Contacts of the strand formed by residues 157 - 164 (chain A) in PDB entry 2VWJ
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 ILE 157 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ILE* 4.1 15.3 - - + -
143A GLU 3.9 5.6 - - - +
144A THR* 4.2 5.2 - - + +
156A PRO* 1.3 76.0 - - - +
158A LEU* 1.3 62.8 + - - +
159A MET 3.3 24.0 - - - +
160A ILE* 4.1 3.1 - - + -
173A TRP* 3.1 13.0 + - - -
187A GLU* 2.8 17.9 + - - +
190A MET* 3.5 15.6 - - + +
191A ILE* 4.1 13.2 - - + -
218A TYR* 3.4 24.9 - - + -
219A LEU* 3.7 29.8 - - + -
222A ARG* 3.6 27.4 - - + +
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Residues in contact with LEU 158 (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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143A GLU* 2.9 11.0 + - + +
144A THR 3.9 1.8 - - - +
145A LEU* 3.5 44.4 - - + +
156A PRO* 3.8 10.3 - - + +
157A ILE* 1.3 79.5 - - - +
159A MET* 1.3 70.5 + - + +
172A THR* 2.9 21.7 + - - -
173A TRP* 3.6 9.5 - - + +
190A MET* 3.4 12.3 - - - +
295A ILE* 3.8 26.9 - - + -
299A TRP* 3.6 54.4 - - + +
308A VAL* 6.3 0.4 - - + -
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Residues in contact with MET 159 (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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142A ILE* 3.3 3.8 - - - -
143A GLU* 3.0 35.6 + - + +
157A ILE* 3.3 5.9 - - - +
158A LEU* 1.3 91.7 - - + +
160A ILE* 1.3 64.4 + - - +
170A VAL* 3.8 24.0 - - + -
171A ILE 3.3 7.4 - - - +
172A THR* 3.8 7.2 - - - +
176A ILE* 4.5 17.0 - - + -
190A MET* 3.5 1.5 - - - -
299A TRP* 5.2 5.2 - - + -
305A LEU* 4.6 8.1 - - + -
308A VAL* 3.6 38.1 - - + +
309A ALA* 4.0 13.5 - - + +
312A SER* 3.9 27.8 - - - +
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Residues in contact with ILE 160 (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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140A PHE* 5.1 0.9 - - + -
141A ASP 3.5 8.5 - - - +
142A ILE* 4.1 15.0 - - + -
157A ILE* 4.1 5.8 - - + -
159A MET* 1.3 80.6 - - - +
161A SER* 1.3 63.9 + - - +
162A TYR* 4.8 0.2 - - - -
170A VAL* 3.7 0.6 - - - -
171A ILE* 2.8 40.1 + - + +
190A MET* 3.9 14.4 - - + -
191A ILE* 3.9 23.6 - - + -
194A PHE* 3.3 57.4 - - + -
219A LEU* 4.1 17.9 - - + -
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Residues in contact with SER 161 (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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140A PHE* 3.2 7.1 - - - +
141A ASP* 2.7 56.2 + - - +
160A ILE* 1.3 75.1 - - - +
162A TYR* 1.3 61.8 + - - +
169A ARG 3.5 12.3 - - - -
170A VAL* 4.1 3.4 - - - +
312A SER* 3.0 45.2 + - - -
316A ALA* 3.7 6.7 - - - +
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Residues in contact with TYR 162 (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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138A LEU* 4.0 21.8 - - + -
139A ALA 3.2 12.6 - - - +
140A PHE* 4.2 6.7 - - + -
160A ILE 4.8 0.2 - - - -
161A SER* 1.3 78.3 - - - +
163A ALA* 1.3 63.9 + - - +
164A ASP* 5.4 0.2 - - - -
167A GLY 5.3 2.7 - - - -
168A ALA* 3.3 2.4 - - - +
169A ARG* 3.0 72.8 + - + +
171A ILE* 3.9 33.4 - - + -
182A ASP* 4.0 6.0 + - - -
194A PHE* 4.6 11.0 - + + -
197A VAL* 3.7 27.1 - - + +
201A LYS* 3.6 26.1 - - - -
316A ALA* 3.7 4.0 - - - +
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Residues in contact with ALA 163 (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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138A LEU* 3.7 3.1 - - - +
139A ALA* 2.9 35.0 + - - +
162A TYR* 1.3 77.7 - - - +
164A ASP* 1.3 65.4 + - - +
167A GLY 3.2 8.1 - - - +
168A ALA* 3.6 20.4 - - + -
316A ALA* 3.5 26.0 - - - +
317A LYS* 3.8 7.6 - - + -
320A TYR* 3.8 8.6 - - + -
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Residues in contact with ASP 164 (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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136A LYS* 2.8 26.2 + - - -
137A MET 3.1 24.9 - - - +
138A LEU* 3.6 12.8 - - + +
162A TYR* 5.4 0.3 - - - -
163A ALA* 1.3 74.4 - - - +
165A GLU* 1.3 66.4 + - - +
166A GLU* 3.0 14.2 + - - +
167A GLY* 2.7 33.5 + - - +
201A LYS* 3.3 28.2 + - - +
320A TYR* 3.8 21.3 - - + -
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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