Contacts of the strand formed by residues 238 - 249 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185H TRP* 3.3 46.4 - - + +
186H ILE 3.3 4.9 - - - +
187H THR* 4.4 3.1 + - - -
189H ALA* 4.9 0.2 - - - -
227H LYS* 3.5 3.9 - - - +
228H GLU* 2.9 37.2 + - + +
230H LYS* 3.2 30.1 + - - +
236H SER* 4.0 3.9 + - - -
237H SER* 1.3 78.3 + - - +
239H ALA* 1.3 63.0 + - - +
501H FAD 3.9 20.8 - - + +
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Residues in contact with ALA 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H TRP 4.4 1.6 - - - +
186H ILE* 3.1 32.6 + - - +
189H ALA* 3.9 6.2 - - + +
190H TRP* 3.4 33.9 - - + +
225H GLY 3.4 11.9 - - - +
226H LYS 3.5 10.8 - - - +
228H GLU* 4.7 5.2 - - - -
238H THR* 1.3 78.6 - - - +
240H ASN* 1.3 70.8 - - - +
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Residues in contact with ASN 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PRO* 4.7 7.1 - - - +
182H THR* 3.7 21.4 - - + +
183H LYS 3.1 13.9 - - - +
184H ALA* 3.3 21.2 - - - +
185H TRP 3.8 1.9 + - - -
224H LEU* 3.4 6.9 - - - +
225H GLY* 2.8 35.4 + - - +
226H LYS 4.8 0.6 + - - -
228H GLU* 4.4 10.2 + - - +
239H ALA* 1.3 77.3 - - - +
241H LEU* 1.3 63.7 - - - +
242H ILE* 4.3 7.0 - - + +
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Residues in contact with LEU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ALA* 4.0 25.8 - - + -
181H GLY 3.6 1.9 - - - +
182H THR* 3.2 3.8 - - - -
183H LYS* 2.8 40.8 + - + -
186H ILE* 3.9 14.8 - - + -
189H ALA* 3.8 26.5 - - + -
195H ALA* 4.2 19.1 - - + -
217H MET* 4.3 14.1 - - + -
222H LEU* 4.0 12.8 - - + -
223H THR 3.9 2.7 - - - -
224H LEU* 3.9 8.5 - - + -
239H ALA 3.9 0.2 + - - -
240H ASN* 1.3 77.8 - - - +
242H ILE* 1.3 61.5 + - - +
243H PHE* 3.8 26.1 - - + -
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Residues in contact with ILE 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H GLY 3.7 2.9 - - - +
182H THR* 4.0 19.5 - - + +
221H GLY 3.3 5.2 - - - +
222H LEU* 3.3 3.3 - - - +
223H THR* 2.8 62.1 + - + +
224H LEU 4.0 4.0 - - - +
225H GLY* 3.8 24.7 - - - +
240H ASN* 4.3 11.0 - - + +
241H LEU* 1.3 74.9 - - - +
243H PHE* 1.3 65.9 + - - +
244H GLU* 5.3 5.3 - - + +
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Residues in contact with PHE 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168H THR* 4.9 4.9 - - + -
179H LEU* 3.7 33.9 - - + +
180H ASN* 3.5 2.8 - - - +
181H GLY* 2.7 48.7 + - - +
183H LYS* 4.1 8.5 - - + -
195H ALA* 6.0 0.2 - - + -
197H VAL* 3.8 36.6 - - + -
215H VAL* 3.9 25.1 - - + -
221H GLY 3.2 4.5 - - - +
222H LEU* 3.8 19.1 - - + -
241H LEU* 3.8 29.4 - - + -
242H ILE* 1.3 76.6 - - - +
244H GLU* 1.3 60.5 + - - +
246H CYS* 3.7 21.5 - - + -
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Residues in contact with GLU 244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H ASN* 3.5 5.8 - - - +
221H GLY* 2.8 23.8 + - - +
242H ILE* 4.1 6.2 + - + +
243H PHE* 1.3 74.1 - - - +
245H ASP* 1.3 80.0 + - - +
246H CYS 3.3 1.1 + - - +
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Residues in contact with ASP 245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H ARG* 5.0 3.9 + - - -
178H VAL* 3.7 19.5 - - + +
179H LEU 3.2 5.9 + - - -
180H ASN* 2.9 34.1 + - - +
220H PRO 5.0 0.3 - - - +
221H GLY* 4.7 1.8 - - - -
244H GLU* 1.3 81.6 - - - +
246H CYS* 1.3 62.5 + - - +
247H ARG* 3.3 7.1 + - - +
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Residues in contact with CYS 246 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177H TRP 3.7 0.9 - - - +
178H VAL* 3.5 0.9 - - - -
179H LEU* 2.7 38.3 + - + +
215H VAL* 4.5 0.4 - - - -
219H THR* 3.5 32.3 - - - -
220H PRO 3.6 11.7 - - - -
221H GLY* 3.6 20.2 - - - +
222H LEU 4.4 0.2 - - - -
243H PHE* 3.7 30.7 - - + -
244H GLU 3.2 0.6 - - - -
245H ASP* 1.3 75.5 - - - +
247H ARG* 1.3 64.0 + - - +
248H ILE* 4.0 10.2 + - - +
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Residues in contact with ARG 247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H ARG* 5.5 2.0 - - - +
173H GLU* 3.9 11.1 + - - +
176H SER* 2.9 40.4 + - - +
177H TRP 3.3 5.6 - - - +
178H VAL* 3.6 23.2 - - + +
219H THR* 4.7 7.4 + - - -
220H PRO* 4.3 6.2 + - - +
245H ASP 3.3 7.7 + - - +
246H CYS* 1.3 74.9 - - - +
248H ILE* 1.3 71.3 + - - +
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Residues in contact with ILE 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H SER* 3.2 8.1 - - - -
177H TRP* 2.9 44.7 + - + +
179H LEU* 4.0 13.5 - - + -
213H PHE* 3.9 32.1 - - + -
214H LEU 4.1 3.4 - - - +
215H VAL* 4.2 27.8 - - + -
216H PRO* 4.4 12.6 - - + -
219H THR* 5.5 1.3 - - + +
246H CYS* 4.5 9.4 - - - +
247H ARG* 1.3 80.6 - - - +
249H PRO* 1.3 72.7 - - + +
252H SER* 3.6 22.4 - - - +
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Residues in contact with PRO 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175H ASP 3.9 5.4 - - - +
176H SER* 4.3 1.1 - - - -
177H TRP* 3.5 5.6 - - - -
216H PRO* 6.0 3.8 - - + -
248H ILE* 1.3 88.4 - - + +
250H LYS* 1.3 65.9 + - - +
251H ASP* 3.4 17.0 - - - +
252H SER* 3.0 39.2 + - - +
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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