Contacts of the helix formed by residues 183 - 193 (chain C) in PDB entry 2V1C
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 PRO 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C PRO 4.3 1.8 - - - +
182C TYR* 1.3 92.3 - - + +
184C PRO* 1.3 71.7 - - + +
185C ALA* 3.2 2.9 - - + +
186C VAL* 2.9 33.5 + - + +
187C LEU* 3.0 10.2 + - - +
210C ASP* 3.8 32.5 - - - +
213C ALA* 5.9 1.6 - - + -
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Residues in contact with PRO 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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182C TYR 4.3 2.5 - - - +
183C PRO* 1.3 87.8 - - + +
185C ALA* 1.3 55.8 + - + +
187C LEU* 3.8 11.7 - - + +
188C ASP* 2.9 31.0 + - - +
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Residues in contact with ALA 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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183C PRO* 3.2 1.9 - - + +
184C PRO* 1.3 80.5 - - + +
186C VAL* 1.3 58.0 + - - +
188C ASP* 3.9 6.5 - - - +
189C PHE* 3.1 27.7 + - - +
205C PRO 5.9 0.7 - - - +
206C VAL* 4.0 18.5 - - + +
207C PRO* 4.6 15.7 - - + -
210C ASP* 4.6 9.9 - - - +
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Residues in contact with VAL 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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182C TYR* 3.6 31.2 - - + -
183C PRO* 2.9 24.9 + - + +
185C ALA* 1.3 75.4 - - - +
187C LEU* 1.3 65.8 + - - +
189C PHE* 3.3 2.8 + - - +
190C LEU* 2.9 30.8 + - + +
206C VAL* 4.7 2.0 - - + -
210C ASP* 3.7 40.4 - - + +
213C ALA* 4.9 5.8 - - + -
214C LEU* 3.7 25.6 - - + +
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Residues in contact with LEU 187 (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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161C PRO 3.8 9.9 - - - +
162C GLU* 3.6 54.5 - - + +
171C LEU* 4.3 15.5 - - + -
181C PRO* 5.7 0.2 - - + -
182C TYR* 3.9 26.0 - - + +
183C PRO 3.0 7.7 + - - +
184C PRO* 3.8 12.6 - - + +
185C ALA 3.4 0.2 - - - -
186C VAL* 1.3 77.1 - - - +
188C ASP* 1.3 58.7 + - - +
190C LEU* 3.3 4.4 + - + +
191C ARG* 2.8 60.3 + - - +
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Residues in contact with ASP 188 (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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184C PRO 2.9 18.4 + - - +
185C ALA* 3.9 7.2 - - - +
187C LEU* 1.3 77.1 - - - +
189C PHE* 1.3 63.5 + - - +
191C ARG* 3.3 5.8 + - - +
192C HIS* 3.1 50.8 + - - +
196C ARG* 2.8 25.9 + - - -
204C GLN* 5.8 1.4 - - - +
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Residues in contact with PHE 189 (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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131C TRP* 3.6 31.6 - + - -
134C LEU* 4.1 11.7 - - + -
135C VAL* 4.2 13.2 - - + -
138C TYR* 3.6 44.9 - + + -
185C ALA 3.1 18.6 + - - +
186C VAL 3.7 3.1 - - - +
187C LEU 3.3 0.2 - - - -
188C ASP* 1.3 79.5 + - - +
190C LEU* 1.3 61.3 + - - +
193C ALA* 2.8 59.2 + - + +
196C ARG* 5.0 4.9 - - - +
201C SER* 5.0 5.4 - - - -
206C VAL* 4.4 8.7 - - + -
214C LEU* 3.4 31.2 - - + -
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Residues in contact with LEU 190 (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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138C TYR* 3.6 36.7 - - + +
148C PRO* 5.8 3.3 - - - +
150C THR* 3.7 15.6 + - - +
169C GLY 5.9 1.6 - - - +
170C GLN 5.2 1.3 - - - +
171C LEU* 3.8 18.8 - - + -
182C TYR* 3.6 37.2 - - + +
186C VAL* 2.9 25.3 + - + +
187C LEU* 3.6 5.6 - - - +
189C PHE* 1.3 78.3 - - + +
191C ARG* 1.3 62.1 + - - +
193C ALA* 4.5 2.7 + - - +
194C VAL* 5.4 6.6 - - - +
214C LEU* 3.8 15.7 - - + -
217C ALA* 4.6 9.9 - - + -
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Residues in contact with ARG 191 (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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150C THR* 3.4 34.0 + - + +
160C ASP* 3.5 29.4 + - - +
161C PRO 3.4 21.6 + - - -
162C GLU* 3.8 16.2 + - - -
171C LEU* 4.9 5.1 - - + +
187C LEU* 2.8 47.2 + - - +
188C ASP* 3.8 3.1 - - - +
190C LEU* 1.3 75.5 - - - +
192C HIS* 1.3 86.6 + - + +
194C VAL 5.7 0.2 - - - -
195C ARG* 3.7 19.3 + - - +
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Residues in contact with HIS 192 (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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188C ASP* 3.1 35.7 + - - +
191C ARG* 1.3 107.9 + - + +
193C ALA* 1.3 60.5 + - - +
194C VAL 3.5 2.5 - - - -
195C ARG* 3.4 29.6 + - + +
196C ARG* 3.0 62.3 + - + +
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Residues in contact with ALA 193 (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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135C VAL* 5.6 4.6 - - + +
138C TYR* 4.7 9.0 - - + -
139C LYS* 3.7 9.1 - - - +
189C PHE* 2.8 62.9 + - + +
190C LEU 4.5 1.2 + - - +
191C ARG 3.9 0.4 - - - -
192C HIS* 1.3 69.4 - - - +
194C VAL* 1.3 67.9 + - + +
195C ARG 3.2 1.0 + - - -
196C ARG* 3.3 19.3 - - - +
201C SER* 4.5 12.8 + - - +
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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