Contacts of the strand formed by residues 189 - 196 (chain A) in PDB entry 2VRF
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 GLU 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ARG* 3.2 40.0 + - + +
118A VAL 3.5 9.0 - - - +
119A VAL* 4.1 11.8 - - + +
167A ASN* 3.1 18.4 + - - +
186A ALA 3.9 3.1 - - - +
187A GLY* 4.4 0.3 - - - -
188A LYS* 1.3 79.0 - - - +
190A VAL* 1.3 66.2 + - - +
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Residues in contact with VAL 190 (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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116A VAL 3.5 0.7 - - - +
117A ARG* 3.3 6.5 - - - +
118A VAL* 2.9 44.3 + - + +
120A LYS* 4.2 12.3 - - - -
126A LEU* 3.7 21.3 - - + -
166A VAL* 4.0 13.2 - - + -
167A ASN* 3.6 3.1 - - - -
183A LEU 4.9 1.1 - - - +
186A ALA* 3.7 27.4 - - + -
187A GLY 4.1 11.2 - - - +
189A GLU* 1.3 82.9 - - - +
191A LEU* 1.3 59.3 + - - +
192A LEU* 3.9 17.3 - - + -
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Residues in contact with LEU 191 (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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115A ARG* 4.1 21.3 - - + +
116A VAL 3.5 26.2 - - - +
117A ARG* 4.1 11.0 - - + +
166A VAL* 3.5 2.1 - - - -
167A ASN* 2.9 39.7 + - - +
190A VAL* 1.3 73.4 - - - +
192A LEU* 1.3 59.5 + - - +
1206A EDO 3.0 29.8 - - - -
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Residues in contact with LEU 192 (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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114A ARG 3.4 1.6 - - - +
115A ARG* 3.3 4.2 - - - -
116A VAL* 2.8 45.0 + - + +
118A VAL* 4.2 22.2 - - + -
126A LEU* 5.0 7.4 - - + -
128A ILE* 5.5 3.1 - - + -
157A LEU* 4.2 20.9 - - + -
163A ILE* 4.1 16.8 - - + -
165A SER 3.4 4.3 - - - +
166A VAL* 3.7 33.0 - - + -
183A LEU* 3.8 16.4 - - + -
190A VAL* 3.9 15.7 - - + -
191A LEU* 1.3 73.3 - - - +
193A GLU* 1.3 61.3 + - - +
194A VAL* 3.8 14.0 + - + -
1206A EDO 4.7 1.1 - - - -
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Residues in contact with GLU 193 (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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113A VAL* 3.0 38.3 - - + +
114A ARG 3.4 3.1 - - - +
115A ARG* 4.5 18.0 + - + +
163A ILE* 3.7 0.7 - - - -
164A LEU* 2.8 34.7 + - + +
165A SER* 2.9 34.1 + - - +
172A ARG* 2.7 31.1 + - - -
191A LEU 4.1 0.8 + - - -
192A LEU* 1.3 73.0 - - - +
194A VAL* 1.3 57.0 + - - +
1206A EDO 3.5 16.1 + - - +
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Residues in contact with VAL 194 (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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113A VAL* 3.4 6.9 - - - +
114A ARG* 2.9 77.7 + - + +
116A VAL* 4.0 9.6 - - + -
157A LEU* 3.9 17.3 - - + -
161A ASP* 4.1 9.4 - - + +
162A ALA 3.1 12.8 - - - +
163A ILE* 4.4 13.2 - - + -
164A LEU* 4.5 1.6 - - - -
192A LEU* 3.9 20.6 - - + -
193A GLU* 1.3 80.1 - - - +
195A LYS* 1.3 60.0 + - - +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-1A SER* 5.0 11.5 - - - +
0A MET* 3.4 31.4 - - + +
112A PRO 4.0 7.9 - - - +
113A VAL* 4.4 9.0 - - + -
114A ARG* 4.5 0.9 - - - +
161A ASP* 4.0 2.2 - - - -
162A ALA* 2.7 43.0 + - + +
164A LEU* 3.9 31.7 - - + +
194A VAL* 1.3 76.0 - - - +
196A PHE* 1.3 71.8 + - - +
197A ILE* 4.1 4.2 - - - +
135B GLU 5.2 6.6 + - - -
137B ARG* 5.5 8.7 - - - +
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Residues in contact with PHE 196 (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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-1A SER 5.8 0.2 + - - -
0A MET* 3.2 48.6 - - + +
112A PRO 4.8 0.6 + - - -
114A ARG* 3.7 5.3 - - - +
158A ARG* 3.6 34.8 - - + +
159A LEU 3.4 23.8 - - - -
160A GLY* 4.0 7.6 - - - -
161A ASP* 3.3 22.6 + - - +
195A LYS* 1.3 79.8 - - - +
197A ILE* 1.3 81.7 + - - +
198A ARG* 3.9 16.4 - - + -
199A GLU 5.6 0.2 - - - -
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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