Contacts of the strand formed by residues 170 - 177 (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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B VAL* 3.4 35.9 - - + +
135B LEU 5.8 0.2 - - - +
160B LEU* 4.6 8.9 - - + +
163B LEU* 3.7 44.0 - - + -
164B GLN* 3.5 38.9 + - + +
167B THR* 3.8 10.3 - - + -
169B SER* 1.3 74.5 - - - +
171B ARG* 1.3 67.5 + - - +
218B GLY* 3.9 12.0 - - - +
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Residues in contact with ARG 171 (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 3.5 2.5 + - - +
134B ASP* 3.5 24.8 + - - +
135B LEU* 3.2 22.9 + - - +
160B LEU* 5.5 1.3 - - - -
170B VAL* 1.3 81.0 - - - +
172B ILE* 1.3 65.1 + - - +
216B LEU* 3.0 28.0 + - - +
217B THR* 3.2 25.3 - - - +
218B GLY* 3.7 3.1 - - - +
257B GLY* 3.1 26.1 + - - -
259B ARG* 3.3 43.6 - - - +
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Residues in contact with ILE 172 (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* 3.2 16.8 - - + +
156B GLY 4.2 11.0 - - - +
159B LEU* 4.6 13.0 - - + -
160B LEU* 3.5 35.4 - - + -
163B LEU* 4.0 16.4 - - + -
171B ARG* 1.3 78.4 - - - +
173B GLY* 1.3 61.3 + - - +
214B LEU* 4.6 1.7 - - - +
215B SER 3.9 0.7 - - - +
216B LEU* 3.4 4.4 - - - -
217B THR* 2.7 40.4 + - + +
219B ASP 4.8 4.5 - - - +
220B ALA* 4.9 4.3 - - - -
223B PHE* 3.5 42.8 - - + -
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Residues in contact with GLY 173 (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 2.9 9.5 + - - +
136B TYR* 3.9 9.9 - - - -
137B TYR* 3.0 23.6 + - - +
172B ILE* 1.3 74.5 - - - +
174B PHE* 1.3 62.0 + - - +
214B LEU* 3.3 16.4 - - - -
216B LEU* 3.3 14.6 - - - +
223B PHE* 4.2 8.3 - - - -
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Residues in contact with PHE 174 (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* 3.1 14.0 + - - -
137B TYR* 3.4 45.1 - + + -
139B MET* 3.8 26.9 - - + -
141B LEU* 5.2 3.8 - - + -
149B LEU* 4.8 4.5 - - + -
152B VAL* 4.9 1.6 - - + -
173B GLY* 1.3 73.3 - - - -
175B GLY* 1.3 72.7 + - - +
176B SER* 4.5 7.4 - - - -
212B HIS* 3.6 0.2 + - - -
213B VAL* 3.0 46.7 + - + -
214B LEU* 2.9 25.1 + - + +
223B PHE* 4.1 21.5 - + + -
227B VAL* 4.1 29.4 - - + -
230B GLN* 4.9 9.9 - - + -
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Residues in contact with GLY 175 (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* 3.3 14.9 + - - -
137B TYR 2.9 8.4 + - - +
138B LEU* 3.3 15.2 - - - -
139B MET* 2.7 34.7 + - - +
174B PHE* 1.3 81.7 - - - +
176B SER* 1.3 54.0 + - - -
211B HIS 3.3 9.0 - - - -
213B VAL 4.2 0.2 - - - -
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Residues in contact with SER 176 (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 3.2 5.4 - - - +
141B LEU* 3.5 33.3 - - - +
174B PHE* 4.5 7.2 - - - -
175B GLY* 1.3 75.7 - - - -
177B PHE* 1.3 61.4 + - - +
208B PHE* 3.3 9.7 - - - -
210B PHE* 3.2 8.0 - - - -
211B HIS* 2.6 64.5 + - - +
213B VAL* 4.1 5.2 - - - +
230B GLN* 4.3 0.5 + - - -
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Residues in contact with PHE 177 (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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138B LEU* 4.0 22.2 - - + -
139B MET 3.1 11.3 + - - -
140B ASP* 3.1 46.6 - - + +
141B LEU 3.0 23.6 + - - -
176B SER* 1.3 79.3 - - - +
178B VAL* 1.3 67.5 + - - +
208B PHE* 3.7 3.4 - - - -
209B SER 3.1 19.5 - - - +
240B GLU* 4.0 7.6 - - + -
241B GLY 3.9 3.1 - - - +
242B GLY* 3.4 27.4 - - - -
245B ALA* 3.6 17.3 - - + -
267B PHE* 3.4 34.1 - + - -
268B THR 4.0 2.5 - - - -
269B SER* 4.6 1.6 - - - -
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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