Contacts of the helix formed by residues 210 - 226 (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 ASP 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C PRO* 3.8 31.1 - - - +
185C ALA* 4.6 5.9 - - - +
186C VAL* 3.7 22.0 - - + +
206C VAL* 3.7 14.6 - - + -
207C PRO* 2.8 27.3 + - - +
209C ALA* 1.3 77.7 - - - +
211C ARG* 1.3 60.4 + - - -
212C PRO* 3.5 2.0 - - - -
213C ALA* 3.6 17.3 + - - +
214C LEU* 3.7 8.5 + - - +
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ASP* 2.7 39.4 + - - -
130C GLU* 3.1 42.7 + - - +
131C TRP* 3.5 27.9 - - - +
134C LEU* 4.1 15.9 - - + -
205C PRO* 4.2 8.1 - - - +
206C VAL* 2.7 30.2 + - + +
207C PRO 3.5 10.1 - - - +
208C SER* 3.6 21.4 - - - +
210C ASP* 1.3 74.9 - - - +
212C PRO* 1.3 72.4 - - + +
213C ALA 3.1 2.5 - - - -
214C LEU* 2.9 20.1 + - - +
215C TRP* 2.9 16.8 + - + -
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Residues in contact with PRO 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C SER 3.4 14.1 - - - +
209C ALA 3.5 10.1 - - - +
210C ASP 3.5 3.6 - - - -
211C ARG* 1.3 93.6 - - + +
213C ALA* 1.3 56.5 + - - +
215C TRP* 3.4 11.1 + - + +
216C ARG* 2.8 44.1 + - + +
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Residues in contact with ALA 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C TYR* 4.1 30.7 + - + -
183C PRO* 5.9 1.3 - - + -
186C VAL* 4.9 5.8 - - + -
210C ASP* 3.6 14.2 + - - +
211C ARG 3.1 0.4 - - - -
212C PRO* 1.3 79.7 - - - +
214C LEU* 1.3 63.4 + - - +
216C ARG* 3.4 7.6 + - - +
217C ALA* 3.1 23.9 + - - +
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Residues in contact with LEU 214 (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* 4.1 12.6 - - + -
134C LEU* 4.0 27.4 - - + -
138C TYR* 2.8 24.6 + - - +
186C VAL* 3.7 29.2 - - + +
189C PHE* 3.4 40.8 - - + -
190C LEU* 3.8 13.2 - - + -
206C VAL* 4.1 18.6 - - + -
210C ASP 4.0 8.7 - - - +
211C ARG* 2.9 10.1 + - - +
213C ALA* 1.3 77.7 - - - +
215C TRP* 1.3 63.3 + - - +
217C ALA* 3.6 1.5 + - - -
218C LEU* 3.3 8.3 + - - +
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Residues in contact with TRP 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C PHE* 4.1 9.2 - + - -
94C LEU* 3.4 31.9 - - + -
130C GLU* 3.0 39.8 + - + -
133C ALA* 4.2 7.4 - - + -
134C LEU* 3.6 43.1 - - + +
137C SER* 4.8 3.1 - - - -
211C ARG 2.9 28.8 + - - -
212C PRO* 3.7 10.1 - - + +
214C LEU* 1.3 76.1 - - - +
216C ARG* 1.3 59.3 + - + +
218C LEU* 3.3 27.9 + - + +
219C GLU* 3.0 34.3 + - - +
232C TRP* 5.2 0.4 - + - -
236C VAL* 3.6 38.8 - - + +
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Residues in contact with ARG 216 (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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212C PRO* 2.8 35.2 + - + +
213C ALA* 3.7 7.9 - - - +
214C LEU 3.3 0.2 - - - -
215C TRP* 1.3 76.7 - - - +
217C ALA* 1.3 60.5 + - - +
219C GLU* 3.4 24.6 + - - +
220C LYS* 3.0 30.5 + - - +
236C VAL* 6.5 0.7 - - - -
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Residues in contact with ALA 217 (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 13.7 - - - +
169C GLY* 3.9 19.9 - - - +
170C GLN 5.7 0.2 - - - +
182C TYR* 4.0 17.2 + - + +
190C LEU* 4.6 12.8 - - + -
213C ALA 3.1 14.8 + - - +
214C LEU* 4.5 1.1 - - - -
216C ARG* 1.3 76.3 - - - +
218C LEU* 1.3 55.6 + - - +
220C LYS* 3.5 4.5 + - - +
221C PHE* 2.8 36.8 + - - +
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Residues in contact with LEU 218 (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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98C PHE* 4.2 13.5 - - + -
134C LEU* 5.2 0.4 - - + -
137C SER* 3.9 21.8 - - - +
138C TYR* 3.3 30.8 + - + +
141C LEU* 3.7 34.1 - - + -
214C LEU 3.3 11.9 + - - +
215C TRP* 3.5 31.6 - - + +
217C ALA* 1.3 75.1 - - - +
219C GLU* 1.3 64.4 + - - +
221C PHE* 4.5 3.1 - - - -
222C VAL* 3.0 40.2 + - + +
