Contacts of the strand formed by residues 194 - 200 (chain G) 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 ALA 194 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123G TYR* 3.1 29.8 - - + +
139G TRP* 3.5 20.9 - - + -
143G PHE* 3.5 11.2 - - + -
149G ILE 3.9 2.4 + - - -
150G GLY* 3.3 3.8 - - - -
151G CYS* 3.0 27.0 + - - -
192G ALA* 3.5 2.1 - - - +
193G SER* 1.3 84.4 - - - +
195G ALA* 1.3 61.7 + - - +
215G VAL 3.3 7.0 - - - -
217G MET* 3.9 4.2 - - - +
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Residues in contact with ALA 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR* 4.4 2.4 - - - -
151G CYS* 3.5 23.6 - - - -
153G ALA* 4.8 1.1 - - + -
194G ALA* 1.3 75.5 - - - +
196G VAL* 1.3 63.8 + - - +
197G VAL* 3.5 21.9 + - + -
213G PHE 3.4 3.5 - - - +
214G LEU* 3.5 3.6 - - - +
215G VAL* 2.9 36.9 + - + +
217G MET* 3.9 9.9 - - + -
241G LEU* 4.1 7.4 - - + -
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Residues in contact with VAL 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU 4.6 5.8 - - - +
123G TYR* 3.7 37.9 - - + +
126G PRO* 4.4 8.7 - - + -
127G ILE* 4.1 4.5 - - + -
151G CYS 3.1 9.1 + - - +
152G PHE* 3.6 3.2 - - + -
153G ALA* 2.7 33.3 + - - +
195G ALA* 1.3 71.7 - - - +
197G VAL* 1.3 58.7 + - - +
198G PHE* 4.0 26.1 - - + -
212G ALA* 4.7 5.2 - - + -
213G PHE 3.3 7.0 - - - +
214G LEU* 4.0 18.6 - - + -
254G LEU* 4.2 18.8 - - + -
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Residues in contact with VAL 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153G ALA* 3.5 6.7 - - + +
168G THR* 5.0 4.3 - - + -
179G LEU* 4.8 8.7 - - + -
183G LYS* 4.1 17.3 - - + -
195G ALA* 3.5 22.7 - - + -
196G VAL* 1.3 77.1 - - - +
198G PHE* 1.3 70.9 + - - +
199G ALA* 5.3 1.3 - - + -
212G ALA* 3.5 2.6 - - - -
213G PHE* 2.8 49.0 + - + +
215G VAL* 3.7 24.5 - - + -
243G PHE* 3.8 32.5 - - + -
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Residues in contact with PHE 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G PRO* 5.9 0.2 - - + -
152G PHE* 3.4 33.9 - + - -
153G ALA 3.0 21.3 + - - +
154G LEU* 3.8 25.8 - - + -
156G GLU* 4.5 0.2 - - - +
166G ALA* 4.5 2.9 - - + +
168G THR* 4.3 0.7 - - - -
183G LYS* 2.6 33.8 + - - +
196G VAL* 4.0 22.0 - - + -
197G VAL* 1.3 74.2 - - - +
199G ALA* 1.3 61.7 + - - +
210G ILE* 4.2 9.9 - - + -
211G SER 3.4 4.5 - - - +
212G ALA* 3.7 20.9 - - + -
260G GLY 3.2 32.8 - - - -
263G ILE* 4.0 8.3 - - + -
264G ALA* 3.6 24.2 - - + -
267G THR* 5.2 0.2 - - - -
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Residues in contact with ALA 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166G ALA* 5.1 1.1 - - - -
168G THR* 3.5 21.5 - - + +
169G THR 3.9 6.5 - - - +
170G ALA* 3.7 25.1 - - + -
179G LEU* 4.9 4.9 - - + -
197G VAL* 4.1 2.9 + - + +
198G PHE* 1.3 74.3 - - - +
200G SER* 1.3 63.5 + - - +
201G THR 3.4 0.5 + - - -
210G ILE* 4.2 5.1 - - - +
211G SER* 2.8 34.9 + - - +
213G PHE* 4.0 10.8 - - + -
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Residues in contact with SER 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B GLY 4.6 4.6 + - - -
166G ALA* 3.7 20.1 - - - +
167G SER* 5.5 0.2 - - - -
168G THR 2.7 18.8 + - - -
169G THR* 3.3 12.3 - - - +
170G ALA 3.0 21.3 + - - +
199G ALA* 1.3 69.8 - - - +
201G THR* 1.3 60.1 + - - +
202G ASP 3.4 22.9 + - - -
209G SER* 3.5 16.0 + - - -
210G ILE* 4.4 7.9 - - - +
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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