Contacts of the strand formed by residues 210 - 216 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154H LEU* 5.7 4.7 - - + -
163H ALA 4.2 2.5 - - - +
164H GLY* 3.5 40.6 - - - +
166H ALA* 3.9 20.6 - - + +
198H PHE* 4.0 17.9 - - + -
199H ALA 3.5 11.2 - - - +
200H SER* 4.7 3.8 - - - -
208H LYS* 3.5 0.8 - - - +
209H SER* 1.3 84.8 - - - +
211H SER* 1.3 71.3 + - - +
258H GLY* 3.1 15.1 + - - +
260H GLY* 2.7 38.8 + - - -
261H PHE* 4.1 19.7 - - + +
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Residues in contact with SER 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H VAL 3.6 1.2 - - - +
198H PHE* 3.2 5.4 - - - -
199H ALA 2.8 31.8 + - - +
201H THR* 3.1 15.6 + - - +
210H ILE* 1.3 71.3 - - - +
212H ALA* 1.3 59.9 + - - +
213H PHE* 3.7 28.0 - - - -
253H ILE* 4.2 10.3 - - - -
256H GLU 5.0 0.9 - - - -
257H PRO* 3.4 7.7 - - - +
258H GLY 2.9 24.5 + - - -
260H GLY* 3.7 9.4 - - - +
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Residues in contact with ALA 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H VAL* 4.5 6.3 - - + -
197H VAL 3.4 5.2 - - - +
198H PHE* 3.7 26.7 - - + -
211H SER* 1.3 73.7 - - - +
213H PHE* 1.3 58.7 + - - +
253H ILE* 3.5 8.7 - - - +
254H LEU* 2.8 53.9 + - + +
260H GLY* 3.9 2.2 - - - -
263H ILE* 4.2 15.5 - - + -
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Residues in contact with PHE 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170H ALA* 3.4 33.4 - - + -
177H TRP* 3.6 32.1 - + + -
179H LEU* 4.8 7.0 - - + -
195H ALA 3.2 4.7 - - - +
196H VAL* 3.4 4.2 - - - +
197H VAL* 2.7 49.9 + - + +
199H ALA* 4.2 11.2 - - + -
201H THR* 3.6 15.9 - - + -
211H SER* 3.7 24.2 - - - -
212H ALA* 1.3 75.9 - - - +
214H LEU* 1.3 63.9 + - - +
215H VAL* 3.7 7.9 + - + -
248H ILE* 3.9 27.8 - - + -
252H SER 3.5 2.5 - - - -
253H ILE* 3.8 21.5 - - + -
254H LEU* 5.5 0.7 - - - -
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Residues in contact with LEU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H TYR* 5.0 0.7 - - + -
127H ILE* 3.7 33.2 - - + -
135H GLN* 3.7 34.1 - - + +
139H TRP* 3.6 54.7 - - + +
195H ALA 3.6 2.7 - - - +
196H VAL* 4.0 15.9 - - + -
213H PHE* 1.3 70.9 - - - +
215H VAL* 1.3 61.1 + - - +
216H PRO* 4.2 2.3 - - - +
248H ILE* 4.1 1.7 - - - +
252H SER* 2.8 38.8 + - - +
254H LEU* 4.4 16.8 - - + -
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Residues in contact with VAL 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H TRP* 3.8 3.1 - - - -
179H LEU* 3.9 22.2 - - + -
194H ALA* 3.2 2.9 - - - +
195H ALA* 2.8 37.7 + - + +
197H VAL* 3.6 28.9 - - + -
213H PHE* 4.0 3.1 - - + +
214H LEU* 1.3 76.7 - - - +
216H PRO* 1.4 79.3 - - + +
217H MET* 4.2 1.2 - - + +
219H THR* 4.3 9.0 - - + -
222H LEU* 4.7 4.7 - - + -
243H PHE* 3.9 21.3 - - + -
246H CYS* 4.5 0.2 - - - -
248H ILE* 4.2 18.6 - - + -
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Residues in contact with PRO 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H TRP* 3.7 21.7 - - + -
193H SER 3.7 9.0 - - - +
214H LEU 4.2 2.5 - - - +
215H VAL* 1.4 95.7 - - + +
217H MET* 1.3 64.6 + - - +
218H PRO 3.7 5.8 - - - +
219H THR* 3.5 29.4 - - - +
248H ILE* 4.4 11.2 - - + -
249H PRO* 6.0 2.2 - - + -
252H 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