Contacts of the strand formed by residues 128 - 135 (chain A) in PDB entry 2VR2
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 ASP 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A THR 3.5 8.0 + - - +
97A MET* 3.2 25.4 - - + -
98A ILE 3.4 1.7 + - - -
127A CYS* 1.3 78.4 - - - +
129A TYR* 1.3 61.9 + - - +
391A ARG* 5.6 0.7 + - - -
392A LYS* 3.1 31.0 + - - -
400A ASP* 4.5 3.3 - - - +
402A ASP* 4.0 4.7 - - - +
442A SER* 4.4 2.6 + - - -
443A ARG* 3.2 40.4 + - - +
460A GLY* 3.9 0.4 - - - -
461A LYS* 3.2 26.5 + - - +
463A ILE* 3.9 15.7 - - + +
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Residues in contact with TYR 129 (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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83A PHE* 5.1 6.1 - + - -
97A MET* 3.7 8.0 - - - +
98A ILE* 3.2 27.1 - - + +
100A ASP 5.4 0.9 - - - -
118A ARG* 3.7 14.4 - - - +
121A ALA* 3.5 25.4 - - + +
122A ASP* 2.7 31.4 + - - -
125A VAL* 3.7 33.4 - - + -
127A CYS 4.3 2.2 - - - +
128A ASP* 1.3 76.4 - - - +
130A SER* 1.3 80.4 + - - +
131A LEU* 3.9 20.0 - - + -
461A LYS 3.1 7.2 + - - -
462A PHE* 3.3 37.6 - + + +
463A ILE* 2.8 26.7 + - - -
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Residues in contact with SER 130 (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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97A MET* 3.8 14.5 - - - +
98A ILE 3.1 5.5 + - - -
99A ILE* 3.3 9.2 - - - -
100A ASP 3.1 22.0 + - - -
129A TYR* 1.3 84.4 - - - +
131A LEU* 1.3 63.1 + - - +
154A GLY 4.4 1.0 + - - -
462A PHE* 3.5 15.2 - - - -
463A ILE 3.0 20.3 + - - -
465A ARG* 2.8 34.0 + - - -
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Residues in contact with LEU 131 (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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83A PHE* 5.1 1.1 - - + -
99A ILE* 4.1 0.2 - - - -
100A ASP* 3.3 31.9 - - + +
101A PHE 4.4 0.4 - - - +
102A ALA* 4.6 4.9 - - + +
114A PHE* 3.6 41.7 - - + +
117A TRP* 4.2 26.0 - - + +
118A ARG* 3.8 21.5 - - + +
129A TYR* 3.9 18.2 - - + -
130A SER* 1.3 85.1 + - - +
132A HIS* 1.3 64.4 + - - +
155A VAL* 4.1 13.9 - - - +
462A PHE* 3.7 4.2 - - + -
465A ARG* 2.8 25.0 + - - -
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Residues in contact with HIS 132 (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 THR 2.8 20.6 + - - -
99A ILE* 3.3 38.9 - - + +
100A ASP 2.7 7.7 + - - +
101A PHE* 3.4 36.1 - + + -
102A ALA* 2.8 25.6 + - - +
131A LEU* 1.3 75.8 - - - +
133A VAL* 1.3 63.0 + - - +
157A SER* 2.6 24.5 + - - +
190A GLN* 3.2 32.5 + - - +
386A PHE* 3.5 27.6 - + - -
465A ARG* 4.8 0.4 - - - -
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Residues in contact with VAL 133 (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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101A PHE* 5.5 0.2 - - - -
102A ALA* 3.7 14.6 - - + +
104A PRO* 5.2 0.4 - - + -
110A LEU* 4.1 19.7 - - + +
114A PHE* 3.9 29.6 - - + -
131A LEU 4.7 0.4 - - - +
132A HIS* 1.3 80.5 - - - +
134A ALA* 1.3 70.0 + - - +
149A LEU* 3.8 23.3 - - + -
155A VAL* 4.1 15.9 - - + -
157A SER 3.4 5.9 + - - -
158A PHE* 3.0 28.0 - - + -
159A LYS* 3.0 19.7 + - - -
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Residues in contact with ALA 134 (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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101A PHE* 5.5 1.0 - - + -
102A ALA 3.1 11.2 + - - +
103A ILE* 3.6 30.7 - - + -
104A PRO* 3.3 23.0 - - + +
110A LEU* 3.6 7.3 - - - +
132A HIS 4.3 0.2 - - - -
133A VAL* 1.3 73.4 - - - +
135A VAL* 1.3 60.9 - - - +
136A THR* 3.4 18.0 + - + -
159A LYS* 3.2 17.0 - - + +
161A PHE* 3.9 7.2 - - + -
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Residues in contact with VAL 135 (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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110A LEU* 4.4 7.9 - - + -
134A ALA* 1.3 70.1 - - - +
136A THR* 1.3 60.5 + - - +
137A TRP 3.4 20.6 - - - +
138A TRP* 3.8 16.2 - - + -
142A VAL* 3.7 13.7 - - + -
146A MET* 3.9 22.2 - - + -
158A PHE* 3.9 22.0 - - + -
159A LYS 2.8 13.9 + - - +
160A MET* 3.6 42.0 - - + +
161A PHE* 4.6 1.7 + - - -
170A VAL* 4.4 8.4 - - + +
178A ALA* 4.6 1.6 - - + -
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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