Contacts of the strand formed by residues 238 - 249 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185B TRP* 3.3 46.4 - - + +
186B ILE 3.3 5.4 - - - +
187B THR* 4.4 2.0 + - - +
189B ALA* 4.9 0.2 - - - -
227B LYS* 3.4 3.6 - - - +
228B GLU* 2.8 38.0 + - + +
230B LYS* 2.9 33.7 + - + +
233B ILE* 5.4 0.2 - - - +
236B SER* 4.3 2.8 + - - -
237B SER* 1.3 75.7 + - - +
239B ALA* 1.3 62.4 + - - +
501B FAD 3.8 22.5 - - + +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TRP 4.3 1.3 - - - +
186B ILE* 3.0 34.9 + - - +
189B ALA* 4.0 6.2 - - + +
190B TRP* 3.4 30.7 - - + +
225B GLY 3.5 4.3 - - - +
226B LYS 3.3 20.0 - - - +
228B GLU* 4.7 6.1 - - - -
238B THR* 1.3 79.7 - - - +
240B ASN* 1.3 71.6 + - - +
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Residues in contact with ASN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B PRO* 4.6 8.9 - - - +
182B THR* 3.6 21.0 - - + +
183B LYS 3.1 11.9 - - - +
184B ALA* 3.2 21.9 - - - +
185B TRP 3.8 1.9 + - - -
224B LEU* 3.4 8.0 - - - +
225B GLY* 2.9 35.5 + - - +
226B LYS 4.6 1.0 + - - -
228B GLU* 4.5 10.9 + - - +
239B ALA* 1.3 77.7 - - - +
241B LEU* 1.3 64.4 + - - +
242B ILE* 4.0 6.8 - - + +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B CYS* 4.8 2.0 - - - -
153B ALA* 4.6 8.7 - - + -
181B GLY 3.7 1.9 - - - +
182B THR* 3.2 3.1 - - - -
183B LYS* 2.7 41.6 + - + -
186B ILE* 3.9 18.8 - - + -
189B ALA* 3.9 19.3 - - + -
195B ALA* 4.2 18.4 - - + -
217B MET* 4.1 20.2 - - + -
222B LEU* 4.0 7.9 - - + -
223B THR 3.9 3.6 - - - -
224B LEU* 3.5 20.0 - - + -
239B ALA 3.8 0.6 + - - -
240B ASN* 1.3 80.1 - - - +
242B ILE* 1.3 60.1 + - - +
243B PHE* 3.9 30.1 + - + -
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B GLY 3.7 3.6 - - - +
182B THR* 3.9 27.4 - - + +
221B GLY 3.4 4.3 - - - +
222B LEU* 3.6 2.5 - - - +
223B THR* 3.0 47.8 + - - +
224B LEU 4.1 2.5 - - - +
225B GLY* 4.0 28.3 - - - +
240B ASN* 4.3 6.5 - - + +
241B LEU* 1.3 74.1 - - - +
243B PHE* 1.3 66.5 + - - +
244B GLU* 3.9 6.3 + - + +
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B THR* 4.7 8.1 - - + -
179B LEU* 3.7 29.6 - - + +
180B ASN* 3.4 3.1 - - - +
181B GLY* 2.7 49.2 + - - +
183B LYS* 4.0 8.5 - - + -
197B VAL* 3.9 38.8 - - + -
215B VAL* 3.8 22.0 - - + -
221B GLY 3.3 2.5 - - - -
222B LEU* 3.5 24.7 - - + -
241B LEU* 3.9 27.4 - - + -
242B ILE* 1.3 73.9 - - - +
244B GLU* 1.3 60.8 + - - +
245B ASP 4.0 0.7 - - - -
246B CYS* 3.6 21.5 - - + -
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B ASN* 3.7 4.7 - - - +
221B GLY* 2.8 24.1 + - - +
242B ILE* 3.9 7.1 + - + +
243B PHE* 1.3 72.8 - - - +
245B ASP* 1.3 75.1 + - + +
246B CYS 3.2 0.6 + - - +
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Residues in contact with ASP 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B VAL* 3.1 24.5 - - - +
179B LEU 3.4 3.0 + - - -
180B ASN* 2.7 20.4 + - - +
220B PRO 4.8 0.7 - - - +
221B GLY* 4.3 3.5 - - - -
244B GLU* 1.3 77.5 - - + +
246B CYS* 1.3 61.9 + - - +
247B ARG* 3.5 26.8 + - - +
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Residues in contact with CYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B TRP 3.5 1.9 - - - +
178B VAL* 3.4 2.3 - - - -
179B LEU* 2.9 40.4 + - + +
215B VAL* 4.7 0.4 - - - -
219B THR* 3.5 32.3 - - - -
220B PRO 3.6 9.9 - - - -
221B GLY* 3.6 17.5 - - - +
243B PHE* 3.6 32.5 - - + -
244B GLU 3.2 0.2 - - - -
245B ASP* 1.3 75.6 - - - +
247B ARG* 1.3 59.8 + - - +
248B ILE* 3.8 12.9 + - - +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B GLU* 3.4 41.8 + - - +
176B SER* 4.0 17.8 + - - +
177B TRP 3.4 4.5 - - - +
178B VAL* 3.8 21.9 - - + +
219B THR* 4.9 6.1 + - - -
220B PRO* 4.2 7.6 + - - +
245B ASP* 3.5 28.6 + - - +
246B CYS* 1.3 74.8 - - - +
248B ILE* 1.3 66.5 + - - +
249B PRO* 4.9 0.2 - - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B SER* 3.1 7.0 - - - -
177B TRP* 2.7 52.6 + - + +
179B LEU* 4.2 15.9 - - + -
213B PHE* 4.0 25.1 - - + -
214B LEU 3.9 9.2 - - - +
215B VAL* 4.3 7.2 - - + -
216B PRO* 4.4 20.0 - - + -
219B THR* 5.4 2.0 - - + +
246B CYS* 4.4 18.6 - - - +
247B ARG* 1.3 79.3 - - - +
249B PRO* 1.3 69.3 - - + +
252B SER* 3.5 27.1 - - - +
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Residues in contact with PRO 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TRP* 6.5 0.7 - - + -
175B ASP 3.7 9.6 - - - +
176B SER* 4.2 2.0 - - - +
177B TRP* 3.7 3.3 - - - -
216B PRO* 6.1 4.0 - - + -
247B ARG 4.9 0.4 - - - +
248B ILE* 1.3 87.6 - - + +
250B LYS* 1.3 59.5 + - - +
251B ASP* 3.7 23.8 - - - +
252B SER* 2.8 42.7 + - - +
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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