Contacts of the strand formed by residues 238 - 249 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185D TRP* 3.5 39.0 - - + +
186D ILE 3.2 4.7 - - - +
187D THR* 4.5 2.9 + - - -
227D LYS* 3.5 3.7 - - - +
228D GLU* 2.9 46.0 + - + +
230D LYS* 3.2 33.0 + - - +
236D SER* 4.0 3.3 + - - -
237D SER* 1.3 77.4 + - - +
239D ALA* 1.3 62.6 + - - +
501D FAD 3.8 21.4 - - + +
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D TRP 4.3 1.3 - - - -
186D ILE* 3.1 36.5 + - - +
189D ALA* 4.0 5.9 - - + +
190D TRP* 3.4 20.0 - - + +
224D LEU* 5.2 0.2 - - + -
225D GLY 3.3 25.6 - - - +
226D LYS 3.4 9.6 - - - +
228D GLU* 4.7 6.3 - - - -
238D THR* 1.3 79.1 - - - +
240D ASN* 1.3 70.2 + - - +
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Residues in contact with ASN 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D PRO* 4.7 6.7 - - - +
182D THR* 3.7 21.2 - - + +
183D LYS 3.1 10.3 - - - +
184D ALA* 3.3 23.1 - - - +
185D TRP 3.9 2.4 + - - -
224D LEU* 3.3 6.9 - - - +
225D GLY* 2.7 38.0 + - - +
226D LYS 4.7 1.0 + - - -
228D GLU* 4.5 10.7 + - - +
239D ALA* 1.3 77.0 - - - +
241D LEU* 1.3 63.1 + - - +
242D ILE* 4.3 7.4 - - + +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D CYS* 4.6 2.9 - - - -
153D ALA* 4.1 23.3 - - + -
181D GLY 3.7 1.6 - - - +
182D THR* 3.3 3.6 - - - -
183D LYS* 2.8 42.0 + - + -
186D ILE* 4.0 12.1 - - + +
189D ALA* 3.8 29.2 - - + -
195D ALA* 4.2 20.4 - - + -
217D MET* 4.1 13.7 - - + -
222D LEU* 4.0 17.0 - - + -
223D THR 3.9 3.4 - - - -
224D LEU* 3.9 9.9 - - + -
239D ALA 3.7 0.6 + - - -
240D ASN* 1.3 74.3 - - - +
242D ILE* 1.3 61.7 + - - +
243D PHE* 3.9 21.5 + - + -
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Residues in contact with ILE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D GLY 3.8 2.9 - - - +
182D THR* 3.8 26.9 - - + +
221D GLY 3.4 2.4 - - - +
222D LEU* 3.4 4.9 - - - +
223D THR* 2.8 59.5 + - - +
224D LEU 3.9 4.0 - - - +
225D GLY* 3.7 31.2 - - - +
240D ASN* 4.3 6.5 - - + +
241D LEU* 1.3 73.3 - - - +
243D PHE* 1.3 66.8 + - - +
244D GLU* 3.9 5.1 + - + +
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Residues in contact with PHE 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D THR* 4.7 7.9 - - + -
179D LEU* 3.6 32.8 - - + +
180D ASN* 3.6 3.2 - - - +
181D GLY* 2.8 43.2 + - - +
183D LYS* 4.0 8.5 - - + -
197D VAL* 3.9 39.0 - - + -
215D VAL* 4.0 22.7 - - + -
221D GLY 3.3 2.0 - - - -
222D LEU* 3.5 25.6 - - + -
241D LEU* 3.9 25.4 - - + -
242D ILE* 1.3 74.3 - - - +
244D GLU* 1.3 60.9 + - - +
246D CYS* 3.7 22.9 - - + -
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Residues in contact with GLU 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D ASN* 3.8 7.2 - - - +
221D GLY* 2.8 26.8 + - - +
242D ILE* 3.9 6.5 + - + +
243D PHE* 1.3 73.5 - - - +
245D ASP* 1.3 74.2 + - + +
246D CYS 3.1 1.0 + - - -
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Residues in contact with ASP 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D VAL* 3.7 20.6 - - + -
179D LEU 3.3 2.7 + - - -
180D ASN* 3.1 17.7 + - - +
220D PRO 5.0 0.2 - - - +
221D GLY* 4.9 1.9 - - - -
244D GLU* 1.3 76.4 - - + +
246D CYS* 1.3 62.7 + - - +
247D ARG* 3.4 12.0 + - - +
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Residues in contact with CYS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TRP 3.5 2.1 - - - +
178D VAL* 3.4 1.8 - - - -
179D LEU* 2.7 43.1 + - + +
219D THR* 3.7 22.0 - - - -
220D PRO 3.4 21.3 - - - -
221D GLY 3.7 17.7 - - - +
243D PHE* 3.7 28.0 - - + -
244D GLU 3.9 1.8 - - - -
245D ASP* 1.3 75.3 - - - +
247D ARG* 1.3 59.7 + - - +
248D ILE* 3.9 11.6 + - - +
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Residues in contact with ARG 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D GLU* 3.1 51.7 + - - +
174D GLY* 5.0 1.0 - - - -
175D ASP* 4.6 4.4 - - - +
176D SER* 3.7 26.8 + - - +
177D TRP 3.3 4.3 - - - -
178D VAL* 3.9 17.2 - - + +
219D THR* 4.7 7.4 + - - -
220D PRO* 4.3 5.6 + - - +
245D ASP 3.4 12.4 + - - +
246D CYS* 1.3 75.2 - - - +
248D ILE* 1.3 66.4 + - - +
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D SER* 3.1 8.0 - - - -
177D TRP* 2.8 45.6 + - + +
179D LEU* 3.9 29.4 - - + -
213D PHE* 4.0 17.9 - - + -
214D LEU 4.4 1.1 - - - +
215D VAL* 4.1 26.7 - - + -
216D PRO* 4.5 11.4 - - + -
219D THR* 5.1 2.0 - - + +
246D CYS* 4.4 12.8 - - - +
247D ARG* 1.3 80.5 - - - +
249D PRO* 1.3 72.8 - - + +
252D SER* 3.6 24.9 - - - +
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Residues in contact with PRO 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ASP 3.7 8.7 - - - +
176D SER* 4.3 2.2 - - - +
177D TRP* 3.6 3.8 - - - -
216D PRO* 5.8 5.4 - - + -
248D ILE* 1.3 88.1 - - + +
250D LYS* 1.3 63.9 + - - +
251D ASP* 3.3 20.0 - - - +
252D SER* 2.6 40.6 + - - +
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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
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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