232C TRP* 4.3 9.4 - - + -
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Residues in contact with GLU 219 (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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215C TRP* 3.0 25.9 + - + +
216C ARG* 3.6 29.0 + - - +
218C LEU* 1.3 76.5 - - - +
220C LYS* 1.3 57.7 + - - +
222C VAL* 4.0 0.5 - - - +
223C THR* 2.9 37.7 + - + +
232C TRP* 4.0 25.8 - - + -
233C ARG* 3.6 32.1 + - + +
236C VAL* 3.7 26.2 - - + +
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Residues in contact with LYS 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C ASP 4.7 1.1 - - - +
166C PRO* 3.0 33.8 + - + +
167C LEU* 3.5 25.6 + - - +
168C GLY 4.2 0.7 - - - +
169C GLY* 3.8 15.3 - - - +
216C ARG 3.0 17.6 + - - +
217C ALA* 4.5 1.1 - - - -
219C GLU* 1.3 72.2 - - - +
221C PHE* 1.3 69.6 + - - +
223C THR* 3.3 9.9 + - - -
224C VAL* 3.1 38.2 + - + +
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Residues in contact with PHE 221 (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* 6.5 0.4 - - + -
141C LEU* 4.1 18.6 - - + -
146C VAL* 3.3 29.4 - - + -
147C ILE 3.8 6.3 - - - -
148C PRO* 3.4 44.4 - - + -
168C GLY 3.8 18.8 - - - -
169C GLY* 3.8 6.7 - - - +
170C GLN* 4.0 18.2 - - + -
217C ALA 2.8 24.1 + - - +
218C LEU* 3.8 4.5 - - - +
220C LYS* 1.3 76.8 - - - +
222C VAL* 1.3 67.9 + - + +
224C VAL* 3.1 1.4 + - - +
225C GLN* 3.0 57.2 + - + +
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Residues in contact with VAL 222 (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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98C PHE* 4.2 11.0 - - + -
102C LEU* 4.6 8.5 - - + -
141C LEU* 4.0 27.4 - - + -
218C LEU* 3.0 30.8 + - + +
219C GLU 4.1 1.8 - - - +
221C PHE* 1.3 84.1 - - + +
223C THR* 1.3 57.4 + - - +
225C GLN* 4.6 0.7 - - - +
226C VAL* 3.0 40.1 + - + +
230C HIS* 3.5 25.2 + - + +
232C TRP* 3.9 15.9 - - + +
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Residues in contact with THR 223 (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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219C GLU 2.9 24.9 + - - +
220C LYS* 3.3 17.7 + - - -
222C VAL* 1.3 76.0 - - + +
224C VAL* 1.3 62.4 + - - +
225C GLN 3.4 0.2 - - - -
226C VAL 3.6 9.4 - - - +
230C HIS* 3.7 25.6 - - + -
232C TRP* 5.5 0.7 - - + -
233C ARG* 3.8 37.7 - - - +
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Residues in contact with VAL 224 (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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167C LEU 3.5 22.9 - - - +
168C GLY* 4.4 13.7 - - - +
220C LYS* 3.1 31.1 + - + +
221C PHE 3.1 4.3 + - - +
223C THR* 1.3 79.5 - - - +
225C GLN* 1.3 76.3 - - + +
226C VAL 4.9 0.2 - - - -
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Residues in contact with GLN 225 (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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104C GLN* 5.0 3.1 + - - -
146C VAL* 3.7 25.7 - - + +
168C GLY 5.1 0.6 + - - -
170C GLN* 4.1 18.8 - - - +
221C PHE* 3.0 47.1 + - + +
222C VAL* 4.7 0.4 - - - -
224C VAL* 1.3 96.7 + - + +
226C VAL* 1.3 62.8 + - + +
227C GLY 4.4 0.3 + - - -
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Residues in contact with VAL 226 (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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101C ALA 3.8 20.2 - - - +
102C LEU* 4.1 31.0 - - + +
104C GLN* 3.7 21.3 - - + +
146C VAL* 4.4 14.4 - - + -
222C VAL* 3.0 19.4 + - + +
223C THR 3.6 10.4 - - - +
224C VAL 5.3 0.2 - - - -
225C GLN* 1.3 87.7 - - + +
227C GLY* 1.3 72.4 + - - +
228C GLY 5.0 0.2 - - - +
230C HIS* 2.9 24.6 + - + -
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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
------------------------------------------------------------
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