Contacts of the helix formed by residues 172 - 186 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 4.4 9.6 - - + +
89C ALA* 3.9 35.9 - - + +
90C ARG 5.0 4.5 - - - +
91C PRO* 5.7 3.6 - - + -
95C CYS* 4.4 11.4 - - - -
97C PHE* 3.8 26.2 - - + -
129C PHE* 3.9 21.5 - - + -
169C ARG* 5.5 4.0 - - - +
170C PRO 3.6 1.1 + - - +
171C VAL* 1.3 77.8 - - - +
173C PHE* 1.3 59.0 + - - +
174C GLN* 3.2 3.6 - - + +
175C GLU* 3.0 22.2 + - + +
176C TYR* 2.8 28.8 + - - -
418C GLU* 3.3 19.7 - - + +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ALA* 5.4 8.1 - - - +
171C VAL 5.8 0.2 - - - -
172C LEU* 1.3 69.9 - - - +
174C GLN* 1.3 57.9 + - - +
176C TYR* 3.1 22.3 + + + +
177C LEU* 2.9 30.2 + - - +
393C LYS* 4.1 17.0 - - + -
394C TYR* 3.6 31.0 - + - -
417C LEU 5.5 1.1 - - - -
418C GLU* 2.9 44.7 + - + +
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Residues in contact with GLN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA 4.4 3.5 + - - +
87C ALA 3.8 9.6 + - - +
88C GLN* 3.4 40.4 - - - +
89C ALA 3.3 26.2 - - - +
90C ARG* 4.8 1.3 - - + +
172C LEU* 3.2 3.2 - - + +
173C PHE* 1.3 76.6 - - - +
175C GLU* 1.3 59.1 + - - +
177C LEU* 3.3 26.5 + - - +
178C ASP* 2.8 58.5 + - - +
181C GLN* 5.2 3.2 - - - +
418C GLU* 4.6 0.6 + - - -
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Residues in contact with GLU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 5.0 1.2 + - - +
91C PRO* 5.2 8.9 - - + +
169C ARG* 4.3 11.4 + - - -
171C VAL* 3.3 19.4 - - + -
172C LEU* 3.0 24.2 + - + +
174C GLN* 1.3 78.6 - - - +
176C TYR* 1.3 59.9 + - - +
178C ASP* 3.4 8.5 + - - +
179C ILE* 3.1 28.8 + - + +
223C ARG* 2.7 37.2 + - - -
251C HIS* 2.8 32.7 + - - +
259C TRP* 4.0 17.7 - - + -
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 3.5 33.8 + - + +
172C LEU 2.8 23.3 + - - -
173C PHE* 3.1 23.1 + + - +
175C GLU* 1.3 75.2 - - - +
177C LEU* 1.3 62.2 + - - +
179C ILE* 3.3 8.7 + - + +
180C ASP* 3.1 27.6 + - - +
212C THR* 3.7 28.9 - - + +
216C ARG* 3.0 25.1 + - - -
227C PHE* 4.3 20.4 - + - -
389C PHE* 3.5 19.0 - + - -
394C TYR* 5.3 6.3 - - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C PHE 2.9 16.2 + - - +
174C GLN* 3.4 32.8 - - - +
176C TYR* 1.3 72.8 - - - +
178C ASP* 1.3 60.2 + - - +
180C ASP* 3.1 11.9 + - + +
181C GLN* 2.9 41.9 + - - +
206C ARG* 5.5 0.2 + - - -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 5.2 0.3 - - - +
90C ARG* 5.3 2.1 - - - +
91C PRO* 4.8 8.7 - - - +
174C GLN* 2.8 47.0 + - - +
175C GLU* 3.8 3.8 - - - +
177C LEU* 1.3 74.1 - - - +
179C ILE* 1.3 61.9 + - - +
181C GLN* 3.4 16.6 + - - +
182C MET* 3.1 22.3 + - - +
256C PRO* 4.3 20.5 - - + +
259C TRP* 3.6 24.5 - - + -
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 4.8 0.7 - - + -
175C GLU* 3.1 24.2 + - + +
176C TYR* 3.4 15.7 - - + +
177C LEU 3.1 0.2 - - - -
178C ASP* 1.3 75.2 - - - +
180C ASP* 1.3 62.4 + - - +
182C MET* 3.3 4.8 + - - +
183C ILE* 3.0 39.9 + - + +
