Contacts of the strand formed by residues 160 - 167 (chain B) in PDB entry 3VI4
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 PHE 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B ILE* 3.4 20.4 - - + -
125B LEU* 3.8 21.8 - - + -
149B LEU* 4.4 4.3 - - + -
150B MET* 3.5 66.5 - - + +
153B MET* 3.7 33.4 - - + -
154B ARG* 4.4 11.5 - - + +
157B THR* 3.5 14.1 - - + -
158B SER 4.0 2.6 + - - -
159B ASP* 1.3 75.4 + - - +
161B ARG* 1.3 87.9 + - - +
162B ILE* 4.1 22.4 - - + -
207B ASN* 3.6 16.8 - - - +
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Residues in contact with ARG 161 (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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123B ILE 2.9 7.3 + - - -
124B ASP* 2.9 27.1 + - - +
125B LEU 2.9 26.6 + - - -
159B ASP* 4.8 4.3 - - - +
160B PHE* 1.3 87.0 - - - +
162B ILE* 1.3 60.6 + - - +
205B LEU* 3.3 31.9 + - + +
206B THR* 3.2 24.3 - - - +
207B ASN* 3.7 7.4 - - + +
246B GLY* 2.9 34.1 + - - -
248B ARG* 2.9 48.6 - - - +
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Residues in contact with ILE 162 (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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125B LEU* 3.5 14.6 - - + +
127B TYR* 5.3 0.9 - - + -
145B LEU* 4.9 2.0 - - + +
146B GLY* 4.4 16.2 - - - +
149B LEU* 3.9 27.8 - - + -
150B MET* 4.8 6.5 - - + +
160B PHE* 4.1 14.1 - - + -
161B ARG* 1.3 74.7 - - - +
163B GLY* 1.3 62.5 + - - +
203B LEU* 4.4 1.0 - - - +
204B SER 4.0 0.7 - - - +
205B LEU* 3.5 4.8 - - - -
206B THR* 2.7 46.8 + - + +
209B GLY* 4.7 10.8 - - - -
212B PHE* 3.6 47.8 - - + -
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Residues in contact with GLY 163 (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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125B LEU 3.0 9.1 + - - +
126B TYR* 3.9 15.0 - - - -
127B TYR* 2.9 30.3 + - - +
162B ILE* 1.3 74.8 - - - +
164B PHE* 1.3 60.7 + - - +
203B LEU* 3.4 15.9 - - - -
204B SER 4.5 0.2 - - - -
205B LEU* 3.5 6.2 - - - +
212B PHE* 3.7 6.8 - - - -
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Residues in contact with PHE 164 (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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126B TYR* 2.7 18.8 + - - -
127B TYR* 3.3 35.0 - + - -
129B MET* 3.7 31.0 - - + -
131B LEU* 5.3 3.6 - - + -
139B LEU* 5.7 3.1 - - + -
142B VAL* 4.8 2.9 - - + -
163B GLY* 1.3 73.5 - - - -
165B GLY* 1.3 61.6 + - - +
166B SER* 4.6 6.3 - - - -
202B VAL* 3.1 30.8 + - + -
203B LEU* 2.9 39.1 + - + +
212B PHE* 3.7 31.4 - + + -
216B VAL* 3.7 28.7 - - + -
219B GLN* 4.4 11.9 - - + -
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Residues in contact with GLY 165 (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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126B TYR* 3.3 16.7 + - - -
127B TYR 2.9 8.2 + - - +
128B LEU* 3.1 9.0 - - - +
129B MET 2.8 26.2 + - - -
164B PHE* 1.3 83.4 - - - +
166B SER* 1.3 61.2 + - - -
199B TYR* 4.3 2.9 - - - -
200B LYS 3.3 11.4 - - - -
202B VAL 4.1 1.3 - - - -
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Residues in contact with SER 166 (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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128B LEU* 4.3 1.8 - - - -
129B MET 3.4 5.2 - - - -
131B LEU* 3.4 33.5 - - - +
164B PHE* 4.6 4.3 - - - -
165B GLY* 1.3 75.6 - - - -
167B PHE* 1.3 60.8 + - - +
197B PHE* 3.3 19.2 - - - -
199B TYR* 3.3 7.4 - - - -
200B LYS* 2.8 41.5 + - - +
202B VAL* 3.9 11.7 - - - +
219B GLN* 4.8 1.4 + - - -
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Residues in contact with PHE 167 (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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128B LEU* 3.6 22.9 - - + -
129B MET 3.2 7.2 + - - -
130B ASP* 3.3 37.0 - - + -
131B LEU* 2.9 25.6 + - - -
166B SER* 1.3 75.4 - - - +
168B VAL* 1.3 69.1 + - - +
197B PHE* 4.2 3.1 - - - -
198B SER 3.2 18.6 - - - +
229B GLU* 3.9 18.4 - - + -
230B GLY 4.3 0.9 - - - +
231B GLY* 3.6 27.8 - - - -
234B ALA* 3.7 14.4 - - + -
256B PHE* 3.5 38.8 - + - -
257B SER 4.3 0.7 - - - -
258B THR* 4.3 5.6 - - - -
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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