Contacts of the strand formed by residues 155 - 161 (chain J) in PDB entry 2VLR
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 155 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12J TYR* 3.5 11.7 + - - -
123J PRO* 4.7 1.6 - - + -
150J PHE* 3.7 47.1 - - + -
153J ASP* 3.9 6.1 + - - +
154J HIS* 1.3 80.2 - - - +
156J GLU* 1.3 71.5 + - - +
157J LEU 5.6 0.2 - - - +
190J LEU* 4.6 15.5 - - + -
212J VAL* 4.1 20.2 - - + -
213J GLN 3.2 12.1 - - - +
214J PHE* 4.0 14.8 - - + -
215J TYR* 4.9 0.4 - - - -
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Residues in contact with GLU 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J LYS* 4.2 15.3 + - - +
12J TYR* 3.9 20.8 - - + +
155J VAL* 1.3 81.9 - - - +
157J LEU* 1.3 63.6 + - - +
158J SER* 5.2 0.7 + - - -
211J GLN* 3.5 2.4 + - - +
212J VAL* 3.5 5.0 - - - -
213J GLN* 3.0 44.6 + - + +
215J TYR* 3.6 28.9 + - + -
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Residues in contact with LEU 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J CYS* 4.4 16.6 - - + +
147J ALA* 4.7 7.9 - - + -
155J VAL* 5.4 1.4 - - + +
156J GLU* 1.3 75.1 - - - +
158J SER* 1.3 73.2 + - - +
159J TRP* 4.0 13.2 - - + +
172J THR* 4.6 13.7 - - + +
190J LEU* 4.1 26.6 - - + +
192J SER* 3.5 39.0 - - - +
210J CYS* 3.9 20.0 - - - -
211J GLN 3.3 5.6 - - - +
212J VAL* 4.3 13.7 - - + +
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Residues in contact with SER 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J GLU 5.2 0.6 + - - -
157J LEU* 1.3 80.0 - - - +
159J TRP* 1.3 64.8 + - - +
160J TRP* 2.8 27.9 + - - -
165J GLU* 3.7 21.5 - - - -
210J CYS* 3.6 4.0 - - - -
211J GLN* 2.8 54.0 + - - +
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Residues in contact with TRP 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J VAL* 4.3 13.5 - - + -
143J LEU* 3.9 31.0 - - + -
144J VAL 4.2 1.6 - - - -
145J CYS* 3.4 42.2 - - + -
157J LEU* 4.0 8.6 - - + +
158J SER* 1.3 73.3 - - - +
160J TRP* 1.3 63.7 + - - +
161J VAL* 4.2 0.9 - - + -
165J GLU* 3.2 11.3 + - - +
166J VAL* 3.1 43.7 + - + +
170J VAL* 3.6 33.0 - - + -
192J SER* 2.9 25.2 + - - -
193J ARG 4.0 5.7 + - - -
194J LEU* 3.7 29.6 - - + -
208J PHE* 5.1 4.3 - - + -
209J ARG 3.6 20.9 - - - -
210J CYS* 4.0 13.2 - - + -
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Residues in contact with TRP 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J SER* 2.8 33.2 + - - -
159J TRP* 1.3 78.6 - - - +
161J VAL* 1.3 63.2 + - - +
162J ASN 4.0 0.6 + - - -
163J GLY* 4.0 10.7 + - - +
164J LYS* 3.6 19.1 - - - +
165J GLU* 3.5 43.5 - - + +
207J HIS* 3.7 2.4 + - - +
208J PHE 3.7 0.7 - - - -
209J ARG* 2.8 73.4 + - + +
211J GLN* 3.9 25.7 + - + +
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Residues in contact with VAL 161 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J TRP* 4.2 0.8 - - + -
160J TRP* 1.3 73.9 - - - +
162J ASN* 1.3 83.9 + - - +
163J GLY 3.4 1.3 - - - -
164J LYS* 2.9 27.6 + - - +
166J VAL* 3.9 31.8 - - + +
194J LEU* 4.3 10.3 - - + -
196J VAL* 6.2 0.4 - - + -
200J PHE* 4.2 20.0 - - + -
207J HIS 3.4 10.8 - - - +
208J PHE* 4.0 28.5 - - + -
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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