Contacts of the strand formed by residues 194 - 200 (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 ALA 194 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.4 27.4 - - + +
139D TRP* 3.5 21.8 - - + -
143D PHE* 3.5 14.7 - - + -
150D GLY* 3.3 3.8 - - - -
151D CYS* 3.0 27.5 + - - -
192D ALA* 3.6 1.9 - - - +
193D SER* 1.3 82.2 - - - +
195D ALA* 1.3 61.4 + - - +
215D VAL 3.3 6.7 - - - -
217D MET* 3.9 5.8 - - - +
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Residues in contact with ALA 195 (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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123D TYR* 4.5 3.5 - - - -
139D TRP* 4.9 0.2 - - - -
151D CYS* 3.4 25.6 - - - +
153D ALA* 5.0 1.1 - - + -
194D ALA* 1.3 74.2 - - - +
196D VAL* 1.3 64.1 + - - +
197D VAL* 3.6 21.8 - - + -
213D PHE 3.3 2.3 - - - +
214D LEU* 3.5 5.2 - - - +
215D VAL* 2.9 35.8 + - + +
217D MET* 3.9 10.1 - - + -
241D LEU* 4.2 7.6 - - + -
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Residues in contact with VAL 196 (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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122D LEU 4.5 6.1 - - - +
123D TYR* 3.9 32.1 - - + +
126D PRO* 4.3 14.8 - - + -
127D ILE* 4.5 1.6 - - + -
151D CYS 3.0 10.1 + - - +
152D PHE* 3.8 3.3 - - + -
153D ALA 2.8 28.8 + - - +
195D ALA* 1.3 72.0 - - - +
197D VAL* 1.3 60.3 + - - +
198D PHE* 3.8 27.8 - - + -
212D ALA* 4.6 6.3 - - + -
213D PHE 3.4 6.3 - - - +
214D LEU* 3.9 19.3 - - + -
254D LEU* 4.4 17.3 - - + -
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Residues in contact with VAL 197 (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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153D ALA* 3.6 9.6 - - + -
168D THR* 5.1 4.0 - - + -
179D LEU* 4.5 10.5 - - + -
183D LYS* 4.3 11.4 - - + -
195D ALA* 3.6 23.6 - - + -
196D VAL* 1.3 72.8 - - - +
198D PHE* 1.3 72.9 + - - +
199D ALA* 5.1 1.6 - - + -
211D SER 3.7 1.2 - - - +
212D ALA* 3.5 1.9 - - - -
213D PHE* 2.7 40.9 + - + -
215D VAL* 3.5 28.9 - - + -
241D LEU* 4.6 0.2 - - + -
243D PHE* 3.9 33.0 - - + -
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Residues in contact with PHE 198 (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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152D PHE* 3.4 37.7 - + - -
153D ALA 3.1 22.6 + - - +
154D LEU* 3.9 22.4 - - + -
166D ALA* 4.7 1.9 - - - +
168D THR* 4.2 0.9 - - - -
183D LYS* 2.8 32.0 + - - +
196D VAL* 3.8 25.1 - - + -
197D VAL* 1.3 75.5 - - - +
199D ALA* 1.3 62.0 + - - +
210D ILE* 4.0 9.4 - - + -
211D SER 3.4 5.2 - - - -
212D ALA* 3.8 21.1 - - + -
260D GLY* 3.4 32.8 - - - -
263D ILE* 4.1 6.5 - - + -
264D ALA* 3.6 20.4 - - + -
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Residues in contact with ALA 199 (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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166D ALA* 5.0 2.0 - - - -
168D THR* 3.4 26.5 - - + +
169D THR 4.1 0.7 - - - +
170D ALA* 3.9 24.2 - - + +
179D LEU* 4.9 4.7 - - + -
197D VAL* 4.1 2.7 + - + -
198D PHE* 1.3 76.4 - - - +
200D SER* 1.3 61.9 + - - +
201D THR* 3.4 1.4 + - - -
210D ILE* 3.5 6.7 - - - +
211D SER* 2.9 32.2 + - - +
213D PHE* 4.0 11.3 - - + -
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Residues in contact with SER 200 (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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166D ALA* 3.7 19.9 + - - +
167D SER* 5.3 0.7 - - - -
168D THR 2.7 17.5 + - - -
169D THR* 3.4 12.7 - - - +
170D ALA 3.0 22.2 + - - +
199D ALA* 1.3 70.7 - - - +
201D THR* 1.3 60.9 + - - +
202D ASP 3.4 19.9 + - - -
209D SER* 3.4 13.5 + - - -
210D ILE* 4.4 6.7 - - - +
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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