Contacts of the strand formed by residues 238 - 249 (chain C) in PDB entry 2VIG
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 THR 238 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C TRP* 3.3 40.6 - - + +
186C ILE 3.4 4.9 - - - +
187C THR* 4.4 1.4 + - - +
227C LYS* 3.3 3.5 - - - +
228C GLU* 2.7 49.0 + - + +
230C LYS* 3.0 32.0 + - - +
233C ILE* 5.6 0.2 - - - +
236C SER* 3.9 2.3 + - - -
237C SER* 1.3 76.1 + - - +
239C ALA* 1.3 61.7 + - - +
501C FAD 3.9 22.7 - - + +
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Residues in contact with ALA 239 (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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185C TRP 4.4 1.1 - - - -
186C ILE* 3.1 34.5 + - - +
189C ALA* 3.8 8.4 - - + +
190C TRP* 3.5 23.6 - - + +
224C LEU* 5.2 0.4 - - + -
225C GLY 3.5 22.4 - - - +
226C LYS 3.6 9.4 - - - +
228C GLU* 4.7 4.5 - - - -
238C THR* 1.3 78.4 - - - +
240C ASN* 1.3 69.1 + - - +
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Residues in contact with ASN 240 (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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157C PRO* 4.5 8.1 - - - +
182C THR* 3.6 21.9 - - + +
183C LYS 3.1 13.7 - - - +
184C ALA* 3.4 19.1 - - - +
185C TRP* 3.9 3.6 + - - -
224C LEU* 3.5 3.6 - - - -
225C GLY* 2.8 39.9 + - - +
226C LYS 4.6 1.0 + - - -
228C GLU* 4.1 11.3 + - - +
239C ALA* 1.3 77.2 - - - +
241C LEU* 1.3 65.1 + - - +
242C ILE* 4.1 6.1 - - + +
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Residues in contact with LEU 241 (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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151C CYS* 4.4 0.2 - - - -
153C ALA* 4.3 16.4 - - + -
181C GLY 3.7 1.9 - - - +
182C THR* 3.2 4.5 - - - -
183C LYS* 2.8 43.2 + - + -
186C ILE* 4.0 11.2 - - + +
189C ALA* 3.8 26.2 - - + -
195C ALA* 4.3 20.0 - - + -
217C MET* 4.1 18.8 - - + -
222C LEU* 3.9 13.2 - - + -
223C THR 3.8 2.5 - - - -
224C LEU* 3.8 11.0 - - + -
239C ALA 3.9 3.1 + - - +
240C ASN* 1.3 80.6 - - - +
242C ILE* 1.3 61.5 + - - +
243C PHE* 4.0 24.5 + - + -
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Residues in contact with ILE 242 (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 GLY 3.7 2.5 - - - +
182C THR* 3.7 27.6 - - + +
221C GLY 3.3 2.3 - - - +
222C LEU* 3.3 7.3 - - - +
223C THR* 2.8 56.0 + - - +
224C LEU 3.8 4.5 - - - +
225C GLY* 3.6 31.6 - - - +
240C ASN* 4.3 5.6 - - + +
241C LEU* 1.3 75.0 - - - +
243C PHE* 1.3 67.0 - - - +
244C GLU* 4.0 5.7 + - + +
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Residues in contact with PHE 243 (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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168C THR* 4.7 7.2 - - + -
179C LEU* 3.4 33.2 - - + +
180C ASN* 3.5 2.8 - - - +
181C GLY* 2.8 48.3 + - - +
183C LYS* 4.0 9.4 - - + -
197C VAL* 4.0 37.7 - - + -
215C VAL* 4.0 20.9 - - + -
221C GLY 3.3 4.9 - - - -
222C LEU* 3.7 22.7 - - + -
241C LEU* 4.0 25.1 - - + -
242C ILE* 1.3 76.3 - - - +
244C GLU* 1.3 59.5 + - - +
246C CYS* 3.7 21.8 - - + -
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Residues in contact with GLU 244 (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 ASN* 3.6 5.2 - - - +
221C GLY* 2.9 23.8 + - - +
242C ILE* 4.0 7.7 + - + +
243C PHE* 1.3 71.1 - - - +
245C ASP* 1.3 72.4 + - + +
246C CYS 3.1 0.9 + - - -
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Residues in contact with ASP 245 (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 ARG* 4.7 8.6 + - - -
178C VAL* 3.8 19.7 - - - +
179C LEU 3.4 3.2 + - - -
180C ASN* 2.7 34.0 + - - +
220C PRO 4.9 0.5 - - - +
221C GLY* 4.7 1.6 - - - -
244C GLU* 1.3 76.9 - - + +
246C CYS* 1.3 62.5 + - - +
247C ARG* 3.5 23.2 + - - +
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Residues in contact with CYS 246 (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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177C TRP 3.6 1.4 - - - +
178C VAL* 3.3 1.9 - - - -
179C LEU* 2.7 39.4 + - - +
215C VAL* 4.9 0.2 - - - -
219C THR* 3.6 22.4 - - - -
220C PRO 3.5 20.9 - - - -
221C GLY 3.4 19.3 - - - +
222C LEU 4.4 0.2 - - - -
243C PHE* 3.7 29.2 - - + -
244C GLU 3.1 1.9 + - - -
245C ASP* 1.3 75.0 - - - +
247C ARG* 1.3 60.8 + - - +
248C ILE* 4.1 14.7 + - - +
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Residues in contact with ARG 247 (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 ARG* 5.3 2.6 - - - +
173C GLU* 3.3 30.5 + - - +
176C SER* 4.0 18.6 + - - +
177C TRP 3.4 4.7 - - - +
178C VAL* 3.2 30.9 - - + +
219C THR* 4.7 6.1 + - - -
220C PRO* 4.3 5.6 + - - +
245C ASP* 3.5 25.2 + - - +
246C CYS* 1.3 77.2 - - - +
248C ILE* 1.3 66.4 + - - +
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Residues in contact with ILE 248 (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 SER* 3.2 6.9 - - - -
177C TRP* 2.9 43.3 + - + +
179C LEU* 3.8 32.8 - - + -
213C PHE* 4.0 16.8 - - + -
214C LEU 4.3 0.7 - - - +
215C VAL* 3.9 16.8 - - + -
216C PRO* 4.3 23.3 - - + -
219C THR* 5.1 2.5 - - - +
246C CYS* 4.3 15.7 - - - -
247C ARG* 1.3 80.4 - - - +
249C PRO* 1.3 71.0 - - + +
252C SER* 3.8 16.4 - - - +
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Residues in contact with PRO 249 (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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175C ASP 3.6 9.9 - - - +
176C SER* 4.3 1.3 - - - +
177C TRP* 3.5 3.6 - - - -
216C PRO* 6.0 3.8 - - + -
248C ILE* 1.3 89.3 - - + +
250C LYS* 1.3 60.6 + - - +
251C ASP* 3.5 15.7 - - - +
252C SER* 2.8 42.3 + - - +
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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