Contacts of the helix formed by residues 172 - 186 (chain A) in PDB entry 2C10
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.1 12.3 - - + +
89A ALA* 3.8 37.9 - - + +
90A ARG 5.1 3.4 - - - +
91A PRO* 5.9 2.7 - - + -
95A CYS* 4.4 7.4 - - - -
97A PHE* 3.7 10.1 - - + -
129A PHE* 3.7 32.8 - - + -
169A ARG* 5.5 3.8 - - - +
170A PRO 3.4 1.0 + - - +
171A VAL* 1.3 73.0 - - - +
173A PHE* 1.3 67.1 + - - +
174A GLN* 3.9 3.4 - - + +
175A GLU* 3.0 23.6 + - + +
176A TYR* 2.9 26.8 + - - -
418A GLU* 3.5 27.6 - - + +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 5.3 7.0 - - - +
171A VAL 4.0 0.2 + - - -
172A LEU* 1.3 69.7 - - - +
174A GLN* 1.3 56.8 + - - +
176A TYR* 3.1 22.3 + + + +
177A LEU* 2.9 30.8 + - - +
393A LYS* 4.1 22.2 - - + -
394A TYR* 4.0 22.9 - + - -
417A LEU 5.5 2.0 - - - -
418A GLU* 2.8 44.1 + - + +
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Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 4.6 3.3 + - - +
87A ALA 3.5 17.2 + - - +
88A GLN* 3.4 33.1 - - - +
89A ALA 3.3 27.6 - - - +
90A ARG* 5.2 1.3 - - + -
172A LEU* 3.1 3.2 - - + +
173A PHE* 1.3 79.3 - - - +
175A GLU* 1.3 56.3 + - - +
177A LEU* 3.1 26.5 + - - +
178A ASP* 3.0 59.3 + - - +
181A GLN* 5.1 3.6 - - - +
418A GLU* 4.7 0.4 + - - -
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 5.0 1.4 + - - +
91A PRO* 5.0 9.0 - - + -
169A ARG* 4.3 12.7 + - - -
171A VAL* 3.3 19.3 - - + -
172A LEU* 3.0 21.5 + - + +
174A GLN* 1.3 78.9 - - - +
176A TYR* 1.3 56.0 + - - +
178A ASP* 3.5 9.1 + - - +
179A ILE* 3.0 32.3 + - - +
223A ARG* 2.7 37.1 + - - -
251A HIS* 2.8 30.5 + - - +
259A TRP* 3.9 19.1 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.5 37.3 + - + +
172A LEU 2.9 23.4 + - - -
173A PHE* 3.1 22.2 + + + +
175A GLU* 1.3 72.8 - - - +
177A LEU* 1.3 60.1 + - + +
179A ILE* 3.4 6.2 + - + +
180A ASP* 3.1 33.2 + - - +
212A THR* 3.7 29.1 - - + +
216A ARG* 3.0 25.3 + - - -
227A PHE* 4.3 19.5 - + - -
389A PHE* 3.5 19.4 - + - -
394A TYR* 5.3 7.0 - - - -
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Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 2.9 15.8 + - + +
174A GLN* 3.1 34.0 + - - +
176A TYR* 1.3 76.1 - - + +
178A ASP* 1.3 60.6 + - - +
180A ASP* 3.2 11.4 + - + +
181A GLN* 2.9 38.0 + - - +
206A ARG* 5.1 5.5 + - - +
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Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 5.2 0.3 - - - +
90A ARG* 5.4 2.1 - - - +
91A PRO* 4.8 7.4 - - - +
174A GLN* 3.0 47.3 + - - +
175A GLU* 3.8 5.0 - - - +
177A LEU* 1.3 72.3 - - - +
179A ILE* 1.3 60.5 + - - +
181A GLN* 3.2 19.6 + - - +
182A MET* 2.9 29.3 + - - +
256A PRO* 4.3 20.8 - - + +
259A TRP* 3.7 21.9 - - + -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.7 0.4 - - + -
175A GLU* 3.0 27.6 + - + +
176A TYR* 3.7 13.0 - - + +
