Contacts of the strand formed by residues 197 - 205 (chain A) in PDB entry 1VIO
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 VAL 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A VAL* 3.7 22.4 - - + -
135A THR 3.6 4.3 - - - -
136A LEU* 4.2 1.6 - - + -
186A VAL* 4.3 3.6 - - + +
187A LYS* 4.1 32.5 + - + -
190A PHE* 3.8 26.0 - - + +
196A LYS* 1.3 81.8 - - - +
198A VAL* 1.3 60.1 + - - +
199A GLY 3.3 29.6 - - - +
200A LEU* 4.1 13.2 - - + -
244A BU1 4.2 17.4 - - - +
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 5.6 1.7 + - - -
135A THR* 2.9 33.6 + - + +
136A LEU 3.8 11.0 - - - +
137A ALA* 3.7 28.3 - - + -
196A LYS* 3.3 11.9 + - + +
197A VAL* 1.3 77.6 - - - +
199A GLY* 1.3 58.4 + - - +
244A BU1 3.7 23.6 - - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLN* 6.2 0.9 - - - -
133A LEU 4.4 1.3 - - - -
134A VAL* 3.6 1.7 - - - -
135A THR* 2.8 41.6 + - - -
197A VAL* 3.3 10.7 - - - +
198A VAL* 1.3 81.7 - - - +
200A LEU* 1.3 59.9 + - - +
244A BU1 4.3 4.3 - - - -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP 4.5 1.6 + - - +
105A THR* 3.5 28.7 - - + +
106A THR* 3.0 27.0 + - - +
132A TYR* 3.7 23.8 - - + -
133A LEU 3.5 2.5 - - - +
134A VAL* 3.7 32.3 - - + -
186A VAL* 3.9 22.9 - - + -
187A LYS* 4.7 10.8 - - + -
197A VAL* 4.1 4.7 - - + -
199A GLY* 1.3 76.4 - - - +
201A HIS* 1.3 60.5 + - - +
243A BU1 4.0 15.3 - - - -
244A BU1 3.6 21.9 - - - +
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Residues in contact with HIS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASN* 4.1 8.3 - - - -
106A THR* 2.9 26.6 + - - +
107A GLY* 3.5 22.9 + - - -
132A TYR* 3.4 3.3 - - - -
133A LEU* 2.7 51.7 + - + +
200A LEU* 1.3 74.6 - - - +
202A ARG* 1.3 66.9 + - - +
203A TRP* 3.6 9.6 + + + +
210A LEU* 3.8 17.3 - - + +
216A GLU* 5.7 1.1 + - - -
245A BU1 3.5 26.3 + - - -
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLY* 2.9 34.4 + - - -
100A ARG 4.4 3.8 + - - -
101A LEU* 3.3 24.4 - - + +
105A THR* 4.9 0.8 - - - +
106A THR 2.9 12.5 + - - +
107A GLY* 3.3 5.4 - - - -
108A LEU* 2.9 57.3 + - + +
109A VAL* 4.2 2.2 - - - +
130A LYS* 4.0 15.9 - - - +
131A THR 3.5 13.7 - - - +
132A TYR* 3.1 44.8 + - + -
201A HIS* 1.3 75.2 + - - +
203A TRP* 1.3 62.6 + - - +
204A LYS 3.9 11.4 - - - +
205A ILE* 3.7 27.6 - - + +
210A LEU* 4.0 0.5 - - - +
243A BU1 5.4 0.2 - - - +
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Residues in contact with TRP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.3 2.2 - - - -
131A THR* 3.1 34.9 + - + +
133A LEU* 3.8 15.2 - - + +
167A GLU* 5.4 1.1 - - - -
175A ASN* 2.9 35.6 + - + -
201A HIS* 3.9 11.0 - + + +
202A ARG* 1.3 74.3 - - - +
204A LYS* 1.3 85.7 + - + +
209A VAL* 3.5 22.3 - - + -
210A LEU* 2.9 37.0 + - + -
245A BU1 3.8 42.6 - - + +
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.0 1.9 - - - +
130A LYS* 3.4 1.7 - - - -
131A THR* 2.9 49.3 + - - +
202A ARG* 3.8 4.4 - - - +
203A TRP* 1.3 99.9 - - + +
205A ILE* 1.3 68.6 + - - +
206A GLY 3.1 25.1 - - - +
207A ASP* 3.6 26.6 + - - +
208A VAL 3.3 14.4 - - - +
209A VAL* 4.1 14.4 - - + +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA 4.5 8.3 - - - +
108A LEU* 3.8 18.1 - - + +
110A LEU* 3.8 33.7 - - + +
121A ILE* 4.1 8.5 - - + -
128A CYS* 3.8 20.4 - - - -
129A GLU 3.4 5.8 - - - +
130A LYS* 4.3 8.5 - - + -
202A ARG* 3.7 38.4 - - - +
204A LYS* 1.3 79.2 - - - +
206A GLY* 1.3 69.6 + - - +
207A ASP 3.2 0.2 + - - -
208A VAL* 2.9 20.5 + - + +
230A LEU* 3.4 19.7 - - + +
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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