Contacts of the strand formed by residues 194 - 200 (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 ALA 194 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H TYR* 3.2 28.2 - - + +
139H TRP* 3.5 22.2 - - + -
143H PHE* 3.5 11.2 - - + -
149H ILE 4.0 0.8 + - - -
150H GLY* 3.2 5.0 - - - -
151H CYS* 3.0 25.1 + - - -
192H ALA* 3.5 2.1 - - - +
193H SER* 1.3 83.6 - - - +
195H ALA* 1.3 61.3 + - - +
215H VAL 3.2 7.9 - - - -
217H MET* 3.9 6.3 - - - +
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Residues in contact with ALA 195 (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* 4.5 2.2 - - - -
151H CYS* 3.4 28.0 - - - +
153H ALA* 4.9 1.1 - - + -
194H ALA* 1.3 76.5 - - - +
196H VAL* 1.3 63.5 + - - +
197H VAL* 3.7 19.8 + - + +
213H PHE 3.2 4.2 - - - +
214H LEU* 3.6 3.8 - - - +
215H VAL* 2.8 33.4 + - + +
217H MET* 3.8 9.8 - - + -
241H LEU* 4.2 7.4 - - + -
243H PHE* 6.0 0.2 - - + -
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H LEU 4.5 1.8 - - - +
123H TYR* 3.8 33.2 - - + +
126H PRO* 4.4 13.2 - - + -
127H ILE* 4.4 2.0 - - + -
151H CYS 3.1 9.8 + - - +
152H PHE* 3.7 8.6 - - + -
153H ALA* 2.8 28.1 + - - +
195H ALA* 1.3 71.0 - - - +
197H VAL* 1.3 60.2 + - - +
198H PHE* 3.9 28.2 - - + -
212H ALA* 4.5 12.1 - - + -
213H PHE 3.4 7.4 - - - +
214H LEU* 4.0 17.5 - - + -
254H LEU* 4.5 11.4 - - + -
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Residues in contact with VAL 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H ALA* 3.7 13.7 - - + +
168H THR* 5.0 4.7 - - + -
179H LEU* 4.5 10.5 - - + -
183H LYS* 4.3 8.3 - - + -
195H ALA* 3.7 20.9 - - + +
196H VAL* 1.3 77.0 - - - +
198H PHE* 1.3 73.4 + - - +
199H ALA* 5.2 1.1 - - + -
212H ALA* 3.4 1.3 - - - -
213H PHE* 2.7 48.1 + - + +
215H VAL* 3.6 25.6 - - + -
241H LEU* 4.7 0.2 - - + -
243H PHE* 3.8 31.4 - - + -
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Residues in contact with PHE 198 (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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126H PRO* 5.9 0.2 - - + -
152H PHE* 3.4 40.4 - + - -
153H ALA 3.1 19.1 + - - +
154H LEU* 3.8 25.6 - - + -
166H ALA* 4.4 2.8 - - + +
168H THR* 4.3 0.2 - - - -
183H LYS* 2.7 33.1 + - - +
196H VAL* 3.9 21.5 - - + -
197H VAL* 1.3 74.5 - - - +
199H ALA* 1.3 61.7 + - - +
210H ILE* 4.0 9.0 - - + -
211H SER 3.2 5.8 - - - +
212H ALA* 3.7 24.2 - - + -
260H GLY* 3.4 31.0 - - - -
263H ILE* 4.0 7.6 - - + -
264H ALA* 3.7 20.9 - - + -
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Residues in contact with ALA 199 (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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166H ALA* 4.8 2.9 - - - -
168H THR* 3.3 32.8 - - + +
169H THR 3.8 12.6 - - - +
170H ALA* 4.0 10.5 - - + +
179H LEU* 5.2 2.9 - - + -
197H VAL* 4.0 2.4 + - + -
198H PHE* 1.3 74.2 - - - +
200H SER* 1.3 63.5 + - - +
201H THR* 3.6 1.0 + - - +
210H ILE* 3.5 6.5 - - - +
211H SER* 2.8 35.7 + - - +
213H PHE* 4.2 7.4 - - + -
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Residues in contact with SER 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H ALA* 3.8 18.2 + - - +
167H SER* 5.2 0.4 - - - -
168H THR 2.7 17.7 + - - -
169H THR* 3.3 12.9 - - - +
170H ALA 2.8 28.2 + - - +
199H ALA* 1.3 70.5 - - - +
201H THR* 1.3 63.8 + - - +
209H SER* 3.3 20.0 + - - -
210H ILE* 4.5 4.5 - - - +
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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