227C PHE* 3.7 41.7 - - + -
249C VAL* 4.4 10.1 - - + -
251C HIS* 3.6 36.1 - - + +
259C TRP* 3.5 21.5 - - + -
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C TYR* 3.1 15.7 + - - +
177C LEU* 3.1 16.1 + - + +
179C ILE* 1.3 78.4 - - - +
181C GLN* 1.3 60.3 + - - +
183C ILE* 4.3 3.1 - - - +
184C PHE* 2.8 48.8 + - + +
206C ARG* 3.8 22.8 + - - +
210C THR* 2.9 35.8 + - - +
227C PHE* 5.4 0.7 - - - -
448D TYR* 4.5 12.0 + - - -
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Residues in contact with GLN 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLN* 5.2 2.0 - - - +
177C LEU* 2.9 28.1 + - - +
178C ASP* 3.7 24.1 + - - +
179C ILE 3.2 0.2 - - - -
180C ASP* 1.3 75.9 - - - +
182C MET* 1.3 58.0 + - - +
185C ASN* 2.8 52.6 + - - +
186C ARG* 4.8 0.8 - - - +
206C ARG* 4.5 11.9 - - - +
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Residues in contact with MET 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ASP 3.1 14.1 + - - +
179C ILE* 3.6 9.2 - - - +
180C ASP 3.3 0.2 - - - -
181C GLN* 1.3 75.9 - - - +
183C ILE* 1.3 56.9 + - - +
186C ARG* 3.1 41.9 + - - +
187C GLU* 3.0 48.6 + - + +
249C VAL* 4.4 11.9 - - - -
259C TRP* 3.7 34.5 - - + +
260C THR* 3.5 37.9 - - - +
261C ILE* 3.8 15.9 - - + +
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Residues in contact with ILE 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ILE* 3.0 35.6 + - + +
180C ASP* 3.8 4.0 - - - +
181C GLN 3.3 0.2 - - - -
182C MET* 1.3 77.5 - - + +
184C PHE* 1.3 74.4 + - + +
187C GLU* 3.2 8.4 + - - -
188C LEU* 2.7 56.5 + - + +
210C THR* 3.8 24.2 - - + -
227C PHE* 4.6 8.1 - - + -
229C LEU* 4.7 1.6 - - + -
247C LEU* 4.1 23.8 - - + -
249C VAL* 4.2 19.3 - - + -
261C ILE* 5.0 4.7 - - + -
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Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP* 2.8 50.8 + - - +
183C ILE* 1.3 81.1 - - + +
185C ASN* 1.3 64.8 + - - +
188C LEU* 3.8 25.6 - - + -
189C PRO* 3.3 19.8 - - - +
201C TYR* 4.5 9.7 + + - -
204C ARG* 5.2 6.4 - - - +
205C GLY 5.9 0.2 - - - -
206C ARG* 3.5 53.2 - - + +
208C LEU* 3.5 39.7 - - + -
209C VAL* 4.3 2.9 - - - -
210C THR* 4.1 15.5 - - + -
229C LEU* 4.3 4.0 - - + -
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Residues in contact with ASN 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLN* 2.8 42.8 + - - +
184C PHE* 1.3 84.1 + - - +
186C ARG* 1.3 63.5 + - + +
189C PRO* 3.3 16.6 - - - +
204C ARG* 4.5 21.4 - - - +
206C ARG* 5.2 5.2 + - - +
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Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C GLN 4.8 0.2 - - - +
182C MET* 3.1 48.9 + - - +
185C ASN* 1.3 85.5 - - + +
187C GLU* 1.3 76.5 + - - +
189C PRO* 4.0 4.1 - - - +
190C GLN* 3.2 23.5 + - - +
256C PRO* 3.3 28.1 + - - +
257C ALA* 4.4 12.2 + - - +
259C TRP* 4.4 11.3 + - - +
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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