAL* 2.7 16.5 + - + +
174B GLU* 1.3 71.7 - - - +
176B GLN* 1.3 58.8 + - - +
177B LEU 3.5 0.2 - - - -
178B ARG* 3.5 36.5 + - + +
179B ARG* 3.3 43.1 + - + +
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Residues in contact with GLN 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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172B GLY 5.2 1.8 - - - +
174B GLU* 2.8 32.2 - - + +
175B HIS* 1.3 80.0 - - - +
177B LEU* 1.3 57.8 + - - +
178B ARG 3.0 1.6 - - - -
179B ARG* 3.2 8.0 + - + +
180B GLU* 2.7 41.0 + - - +
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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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163B LEU* 4.4 21.3 - - + -
168B LEU* 4.8 15.3 - - + -
174B GLU* 3.5 25.2 + - + +
175B HIS 3.5 0.4 - - - -
176B GLN* 1.3 80.4 - - - +
178B ARG* 1.3 67.0 + - + +
180B GLU* 3.4 3.9 + - - +
181B VAL* 3.0 46.8 + - + +
205B VAL* 4.7 20.9 - - + -
207B LEU* 4.6 1.8 - - + -
1388B HPM 3.5 31.9 - - + -
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Residues in contact with ARG 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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174B GLU 4.3 10.8 - - - +
175B HIS* 3.5 36.5 + - + +
176B GLN 3.0 0.2 - - - -
177B LEU* 1.3 85.9 - - + +
179B ARG* 1.3 68.4 + - + +
181B VAL* 3.2 14.6 + - - +
182B GLU* 3.2 13.9 + - - +
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Residues in contact with ARG 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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175B HIS* 3.3 36.7 + - + +
176B GLN* 3.2 10.2 + - + +
178B ARG* 1.3 79.9 - - + +
180B GLU* 1.3 62.3 - - - +
182B GLU* 2.7 42.4 + - - +
183B ILE* 3.1 41.3 + - + +
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Residues in contact with GLU 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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176B GLN* 2.7 22.9 + - - +
177B LEU* 3.5 9.9 - - - +
179B ARG* 1.3 75.0 - - - +
181B VAL* 1.3 60.0 + - - +
183B ILE* 3.4 19.4 + - - +
184B GLN* 2.9 52.2 + - - +
251B VAL* 5.8 2.8 - - - +
273B ASP 3.7 19.9 - - - +
1388B HPM 3.9 14.6 - - + -
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Residues in contact with VAL 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* 3.0 41.6 + - + +
178B ARG* 3.2 7.6 + - - +
180B GLU* 1.3 74.6 - - - +
182B GLU* 1.3 63.7 + - - +
185B SER* 3.0 26.3 + - - -
195B LEU* 3.7 11.4 - - + +
198B TYR* 3.5 47.1 - - + -
205B VAL* 6.0 0.7 - - + -
207B LEU* 4.0 19.7 - - + -
1388B HPM 4.1 11.2 - - + -
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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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178B ARG 3.2 8.2 + - - +
179B ARG* 2.7 50.7 + - - +
181B VAL* 1.3 81.4 - - - +
183B ILE* 1.3 63.6 + - + +
185B SER* 2.9 20.5 + - - -
186B HIS* 3.4 26.5 + - + +
198B TYR* 6.3 0.4 - - - -
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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 ARG* 3.1 31.9 + - + +
180B GLU* 3.7 20.0 - - - +
182B GLU* 1.3 79.1 - - + +
184B GLN* 1.3 65.4 + - - +
186B HIS* 3.1 16.7 + - - +
187B LEU* 3.3 21.4 - - + +
251B VAL* 4.0 33.2 - - + -
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Residues in contact with GLN 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 GLU* 2.9 40.1 + - - +
181B VAL 3.9 2.7 - - - +
183B ILE* 1.3 74.6 - - - +
185B SER* 1.3 58.7 + - - +
186B HIS 3.1 5.6 + - - -
187B LEU* 3.2 45.8 + - - +
192B ILE* 4.5 9.7 - - - +
193B LEU 5.2 7.9 - - - +
195B LEU* 3.9 17.9 + - + +
273B ASP 2.9 36.6 + - - +
1388B HPM 3.5 23.9 - - + -
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Residues in contact with SER 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 VAL* 3.0 16.0 + - - -
182B GLU* 2.9 21.7 + - - -
184B GLN* 1.3 75.1 - - - +
186B HIS* 1.3 70.1 + - - +
187B LEU 4.8 2.6 - - - +
195B LEU* 3.9 26.9 - - - +
196B TYR 6.4 0.2 - - - -
197B GLY* 6.3 2.2 - - - -
198B TYR* 5.8 6.7 - - - -
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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