Contacts of the strand formed by residues 194 - 200 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A TYR* 3.3 28.5 - - + +
139A TRP* 3.5 21.3 - - + -
143A PHE* 3.5 13.6 - - + -
150A GLY* 3.2 6.2 - - - -
151A CYS 3.1 20.8 + - - -
192A ALA* 3.5 5.7 - - - +
193A SER* 1.3 79.4 - - - +
195A ALA* 1.3 61.0 + - - +
215A VAL 3.2 8.3 - - - +
217A MET* 3.9 6.2 - - - +
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 4.3 2.6 - - - -
151A CYS* 3.5 26.9 - - - +
152A PHE 5.2 0.2 - - - +
153A ALA* 5.2 0.9 - - + -
194A ALA* 1.3 75.0 - - - +
196A VAL* 1.3 63.7 + - - +
197A VAL* 3.6 20.6 - - + +
213A PHE 3.3 3.3 - - - +
214A LEU* 3.5 4.7 - - - +
215A VAL* 2.9 34.2 + - + +
217A MET* 3.8 10.1 - - + -
222A LEU* 6.2 0.2 - - + -
241A LEU* 4.2 7.4 - - + -
243A PHE* 5.9 0.2 - - + -
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Residues in contact with VAL 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU 4.2 6.7 - - - +
123A TYR* 3.7 36.8 - - + +
126A PRO* 4.2 13.2 - - + -
127A ILE* 4.4 1.3 - - + -
151A CYS 3.0 9.4 + - - +
152A PHE* 3.6 3.0 - - + -
153A ALA 2.7 32.4 + - - +
195A ALA* 1.3 70.1 - - - +
197A VAL* 1.3 59.0 + - - +
198A PHE* 4.0 25.7 - - + -
212A ALA* 4.6 5.4 - - + -
213A PHE 3.4 6.7 - - - +
214A LEU* 3.8 17.0 - - + -
254A LEU* 4.3 20.0 - - + -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ALA* 3.7 10.8 - - + +
168A THR* 5.3 1.8 - - + -
179A LEU* 4.3 12.1 - - + -
183A LYS* 4.5 8.3 - - + -
195A ALA* 3.6 24.0 - - + -
196A VAL* 1.3 78.5 - - - +
198A PHE* 1.3 73.0 + - - +
199A ALA* 5.2 2.5 - - + -
211A SER 3.6 1.0 - - - +
212A ALA* 3.4 3.2 - - - -
213A PHE* 2.7 46.8 + - + +
215A VAL* 3.7 22.0 - - + -
243A PHE* 3.9 32.8 - - + -
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Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.4 40.8 - + - -
153A ALA 3.0 24.1 + - - +
154A LEU* 3.9 23.3 - - + -
166A ALA* 4.7 2.9 - - + +
168A THR* 4.5 0.5 - - - -
183A LYS* 2.6 33.5 + - - +
196A VAL* 4.0 21.8 - - + -
197A VAL* 1.3 73.8 - - - +
199A ALA* 1.3 60.3 + - - +
210A ILE* 4.0 9.2 - - + -
211A SER 3.4 1.6 - - - -
212A ALA* 3.6 24.0 - - + -
260A GLY* 3.2 33.7 - - - -
263A ILE* 4.2 7.4 - - + -
264A ALA* 3.6 17.5 - - + -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 5.2 1.6 - - - -
168A THR* 3.6 20.9 - - + +
169A THR 3.8 3.6 - - - +
170A ALA* 3.7 28.5 - - + +
179A LEU* 4.7 6.5 - - + -
197A VAL* 4.0 1.7 + - + -
198A PHE* 1.3 73.9 - - - +
200A SER* 1.3 62.9 + - - +
201A THR* 3.4 2.4 + - - +
210A ILE* 3.4 6.2 - - - +
211A SER* 2.9 32.7 + - - +
213A PHE* 4.1 9.0 - - + -
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Residues in contact with SER 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA* 3.6 20.2 + - - +
167A SER* 5.1 0.7 - - - -
168A THR 2.7 18.2 + - - -
169A THR* 3.4 13.1 - - - +
170A ALA 2.9 22.7 + - - +
199A ALA* 1.3 69.5 - - - +
201A THR* 1.3 60.0 + - - +
202A ASP 4.0 4.3 + - - -
203A ARG* 4.4 12.5 + - - +
209A SER* 3.4 22.7 + - - -
210A ILE* 4.4 5.1 - - - +
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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