Contacts of the strand formed by residues 192 - 200 (chain B) in PDB entry 1VAV
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 LEU 192 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B ASN* 3.4 0.4 - - - -
74B TRP* 2.6 81.1 + - + +
76B TYR* 4.3 22.7 - - + +
103B ILE* 4.2 8.7 - - + -
104B HIS 3.1 14.1 - - - +
105B SER* 4.1 8.7 - - - -
116B LEU* 4.2 20.4 - - + -
164B VAL* 4.4 2.9 - - + -
183B LEU* 5.2 0.4 - - + -
187B TRP* 4.1 28.5 - - + +
190B GLN* 3.9 11.9 - - + +
191B GLY* 1.3 77.0 - - - +
193B TYR* 1.3 64.2 + - - +
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Residues in contact with TYR 193 (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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63B ARG* 3.4 44.2 - - + +
64B GLU* 4.3 1.8 - - + +
72B TYR 3.1 24.0 - - - +
73B ASN* 3.1 15.5 - - - -
74B TRP* 3.6 8.0 - - - +
103B ILE* 3.4 1.5 - - - -
104B HIS* 2.7 83.6 + - + +
105B SER 3.8 19.2 + - - -
106B ASP* 4.1 3.4 - - - -
191B GLY 4.3 0.2 - - - -
192B LEU* 1.3 74.1 - - - +
194B PHE* 1.3 69.1 + - - +
195B LYS* 3.6 20.7 + - + +
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Residues in contact with PHE 194 (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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7B TRP* 3.9 13.0 - - + -
64B GLU* 3.0 44.1 + - - +
74B TRP* 3.9 22.2 - + - -
81B ASN* 3.9 5.4 - - + -
82B TRP 3.4 44.0 - - - -
83B LEU* 3.5 26.2 - - + -
102B GLN 3.5 8.1 - - - -
103B ILE* 3.5 27.1 - - + -
162B ILE* 3.7 14.1 - - + -
163B GLY* 4.4 0.9 - - - -
193B TYR* 1.3 74.3 - - - +
195B LYS* 1.3 66.5 + - - +
220B VAL* 3.4 24.9 - - + -
222B HIS* 4.0 5.2 - + - -
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Residues in contact with LYS 195 (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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7B TRP* 4.0 2.7 - - - -
10B THR* 5.5 4.2 + - - -
59B ARG* 3.3 20.2 - - - +
61B GLU* 2.8 43.0 + - - +
62B LEU 3.1 15.0 - - - +
63B ARG* 4.0 16.9 - - + +
83B LEU* 3.8 4.7 - - - +
101B GLY* 3.3 2.9 - - - -
102B GLN* 2.9 44.5 + - + +
104B HIS* 4.5 14.4 + - + +
193B TYR* 3.6 29.9 + - + +
194B PHE* 1.3 81.6 - - - +
196B ALA* 1.3 63.3 + - - +
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Residues in contact with ALA 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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7B TRP* 4.2 8.5 - - + -
43B PHE* 4.9 1.6 - - - -
61B GLU* 4.0 4.6 - - - +
62B LEU* 2.8 42.9 + - + +
83B LEU* 4.7 2.2 - - + -
100B ILE 3.9 5.6 - - - -
101B GLY* 4.2 1.1 - - - -
160B TYR* 3.7 16.8 - - - +
195B LYS* 1.3 77.5 - - - +
197B GLY* 1.3 59.2 + - - +
215B PHE* 4.5 3.4 - - + -
218B LEU* 4.2 32.3 - - + -
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Residues in contact with GLY 197 (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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43B PHE* 3.9 18.6 - - - -
60B SER 3.8 7.2 - - - -
61B GLU* 4.4 2.4 - - - +
99B ILE 4.1 1.3 - - - -
100B ILE* 3.2 30.5 + - - +
196B ALA* 1.3 77.6 - - - +
198B LEU* 1.3 70.0 + - - +
215B PHE* 3.8 12.0 - - - -
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Residues in contact with LEU 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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43B PHE* 3.7 19.3 - - + +
45B VAL* 3.7 15.1 - - + +
59B ARG* 3.3 3.5 - - - +
60B SER 2.9 40.1 + - - +
61B GLU* 4.4 2.3 - - - +
98B MET* 3.8 20.9 - - + -
99B ILE 3.5 1.8 - - - +
100B ILE* 4.0 13.9 - - + -
197B GLY* 1.3 82.5 - - - +
199B TYR* 1.3 59.9 + - - +
200B LEU* 4.0 5.2 - - + -
211B GLY* 3.6 34.3 - - - +
212B ARG* 3.7 16.6 - - - -
213B ALA* 3.7 20.4 - - + +
215B PHE* 5.2 0.2 - - + -
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Residues in contact with TYR 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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55B SER* 2.6 27.1 + - - -
57B PHE* 3.6 17.1 - + + -
58B PRO 3.8 1.1 - - - -
59B ARG* 3.4 45.6 + - + -
61B GLU* 3.8 18.6 - - - +
98B MET* 4.7 0.2 - - - -
99B ILE* 2.9 53.4 + - + +
102B GLN* 3.7 20.4 - - - -
118B LYS* 5.9 4.9 - - + -
198B LEU* 1.3 73.6 - - - +
200B LEU* 1.3 73.4 + - - +
201B GLN* 4.0 12.8 - - - -
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Residues in contact with LEU 200 (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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45B VAL* 3.5 51.6 - - + +
47B VAL* 3.8 14.8 - - - -
57B PHE* 3.0 16.2 - - - +
58B PRO* 3.2 25.8 + - + +
93B PRO* 3.7 24.9 - - + -
97B ARG 4.4 3.1 - - - -
98B MET* 3.9 26.0 - - + +
198B LEU* 4.7 0.7 - - + -
199B TYR* 1.3 81.6 - - - +
201B GLN* 1.3 73.5 + - - +
202B ASP 3.5 12.8 - - - +
211B GLY 4.3 3.4 - - - +
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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