Contacts of the strand formed by residues 210 - 216 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154E LEU* 5.5 3.4 - - + -
163E ALA 3.8 7.6 - - - +
164E GLY* 3.4 39.9 - - - +
166E ALA* 4.3 14.6 - - + +
198E PHE* 3.9 21.3 - - + -
199E ALA 3.4 13.5 - - - +
200E SER* 4.5 4.5 - - - -
209E SER* 1.3 87.6 - - - +
211E SER* 1.3 68.7 + - - +
258E GLY* 3.1 12.7 + - - +
260E GLY* 2.7 36.5 + - - -
261E PHE* 4.0 22.2 + - + +
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Residues in contact with SER 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E PHE* 3.4 5.1 - - - -
199E ALA 2.9 30.0 + - - +
201E THR* 2.7 37.1 + - - +
210E ILE* 1.3 72.7 - - - +
212E ALA* 1.3 59.5 + - - +
213E PHE* 3.7 16.4 - - - -
253E ILE* 3.9 12.3 - - - -
256E GLU 4.7 1.1 - - - -
257E PRO* 3.2 7.6 - - - +
258E GLY 2.9 17.5 + - - +
259E MET 4.9 0.2 - - - +
260E GLY* 3.8 8.7 - - - +
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Residues in contact with ALA 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E VAL* 4.4 2.2 - - + -
197E VAL 3.4 5.6 - - - +
198E PHE* 3.7 26.9 - - + -
211E SER* 1.3 73.5 - - - +
213E PHE* 1.3 58.3 + - - +
253E ILE* 3.4 10.2 - - - +
254E LEU* 2.7 60.3 + - + +
260E GLY* 4.0 3.0 - - - +
263E ILE* 4.2 11.7 - - + -
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Residues in contact with PHE 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ALA* 3.3 33.9 - - + -
177E TRP* 3.6 34.3 - + + -
179E LEU* 4.7 6.5 - - + -
195E ALA 3.3 4.2 - - - +
196E VAL* 3.4 3.4 - - - -
197E VAL* 2.8 45.1 + - + +
199E ALA* 4.1 11.0 - - + -
201E THR* 3.9 7.6 - - + -
211E SER* 3.7 35.9 - - - -
212E ALA* 1.3 74.3 - - - +
214E LEU* 1.3 63.1 + - - +
215E VAL* 3.7 8.0 + - + +
248E ILE* 4.0 24.9 - - + -
252E SER 3.4 2.2 - - - -
253E ILE* 3.7 26.0 - - + -
254E LEU* 5.1 0.2 - - - -
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Residues in contact with LEU 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E TYR* 5.1 1.1 - - + -
127E ILE* 3.8 31.0 - - + -
135E GLN* 3.9 32.3 - - + +
139E TRP* 3.7 55.7 - - + +
195E ALA 3.5 3.4 - - - +
196E VAL* 3.9 18.6 - - + -
213E PHE* 1.3 71.7 - - - +
215E VAL* 1.3 58.1 + - - +
216E PRO* 4.2 1.9 - - - +
248E ILE* 3.7 3.8 - - - +
252E SER* 2.8 37.6 + - - +
254E LEU* 4.5 16.4 - - + -
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Residues in contact with VAL 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TRP* 3.8 4.1 - - - -
179E LEU* 4.0 21.5 - - + -
194E ALA* 3.3 2.4 - - - -
195E ALA* 2.9 40.8 + - + +
197E VAL* 3.6 25.6 - - + -
213E PHE* 4.0 5.6 - - + +
214E LEU* 1.3 77.7 - - - +
216E PRO* 1.4 80.0 - - + +
217E MET* 5.1 1.1 - - + -
219E THR* 4.2 9.9 - - + -
222E LEU* 4.4 4.5 - - + -
243E PHE* 4.0 21.5 - - + -
248E ILE* 4.1 15.0 - - + -
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Residues in contact with PRO 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E TRP* 3.7 21.1 - - + -
193E SER 3.8 8.1 - - - +
214E LEU 4.2 2.2 - - - +
215E VAL* 1.4 91.8 - - + +
217E MET* 1.3 65.5 + - - +
218E PRO 3.6 7.2 - - - +
219E THR* 3.3 40.5 - - - +
222E LEU* 3.9 0.5 - - - +
248E ILE* 4.7 9.9 - - + -
249E PRO* 6.0 3.8 - - + -
252E SER* 5.9 0.4 - - - +
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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