Contacts of the strand formed by residues 123 - 130 (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 ILE 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 3.6 6.3 + - + +
122B PRO* 1.3 75.1 - - - +
124B ASP* 1.3 78.4 + - - +
125B LEU* 4.2 0.9 - - + +
153B MET* 3.7 22.0 - - + -
156B ILE* 5.0 4.0 - - + +
157B THR* 3.8 18.4 + - + -
159B ASP 2.9 10.0 + - - +
160B PHE* 3.4 22.7 - - + -
161B ARG 2.9 25.1 + - - -
248B ARG* 4.1 0.6 + - - -
251B THR* 3.2 20.9 - - - +
253B LEU* 4.1 21.5 - - + -
355B TYR* 3.9 31.0 - - + +
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Residues in contact with ASP 124 (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* 1.3 74.0 - - - +
125B LEU* 1.3 53.8 + - - +
126B TYR 4.2 0.2 - - - -
161B ARG* 2.9 35.6 + - - +
205B LEU* 3.6 19.6 - - + +
247B TRP* 3.7 12.7 - - + -
248B ARG* 2.9 50.4 + - - +
250B VAL* 3.8 9.5 - - + +
251B THR 3.1 10.5 + - - +
252B ARG* 3.5 1.6 - - + -
253B LEU* 2.8 32.1 + - - -
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Residues in contact with LEU 125 (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* 4.0 2.0 - - + -
124B ASP* 1.3 74.4 - - - +
126B TYR* 1.3 69.2 + - - +
127B TYR* 3.9 11.7 - - + +
149B LEU* 4.3 21.8 - - + -
153B MET* 5.1 3.4 - - + -
160B PHE* 3.8 19.7 - - + -
161B ARG 2.9 7.7 + - - -
162B ILE* 3.5 8.7 - - + -
163B GLY 3.0 22.2 + - - -
205B LEU* 3.4 4.9 - - - +
253B LEU* 3.2 23.8 - - + +
255B VAL* 3.7 33.0 - - + -
351B ILE* 3.9 23.8 - - + -
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Residues in contact with TYR 126 (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* 1.3 74.8 - - - +
127B TYR* 1.3 59.8 + - - +
128B LEU* 4.2 9.0 - - + -
163B GLY* 3.8 11.2 - - - -
164B PHE 2.7 17.2 + - - -
165B GLY* 3.3 23.0 - - - -
199B TYR* 3.2 13.6 + - - -
201B ASN* 2.7 23.9 + - - -
203B LEU 3.5 18.6 - - - -
204B SER* 4.8 1.8 - - - -
205B LEU* 4.5 4.5 - - + -
238B VAL* 4.0 26.7 - - + -
245B ILE* 3.8 27.4 - - + -
247B TRP* 3.6 22.6 - - + -
253B LEU 2.6 10.9 + - - +
254B LEU* 3.4 9.0 - - + +
255B VAL 2.6 32.3 + - - -
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Residues in contact with TYR 127 (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* 3.9 10.2 - - + +
126B TYR* 1.3 71.1 - - - +
128B LEU* 1.3 58.6 + - - +
129B MET* 3.7 32.6 - - + -
142B VAL* 4.4 9.2 - - + +
145B LEU* 3.9 26.9 - - + -
149B LEU* 5.4 0.7 - - + -
162B ILE* 5.3 0.7 - - + -
163B GLY 2.9 17.0 + - - +
164B PHE* 3.3 28.2 - + + -
165B GLY 2.9 24.0 + - - -
212B PHE* 4.5 6.3 - - + -
255B VAL* 3.5 32.1 - - + -
257B SER* 3.3 16.6 + - - -
344B SER* 4.6 5.5 + - - -
347B VAL* 3.4 34.4 - - + +
351B ILE* 4.2 5.8 - - + -
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Residues in contact with LEU 128 (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* 3.6 4.2 + - + -
127B TYR* 1.3 71.6 - - - +
129B MET* 1.3 61.1 + - - +
165B GLY* 3.1 24.7 - - - +
166B SER 4.3 0.7 - - - -
167B PHE* 3.6 28.0 - - + -
199B TYR* 4.2 12.6 - - + -
234B ALA* 3.9 11.7 - - + -
235B ILE* 3.8 30.7 - - + +
238B VAL* 3.8 21.5 - - + -
254B LEU* 3.6 19.5 - - + -
255B VAL 2.6 15.9 + - - +
256B PHE* 3.4 6.3 - - + -
257B SER 3.1 23.9 + - - +
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Residues in contact with MET 129 (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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127B TYR* 3.7 23.3 + - + +
128B LEU* 1.3 75.1 - - - +
130B ASP* 1.3 71.5 + - - +
131B LEU* 3.3 16.2 + - + -
135B MET* 3.8 24.7 - - + -
138B ASP* 4.1 7.9 - - + +
139B LEU* 4.1 26.0 - - + +
142B VAL* 4.3 14.4 - - + -
164B PHE* 3.7 29.2 - - + -
165B GLY 2.8 11.1 + - - -
166B SER* 3.4 5.5 - - - -
167B PHE* 3.2 24.1 + - - -
257B SER* 3.4 20.6 - - - +
344B SER* 5.7 0.7 - - - +
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Residues in contact with ASP 130 (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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129B MET* 1.3 73.6 - - - +
131B LEU* 1.3 67.4 + - - +
132B SER* 2.5 44.2 + - - -
135B MET* 3.3 32.3 - - + +
167B PHE* 3.3 19.9 - - + +
168B VAL* 6.2 0.2 - - - -
229B GLU* 3.4 22.1 - - - +
257B SER 3.0 17.3 + - - +
258B THR* 2.7 30.5 + - - +
259B ASP* 3.8 6.1 - - - +
260B ALA 4.5 0.3 + - - -
502B MG 3.8 0.2 - - - -
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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