Contacts of the strand formed by residues 251 - 258 (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 THR 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 3.9 19.2 + - + +
122B PRO 2.9 17.0 + - - -
123B ILE* 3.2 19.2 - - - +
124B ASP 3.1 25.5 + - - +
250B VAL* 1.3 78.1 - - - +
252B ARG* 1.3 57.5 + - - +
253B LEU* 4.2 2.0 - - - -
312B GLN* 4.2 14.8 - - - +
355B TYR* 4.9 12.5 + - + +
429B GLY 4.6 4.9 - - - +
430B PHE* 3.7 34.5 - - + -
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Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 3.5 4.9 - - + -
239B ALA 5.6 0.2 + - - -
247B TRP* 3.6 51.1 - - + +
248B ARG 3.0 23.4 + - - +
249B ASN* 2.9 29.9 + - - +
250B VAL 3.3 14.9 + - - +
251B THR* 1.3 75.0 - - - +
253B LEU* 1.3 63.2 + - - +
309B ASN* 2.8 49.1 + - - +
310B ASN* 3.5 19.2 + - + +
311B ILE* 4.0 6.7 - - + +
312B GLN* 2.9 35.1 + - - +
429B GLY 5.0 0.2 + - - -
503B NAG 4.5 4.6 + - - +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 4.1 20.4 - - + -
124B ASP 2.8 13.3 + - - +
125B LEU* 3.2 28.2 - - + -
126B TYR 2.6 32.6 + - - -
153B MET* 4.8 4.9 - - + -
247B TRP* 3.7 6.4 - - - -
251B THR* 5.4 2.5 - - - +
252B ARG* 1.3 81.5 - - - +
254B LEU* 1.3 55.8 + - - +
312B GLN* 3.3 27.4 - - + +
314B ILE* 4.2 15.7 - - + -
351B ILE* 5.3 1.3 - - + -
355B TYR* 3.8 37.2 - - + -
358B LEU* 4.2 10.3 - - + -
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Residues in contact with LEU 254 (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* 3.4 22.0 - - + +
128B LEU* 3.6 33.2 - - + -
235B ILE* 4.1 37.2 - - + +
238B VAL* 4.4 10.5 - - + -
239B ALA 5.9 0.4 - - - +
247B TRP* 5.0 5.2 - - + -
252B ARG 4.2 0.4 + - - -
253B LEU* 1.3 72.3 - - - +
255B VAL* 1.3 66.0 + - - +
256B PHE* 3.5 2.4 + - + +
306B LEU* 4.7 1.8 - - + -
311B ILE* 3.5 27.6 - - + +
312B GLN 2.8 10.4 + - - +
313B THR* 3.4 14.3 - - + +
314B ILE* 2.8 27.3 + - - -
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU* 3.7 35.7 - - + -
126B TYR 2.6 11.0 + - - +
127B TYR* 3.5 34.1 - - + -
128B LEU* 2.6 34.8 + - - +
254B LEU* 1.3 75.6 - - - +
256B PHE* 1.3 57.6 + - - +
257B SER* 4.6 1.8 - - - -
314B ILE* 3.7 20.9 - - + +
316B ALA* 4.5 15.0 - - + -
351B ILE* 3.9 22.0 - - + -
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Residues in contact with PHE 256 (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* 3.4 9.4 - - + -
167B PHE* 3.5 37.9 - + - -
231B GLY* 3.8 17.0 - - - -
232B PHE* 5.0 7.2 - + - -
235B ILE* 3.5 34.5 - - + -
254B LEU* 3.5 6.9 + - + -
255B VAL* 1.3 71.2 - - - +
257B SER* 1.3 60.2 + - - +
258B THR* 3.3 26.5 - - + -
262B PHE* 5.4 3.1 - - + -
313B THR* 4.6 8.3 - - + -
314B ILE 3.0 11.0 + - - +
315B PHE* 3.5 26.7 - + + -
316B ALA 3.0 22.3 + - - +
317B VAL* 4.7 0.7 - - - +
325B TYR* 3.9 16.8 - + - -
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Residues in contact with SER 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 3.3 27.7 + - - -
128B LEU 3.1 6.3 + - - +
129B MET* 3.4 17.7 - - - +
130B ASP* 3.0 25.8 + - - +
135B MET* 4.4 5.9 - - - +
167B PHE* 4.3 1.4 - - - -
255B VAL* 3.9 2.7 + - - -
256B PHE* 1.3 74.9 - - - +
258B THR* 1.3 62.9 + - - +
316B ALA* 3.1 29.2 - - - -
340B LEU* 5.0 6.1 - - - -
344B SER* 5.6 0.3 + - - -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP* 2.7 33.4 + - - -
135B MET* 4.1 7.2 - - - +
167B PHE* 4.3 5.0 - - - -
229B GLU* 4.8 1.6 - - - +
256B PHE* 3.3 32.1 - - + -
257B SER* 1.3 74.9 - - - +
259B ASP* 1.3 64.6 + - - +
260B ALA* 3.3 12.6 + - - +
261B GLY 4.9 0.7 + - - -
316B ALA 3.3 3.9 + - - +
317B VAL* 3.3 34.9 - - + +
318B THR* 3.6 2.7 + - - +
325B TYR* 3.5 16.2 - - - +
340B LEU* 4.8 2.2 - - - +
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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