Contacts of the strand formed by residues 194 - 200 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TYR* 3.2 30.7 - - + +
139B TRP* 3.7 20.2 - - + -
143B PHE* 3.5 13.0 - - + -
150B GLY* 3.3 4.9 - - - -
151B CYS* 3.1 26.2 + - - -
192B ALA* 3.5 2.6 - - - +
193B SER* 1.3 81.8 - - - +
195B ALA* 1.3 61.7 + - - +
215B VAL 3.2 7.4 - - - -
217B MET* 3.7 5.1 - - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 4.5 3.2 - - - -
139B TRP* 5.2 0.2 - - - -
151B CYS* 3.2 28.5 - - - -
153B ALA* 5.0 2.2 - - + -
194B ALA* 1.3 72.4 - - - +
196B VAL* 1.3 64.0 + - - +
197B VAL* 3.7 19.4 + - + +
213B PHE 3.4 1.9 - - - +
214B LEU* 3.6 4.2 - - - +
215B VAL* 2.9 34.3 + - + +
217B MET* 3.7 10.3 - - - -
241B LEU* 4.2 9.6 - - + -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B LEU 4.1 11.0 - - - +
123B TYR* 3.7 39.0 - - + +
126B PRO* 4.4 9.0 - - + -
127B ILE* 4.5 0.9 - - + -
151B CYS 2.8 12.6 + - - +
152B PHE* 3.6 3.7 - - + -
153B ALA* 2.8 32.7 + - - +
195B ALA* 1.3 71.2 - - - +
197B VAL* 1.3 56.3 + - - +
198B PHE* 4.1 24.3 - - + -
212B ALA* 4.5 6.5 - - + -
213B PHE 3.4 7.0 - - - +
214B LEU* 4.2 11.4 - - + -
254B LEU* 4.2 21.5 - - + -
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 3.5 11.9 - - + +
168B THR* 5.1 3.8 - - + -
179B LEU* 4.6 11.0 - - + -
183B LYS* 4.2 11.2 - - + -
195B ALA* 3.7 20.2 - - + +
196B VAL* 1.3 77.2 - - - +
198B PHE* 1.3 70.7 + - - +
199B ALA* 5.3 0.9 - - + -
211B SER 3.6 1.6 - - - +
212B ALA* 3.5 2.6 - - - -
213B PHE* 2.8 36.1 + - + +
215B VAL* 3.2 32.8 - - + -
243B PHE* 3.9 30.7 - - + -
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Residues in contact with PHE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 5.9 0.2 - - + -
152B PHE* 3.4 34.1 - + - -
153B ALA 3.0 22.1 + - - +
154B LEU* 3.7 25.6 - - + -
166B ALA* 4.5 4.4 - - + +
168B THR* 4.3 1.9 - - - -
183B LYS* 2.9 31.2 + - - +
196B VAL* 4.1 21.5 - - + -
197B VAL* 1.3 73.8 - - - +
199B ALA* 1.3 62.0 + - - +
210B ILE* 4.1 8.5 - - + -
211B SER 3.3 6.3 - - - +
212B ALA* 3.8 18.8 - - + -
260B GLY* 3.1 33.4 - - - -
263B ILE* 4.2 7.2 - - + -
264B ALA* 3.3 26.7 - - + -
267B THR* 5.2 0.7 - - - -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA* 5.4 0.9 - - - -
168B THR* 3.7 15.5 - - + +
169B THR 4.0 5.8 - - - +
170B ALA* 3.7 31.2 - - + +
179B LEU* 4.8 5.6 - - + -
197B VAL* 3.9 2.0 + - + +
198B PHE* 1.3 76.0 - - - +
200B SER* 1.3 61.5 + - - +
201B THR* 3.4 2.8 + - - +
210B ILE* 3.5 4.6 - - - +
211B SER* 2.8 38.2 + - - +
213B PHE* 3.9 10.8 - - + -
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA* 3.6 20.2 + - - +
167B SER* 5.1 0.9 - - - -
168B THR 2.7 19.0 + - - -
169B THR* 3.4 13.9 - - - +
170B ALA 3.1 20.8 + - - +
199B ALA* 1.3 70.1 - - - +
201B THR* 1.3 63.2 + - - +
209B SER* 3.4 13.7 + - - -
210B ILE* 4.4 7.8 - - - +
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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