Contacts of the strand formed by residues 135 - 140 (chain A) in PDB entry 2VRB
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 TYR 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.2 9.9 - - - +
128A ILE* 4.0 19.7 - - + -
129A ARG* 2.8 42.1 + - + -
133A ILE 3.9 9.4 - - - +
134A PRO* 1.3 73.3 - - - +
136A THR* 1.3 65.7 + - - +
137A PHE* 3.5 35.9 - + + -
191A HIS 3.6 0.2 - - - +
192A GLU* 3.6 1.4 - - - -
193A ASN* 2.7 66.4 + - + +
194A LYS* 3.4 26.0 + - - -
195A THR* 4.2 3.1 + - - -
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Residues in contact with THR 136 (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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102A ILE 2.9 7.7 + - - -
103A ALA* 3.1 11.6 - - - +
104A TYR 3.0 25.5 + - - -
135A TYR* 1.3 71.8 + - - +
137A PHE* 1.3 66.6 + - - +
138A LEU* 3.5 10.3 + - + -
185A VAL* 3.7 30.6 - - + +
191A HIS* 2.6 22.6 + - - +
192A GLU* 4.5 1.4 - - - +
194A LYS 3.4 4.7 - - - +
196A TYR* 3.8 30.5 - - + -
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Residues in contact with PHE 137 (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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102A ILE 5.7 0.2 - - - -
104A TYR* 3.8 12.3 - + + +
106A GLY 6.1 0.2 - - - +
125A GLU* 3.5 59.9 - - + +
128A ILE* 3.8 34.5 - - + -
129A ARG* 3.7 24.5 - - + -
135A TYR* 3.5 31.2 - + + -
136A THR* 1.3 78.7 - - - +
138A LEU* 1.3 61.1 + - - +
139A ARG* 3.4 3.9 + - + -
194A LYS 2.9 8.5 + - - +
195A THR* 3.5 27.9 - - + +
196A TYR* 2.9 31.5 + - - +
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Residues in contact with LEU 138 (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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71A LEU* 3.7 30.1 - - + -
103A ALA* 4.0 9.9 - - + -
104A TYR 2.9 13.7 + - - +
105A THR* 3.3 10.8 - - + -
106A GLY 2.8 21.2 + - - -
136A THR* 4.1 16.6 - - + +
137A PHE* 1.3 69.1 - - - +
139A ARG* 1.3 60.1 + - - +
140A ASN* 3.2 11.4 + - - +
181A ALA 4.6 1.1 - - - +
182A ALA* 3.7 26.2 - - + +
185A VAL* 4.1 25.8 - - + -
196A TYR* 4.3 5.4 - - + -
198A LEU* 3.7 24.7 - - + -
270A LEU* 5.2 0.4 - - + -
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Residues in contact with ARG 139 (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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106A GLY* 4.7 0.4 - - - -
107A TYR 3.7 19.2 + - - +
108A ALA* 3.4 18.8 - - - +
109A PHE* 4.1 2.0 - - - +
110A ALA* 3.9 11.4 - - - +
111A GLU* 2.7 44.8 + - - -
122A LEU* 3.6 10.7 - - - +
125A GLU* 2.9 42.5 + - - +
137A PHE 4.2 2.9 - - - +
138A LEU* 1.3 72.4 - - - +
140A ASN* 1.3 63.9 + - - +
195A THR* 3.5 25.8 - - + +
196A TYR 2.9 19.4 + - - +
197A ASN* 3.3 20.6 + - - +
198A LEU* 2.8 26.6 + - - +
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Residues in contact with ASN 140 (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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12A LEU* 4.0 18.0 - - - +
105A THR* 3.9 21.7 - - - +
106A GLY 3.3 12.0 + - - +
107A TYR* 3.5 12.3 - - - -
108A ALA 3.2 15.6 + - - -
138A LEU* 3.2 15.4 + - - +
139A ARG* 1.3 72.3 - - - +
141A ALA* 1.3 70.1 + - - +
143A TYR* 4.6 4.4 + - - -
178A LEU* 3.4 38.4 + - + +
198A LEU* 3.5 16.9 - - - +
1286A NAP 4.5 7.0 + - - +
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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