Contacts of the strand formed by residues 133 - 140 (chain B) in PDB entry 3V4V
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 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR 3.6 4.9 - - - +
132B PRO* 1.3 82.2 - - - +
134B ASP* 1.3 81.6 + - - +
135B LEU* 4.1 7.2 - - + +
163B LEU* 5.1 8.1 - - + -
167B THR* 4.3 7.6 + - + -
169B SER 3.5 5.9 + - - -
170B VAL* 3.4 31.0 - - + +
171B ARG 3.5 5.9 + - - -
259B ARG* 3.3 7.5 + - - +
261B VAL* 3.6 0.8 - - - +
262B SER* 3.6 10.3 - - - +
264B LEU* 4.4 17.3 - - + -
367B TYR* 3.2 37.0 - - + +
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 1.3 73.3 - - - +
135B LEU* 1.3 60.2 + - - +
171B ARG* 3.5 12.9 + - - +
216B LEU* 3.3 26.7 - - + +
257B GLY 3.7 1.6 - - - +
258B TRP* 3.5 11.8 - - + -
259B ARG* 2.6 71.3 + - - +
261B VAL* 3.8 4.3 - - + +
262B SER 3.2 9.8 + - - +
263B ARG* 4.8 1.6 - - + -
264B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.0 10.4 - - + -
134B ASP* 1.3 71.4 - - - +
136B TYR* 1.3 66.7 + - - +
137B TYR* 4.0 3.5 + - + +
159B LEU* 3.7 29.8 - - + -
163B LEU* 4.3 16.4 - - + -
170B VAL* 5.8 0.2 - - + -
171B ARG 3.2 8.1 + - - +
172B ILE* 3.2 15.9 - - + +
173B GLY 2.9 24.6 + - - +
216B LEU* 3.2 3.2 - - - +
264B LEU* 3.5 28.7 - - + -
266B VAL* 3.5 26.2 - - + +
363B ILE* 4.1 22.4 - - + -
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Residues in contact with TYR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ASP 4.0 0.2 + - - -
135B LEU* 1.3 74.2 - - - +
137B TYR* 1.3 64.2 + - - +
138B LEU* 3.4 26.0 + - + -
173B GLY* 3.8 13.7 - - - -
174B PHE 3.1 21.3 + - - -
175B GLY* 3.3 12.0 - - - -
210B PHE* 3.9 3.3 - + - -
212B HIS* 2.6 46.0 + + - +
214B LEU 4.2 0.7 - - - -
216B LEU* 4.2 4.7 - - + -
249B ALA* 4.6 5.2 - - + -
256B ILE* 3.6 32.4 - - + +
258B TRP* 3.6 23.6 - + + -
264B LEU 3.3 8.2 + - - +
265B LEU* 3.5 19.7 - - + +
266B VAL 2.9 23.6 + - - -
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.0 5.8 + - + +
136B TYR* 1.3 70.5 - - - +
138B LEU* 1.3 58.8 + - - +
139B MET* 3.4 34.1 - - + +
152B VAL* 3.7 28.0 - - + +
159B LEU* 5.7 6.3 - - + -
173B GLY 3.0 15.4 + - - +
174B PHE* 3.4 29.3 - + + -
175B GLY 2.9 26.2 + - - +
223B PHE* 5.0 8.3 - + + -
266B VAL* 3.7 22.7 - - + -
268B THR* 3.2 34.2 + - + +
356B SER* 4.7 5.7 + - - -
359B VAL* 4.1 19.5 - - + +
363B ILE* 4.7 7.9 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B TYR* 3.4 13.1 + - + -
137B TYR* 1.3 71.2 - - - +
139B MET* 1.3 59.8 + - - +
175B GLY 3.3 23.1 - - - +
176B SER 4.1 0.4 - - - +
177B PHE* 4.0 14.6 - - + -
210B PHE* 3.6 24.5 - - + -
245B ALA* 3.7 23.1 - - + +
246B ILE* 3.8 29.8 - - + +
249B ALA* 4.8 4.3 - - + -
265B LEU* 3.8 20.6 - - + -
266B VAL 2.8 13.3 + - - +
267B PHE* 3.6 6.6 - - + -
268B THR* 3.1 25.4 + - - -
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TYR* 3.4 26.2 + - + +
138B LEU* 1.3 71.8 - - - +
140B ASP* 1.3 72.4 + - - +
141B LEU* 3.5 7.0 + - + +
145B MET* 4.0 11.7 - - + +
148B ASP* 3.6 33.2 - - + +
149B LEU* 3.7 38.8 - - + +
152B VAL* 4.2 11.7 - - + -
174B PHE* 3.8 18.2 - - + -
175B GLY 2.7 10.3 + - - -
176B SER* 3.2 5.9 - - - -
177B PHE* 3.1 28.6 + - - -
268B THR* 3.4 13.2 - - - +
356B SER* 5.1 0.2 - - - +
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Residues in contact with ASP 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MET* 1.3 72.2 - - - +
141B LEU* 1.3 64.8 + - - +
142B SER* 2.3 28.3 + - - -
145B MET* 3.1 42.1 - - + +
177B PHE* 3.1 35.5 - - + +
240B GLU* 3.1 25.5 - - - +
268B THR 3.2 23.3 + - - +
269B SER* 4.0 8.7 - - - +
270B ASP* 4.1 4.9 - - - +
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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