Contacts of the strand formed by residues 210 - 216 (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 ILE 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154D LEU* 5.9 2.9 - - + -
163D ALA 4.3 2.2 - - - +
164D GLY* 3.7 38.4 - - - +
166D ALA* 4.0 18.2 - - + +
198D PHE* 4.0 13.0 - - + -
199D ALA 3.5 19.3 - - - +
200D SER* 4.5 5.4 - - - -
208D LYS 3.5 0.6 - - - -
209D SER* 1.3 87.6 - - - +
211D SER* 1.3 69.3 + - - +
258D GLY* 3.1 13.2 + - - +
260D GLY* 2.7 37.2 + - - -
261D PHE* 4.0 22.3 - - + +
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Residues in contact with SER 211 (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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197D VAL 3.7 1.2 - - - +
198D PHE* 3.4 5.2 - - - -
199D ALA 2.9 30.1 + - - -
201D THR* 2.9 21.2 + - - +
210D ILE* 1.3 72.1 - - - +
212D ALA* 1.3 60.4 + - - +
213D PHE* 3.7 25.5 - - - -
253D ILE* 4.0 13.0 - - - -
256D GLU 4.9 1.1 - - - -
257D PRO* 3.4 6.9 - - - +
258D GLY 3.0 19.4 + - - +
260D GLY* 3.8 9.2 - - - +
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Residues in contact with ALA 212 (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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196D VAL* 4.6 2.9 - - + -
197D VAL 3.5 4.5 - - - -
198D PHE* 3.8 26.5 - - + -
211D SER* 1.3 75.0 - - - +
213D PHE* 1.3 56.7 + - - +
253D ILE* 3.4 9.0 - - - +
254D LEU* 2.7 46.1 + - + +
256D GLU 5.7 0.2 + - - -
260D GLY* 4.0 2.4 - - - +
263D ILE* 3.8 27.8 - - + -
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Residues in contact with PHE 213 (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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170D ALA* 3.5 32.3 - - + -
177D TRP* 3.6 35.4 - + + -
179D LEU* 4.9 5.4 - - + -
195D ALA 3.3 4.9 - - - +
196D VAL* 3.4 3.1 - - - +
197D VAL* 2.7 44.8 + - + +
199D ALA* 4.0 12.3 - - + -
201D THR* 3.9 7.9 - - + -
211D SER* 3.7 35.0 - - - -
212D ALA* 1.3 78.7 - - - +
214D LEU* 1.3 64.4 + - - +
215D VAL* 3.7 7.9 + - + +
248D ILE* 4.0 27.6 - - + -
252D SER 3.6 2.2 - - - -
253D ILE* 4.0 20.0 - - + -
254D LEU 4.4 0.2 - - - +
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Residues in contact with LEU 214 (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* 5.4 0.2 - - + -
127D ILE* 4.0 20.6 - - + -
135D GLN* 4.0 26.5 - - + +
139D TRP* 3.5 61.3 - - + +
195D ALA 3.5 4.0 - - - +
196D VAL* 3.9 27.4 - - + -
213D PHE* 1.3 71.1 - - - +
215D VAL* 1.3 60.3 + - - +
216D PRO* 4.2 2.4 - - - +
248D ILE* 4.4 0.9 - - - +
252D SER* 2.8 40.0 + - - +
254D LEU* 4.2 18.4 - - + -
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Residues in contact with VAL 215 (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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139D TRP* 3.8 3.3 - - - -
179D LEU* 4.1 15.7 - - + -
194D ALA* 3.3 3.3 - - - +
195D ALA* 2.9 35.2 + - + +
197D VAL* 3.5 33.0 - - + -
213D PHE 3.8 7.0 - - - +
214D LEU* 1.3 77.8 - - - +
216D PRO* 1.4 79.5 - - + +
217D MET* 4.1 2.0 - - + +
219D THR* 4.4 6.5 - - + -
222D LEU* 5.0 3.1 - - + -
243D PHE* 4.0 23.1 - - + -
248D ILE* 4.1 18.6 - - + -
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Residues in contact with PRO 216 (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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139D TRP* 3.7 18.4 - - + -
193D SER 3.9 7.6 - - - +
214D LEU 4.2 2.5 - - - +
215D VAL* 1.4 93.7 - - + +
217D MET* 1.3 63.8 + - - +
218D PRO 3.7 7.2 - - - +
219D THR* 3.4 37.2 - - - +
222D LEU* 4.2 0.7 - - - +
248D ILE* 4.5 10.5 - - + -
249D PRO* 5.8 5.6 - - + -
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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