Contacts of the strand formed by residues 187 - 196 (chain E) in PDB entry 3VXR
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 187 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLY 3.0 24.3 + - - -
149E PHE* 2.6 42.3 + - + +
150E TYR* 2.6 37.2 - + - -
152E ASP* 3.7 29.8 + - + +
175E PRO* 4.0 17.0 - - + -
176E LEU 3.2 20.4 - - - +
177E LYS* 3.9 32.8 + - + -
178E GLU* 3.7 3.6 - - - -
185E SER 3.5 13.3 + - - -
186E ARG* 1.3 74.3 - - - +
188E ALA* 1.3 60.9 + - - +
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Residues in contact with ALA 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TRP* 3.5 34.5 - - + -
146E ALA 3.1 10.3 - - - +
147E THR* 4.4 2.2 - - + -
149E PHE* 3.9 2.5 - - - -
172E ASP* 5.3 0.5 - - - +
175E PRO* 3.4 5.4 - - - +
176E LEU* 2.9 39.8 + - + +
178E GLU* 3.8 17.5 - - + +
187E TYR* 1.3 74.8 - - - +
189E LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D TRP* 5.6 0.7 - - - -
144E CYS 3.8 0.9 - - - +
145E LEU* 3.6 4.7 - - - +
146E ALA* 2.8 43.7 + - + +
149E PHE* 4.0 14.1 - - + -
154E VAL* 3.7 27.6 - - + +
156E LEU* 4.1 27.3 - - + +
171E THR* 4.1 10.8 - - + -
172E ASP* 3.6 40.4 - - + +
174E GLN 4.0 0.2 - - - -
175E PRO* 3.8 24.7 - - + -
176E LEU* 6.3 0.2 - - - -
188E ALA* 1.3 75.5 - - - +
190E SER* 1.3 64.6 + - - +
211E VAL* 6.0 0.2 - - + -
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Residues in contact with SER 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D THR* 3.4 15.2 - - - +
175D VAL* 3.8 13.7 - - - +
177D TRP* 4.8 0.4 - - - -
143E VAL* 4.6 1.3 - - - -
144E CYS 3.1 9.4 - - - -
145E LEU* 3.8 16.8 - - - -
156E LEU* 4.6 1.1 - - - -
171E THR* 3.6 5.4 - - - +
172E ASP* 2.7 50.3 + - - +
189E LEU* 1.3 74.7 - - - +
191E SER* 1.3 63.5 + - - +
192E ARG* 2.8 18.7 + - - -
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Residues in contact with SER 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E VAL* 3.2 6.6 - - - +
144E CYS* 2.6 36.9 + - - +
156E LEU* 3.4 30.6 - - - +
158E TRP* 2.9 26.2 + - - -
169E VAL* 4.1 0.3 - - - +
170E CYS 3.3 8.3 + - - -
171E THR* 2.8 20.2 + - - -
190E SER* 1.3 76.1 - - - +
192E ARG* 1.3 67.4 + - - +
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Residues in contact with ARG 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 4.0 1.6 - - + -
157D THR* 4.2 2.6 + - - -
158D ASP 4.4 0.4 + - - -
160D CYS* 3.7 12.1 - - - +
162D LEU* 4.4 11.7 - - + -
173D SER* 2.8 55.7 + - - +
174D ALA* 3.9 5.9 - - - +
175D VAL* 3.5 18.2 - - - +
141E THR* 3.7 23.6 - - + -
142E LEU 3.2 3.1 - - - +
143E VAL* 3.8 14.4 - - + -
158E TRP* 3.7 5.8 + - - -
168E GLY 3.6 1.8 - - - +
169E VAL* 3.4 5.4 - - - -
170E CYS* 2.8 39.9 + - - +
172E ASP* 2.8 25.7 + - - +
190E SER* 2.8 32.8 + - - -
191E SER* 1.3 76.1 + - - +
193E LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E THR* 4.3 1.1 - - - -
142E LEU* 2.7 49.1 + - + +
158E TRP* 3.6 45.7 - - + +
160E VAL* 3.8 25.1 - - + -
165E VAL* 4.2 7.2 - - + -
167E SER 3.9 13.9 - - - +
168E GLY 3.5 2.5 - - - +
169E VAL* 3.9 19.7 - - + -
192E ARG* 1.3 73.7 - - - +
194E ARG* 1.3 66.7 + - - +
195E VAL* 4.5 9.6 - - + -
207E PHE* 3.9 17.5 - - + -
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Residues in contact with ARG 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D THR* 4.0 7.5 + - - +
139D ASP* 2.7 42.0 + - - -
162D LEU* 3.7 23.8 - - + -
164D MET* 3.4 33.3 - - + +
169D PHE* 3.5 13.3 - - - -
171D SER* 3.0 21.8 + - - -
133E GLU* 2.9 28.3 + - - +
137E THR* 3.7 16.8 + - - -
139E LYS* 3.5 13.6 - - + +
140E ALA 3.3 8.3 - - - +
141E THR* 3.1 15.9 + - - +
167E SER 5.0 0.7 - - - +
168E GLY* 3.2 14.4 + - - -
192E ARG 4.2 0.6 - - - -
193E LEU* 1.3 76.6 - - - +
195E VAL* 1.3 70.3 + - - +
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D MET* 3.5 12.1 - - - +
167D MET* 5.2 0.2 - - - -
139E LYS* 3.5 3.6 - - - +
140E ALA 2.8 40.1 + - - +
142E LEU* 4.7 4.9 - - + -
160E VAL* 5.8 2.0 - - + -
193E LEU* 4.5 15.3 - - + -
194E ARG* 1.3 78.2 - - - +
196E SER* 1.3 72.7 + - - +
199E PHE* 3.9 27.1 - - + -
200E TRP* 4.0 22.4 - - + +
207E PHE* 4.1 18.2 - - + -
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Residues in contact with SER 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 3.9 4.2 - - - +
167D MET* 3.7 26.9 - - - +
138E GLN 3.9 7.0 - - - -
139E LYS* 4.4 2.0 - - - +
140E ALA 4.5 0.4 - - - -
195E VAL* 1.3 80.0 - - - +
197E ALA* 1.3 64.9 + - - +
198E THR* 3.2 21.5 + - - -
199E PHE* 3.0 24.0 + - - +
200E TRP 3.1 9.4 + - - -
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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