177A LEU 3.3 0.4 - - - -
178A ASP* 1.3 76.0 - - - +
180A ASP* 1.3 58.6 + - - +
182A MET* 3.3 6.4 + - - +
183A ILE* 2.9 40.9 + - + +
227A PHE* 3.6 44.4 - - + -
249A VAL* 4.0 12.3 - - + -
251A HIS* 3.6 34.1 - - + +
259A TRP* 3.7 19.7 - - + -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.1 16.5 + - - +
177A LEU* 3.5 13.8 - - + +
179A ILE* 1.3 77.2 - - - +
181A GLN* 1.3 59.4 + - - +
183A ILE* 4.3 3.5 - - - +
184A PHE* 2.8 50.0 + - + +
206A ARG* 3.8 25.6 + - - +
210A THR* 2.9 34.5 + - - +
227A PHE* 5.5 1.0 - - - -
448B TYR* 4.3 13.5 + - - -
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A GLN* 5.1 3.8 - - - +
177A LEU* 2.9 21.4 + - - +
178A ASP* 3.2 26.3 + - - +
180A ASP* 1.3 75.5 - - - +
182A MET* 1.3 58.2 + - - +
185A ASN* 2.8 50.4 + - - +
186A ARG* 4.8 0.8 - - - +
206A ARG* 4.1 12.7 - - - +
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Residues in contact with MET 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP 2.9 14.4 + - - +
179A ILE* 3.5 9.6 - - - +
181A GLN* 1.3 76.1 - - - +
183A ILE* 1.3 56.9 + - - +
186A ARG* 2.9 56.0 + - - +
187A GLU* 2.9 38.7 + - + +
249A VAL* 4.2 18.2 - - - -
256A PRO 5.9 0.2 - - - +
259A TRP* 3.5 46.4 - - + +
260A THR* 3.5 23.3 - - - +
261A ILE* 3.9 4.5 - - + +
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Residues in contact with ILE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ILE* 2.9 36.9 + - + +
180A ASP* 3.2 3.8 + - - +
182A MET* 1.3 77.1 - - + +
184A PHE* 1.3 70.2 + - + +
187A GLU* 3.2 9.2 + - - -
188A LEU* 2.6 58.0 + - + +
210A THR* 3.9 22.4 - - + -
227A PHE* 4.6 9.6 - - + -
229A LEU* 4.8 1.3 - - + -
247A LEU* 4.1 24.5 - - + -
249A VAL* 4.1 18.8 - - + -
261A ILE* 5.1 4.3 - - + -
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ASP* 2.8 45.6 + - - +
183A ILE* 1.3 76.4 - - + +
185A ASN* 1.3 65.4 + - - +
188A LEU* 4.0 23.8 - - + -
189A PRO* 3.4 15.8 - - - +
201A TYR* 4.4 10.3 + + - -
204A ARG* 6.1 0.3 - - - -
205A GLY 4.7 6.3 - - - +
206A ARG* 3.6 46.4 - - + +
208A LEU* 3.5 39.0 - - + -
209A VAL* 4.2 2.7 - - - -
210A THR* 3.8 31.4 - - + -
229A LEU* 4.2 4.3 - - + -
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Residues in contact with ASN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLN* 2.8 39.1 + - + +
184A PHE* 1.3 89.7 + - - +
186A ARG* 1.3 63.6 + - + +
189A PRO* 3.3 16.1 - - - +
204A ARG* 4.9 27.6 + - - +
206A ARG* 5.4 4.9 + - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLN 4.8 0.4 - - - +
182A MET* 2.9 46.2 + - - +
185A ASN* 1.3 83.0 - - + +
187A GLU* 1.3 75.1 + - + +
189A PRO* 4.0 3.6 - - - +
190A GLN* 3.2 23.4 + - - +
256A PRO 3.7 21.0 + - - -
257A ALA* 4.1 13.7 + - - +
259A TRP 3.9 15.0 + - - -
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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