Contacts of the strand formed by residues 311 - 318 (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 311 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B VAL* 6.1 0.2 - - + -
239B ALA* 4.1 11.2 - - + -
247B TRP* 3.9 34.1 - - + +
252B ARG* 3.9 12.3 - - + +
253B LEU 4.9 0.2 - - - -
254B LEU* 3.5 36.1 - - + +
306B LEU* 3.0 46.8 + - + +
307B SER* 5.6 0.5 - - - -
309B ASN* 3.4 32.1 - - + +
310B ASN* 1.3 74.3 - - - +
312B GLN* 1.3 64.3 + - - +
313B THR* 3.8 8.8 + - - +
332B ILE* 5.9 0.2 - - - +
333B PRO 5.1 2.9 - - - +
334B LYS* 4.1 5.9 - - - +
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Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B THR* 4.2 11.2 - - - +
252B ARG 2.9 28.1 + - - +
253B LEU* 3.3 22.4 - - + +
254B LEU 2.8 26.2 + - - +
310B ASN 3.6 0.4 + - - +
311B ILE* 1.3 73.3 - - - +
313B THR* 1.3 60.1 - - - +
314B ILE* 3.9 1.0 + - - +
334B LYS* 3.3 50.1 - - + +
355B TYR* 5.7 3.7 - - - -
358B LEU* 3.9 22.7 + - + +
359B SER* 5.6 1.6 - - - +
428B LEU 4.5 0.2 + - - -
429B GLY* 3.9 25.6 - - - +
430B PHE* 5.8 5.1 - - - -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 5.3 2.9 - - + -
254B LEU* 3.4 27.4 - - + +
256B PHE* 4.6 4.7 - - + -
306B LEU* 3.3 28.6 - - + +
311B ILE* 3.8 7.1 + - - +
312B GLN* 1.3 73.3 - - - +
314B ILE* 1.3 64.8 + - - +
315B PHE* 3.8 33.6 - - + -
332B ILE* 4.4 2.8 - - - +
334B LYS 3.6 6.3 + - - -
335B SER* 3.3 12.3 - - - +
336B ALA 2.8 27.7 + - - +
358B LEU* 4.9 0.3 - - - +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 4.2 27.6 - - + -
254B LEU 2.8 13.1 + - - +
255B VAL* 3.7 25.5 - - + -
256B PHE* 3.0 29.5 + - - +
312B GLN 4.9 0.7 - - - +
313B THR* 1.3 76.0 - - - +
315B PHE* 1.3 68.5 + - - +
316B ALA* 3.4 6.5 + - + +
336B ALA* 3.3 4.9 - - + +
337B VAL 5.5 0.2 - - - +
338B GLY 5.6 1.3 - - - +
350B LEU* 5.2 4.9 - - + +
351B ILE* 4.2 21.3 - - + +
354B ALA* 3.7 34.1 - - + -
355B TYR 4.5 1.1 - - - +
358B LEU* 4.1 16.8 - - + -
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Residues in contact with PHE 315 (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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232B PHE* 6.0 0.2 - + - -
235B ILE* 4.7 9.0 - - + -
256B PHE* 3.5 33.2 - + + -
313B THR* 3.8 24.9 - - + -
314B ILE* 1.3 71.8 - - - +
316B ALA* 1.3 60.7 + - - +
317B VAL* 3.3 5.5 + - + -
325B TYR* 4.0 29.8 - + + -
328B LEU* 3.8 21.3 - - + -
329B LYS* 4.5 7.2 - - + -
332B ILE* 3.4 33.2 - - + -
335B SER* 4.3 13.5 - - - -
336B ALA 2.6 28.2 + - - +
337B VAL* 3.4 11.8 - - + +
338B GLY 2.9 29.7 + - - +
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Residues in contact with ALA 316 (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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255B VAL* 4.5 12.3 - - + -
256B PHE 3.0 8.6 + - - +
257B SER* 3.1 38.7 - - - -
258B THR 3.3 4.5 + - - +
314B ILE* 3.4 4.7 + - + +
315B PHE* 1.3 69.1 - - - +
317B VAL* 1.3 60.7 + - - +
340B LEU* 3.9 16.8 - - + +
347B VAL* 4.8 4.5 - - + -
350B LEU* 3.5 28.3 - - + -
351B ILE* 6.2 0.7 - - + -
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Residues in contact with VAL 317 (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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256B PHE 4.7 1.6 - - - +
258B THR* 3.3 22.9 - - + +
315B PHE* 3.3 14.5 + - + +
316B ALA* 1.3 80.1 - - - +
318B THR* 1.3 63.7 + - - +
321B PHE* 3.8 8.7 - - + +
322B GLN* 3.2 27.5 + - - +
325B TYR* 3.6 56.5 - - + -
337B VAL* 4.7 0.4 - - + -
338B GLY 3.3 1.5 + - - +
340B LEU* 2.8 27.9 + - - -
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Residues in contact with THR 318 (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 ASP* 6.0 0.2 - - - +
258B THR 3.6 1.4 + - - -
259B ASP* 3.6 40.3 + - + +
317B VAL* 1.3 79.8 - - - +
319B GLU* 1.3 66.9 + - - +
320B GLU* 3.9 15.7 - - - +
321B PHE* 3.1 14.9 + - - +
322B GLN* 3.5 10.6 + - - -
340B LEU* 3.5 26.5 - - + +
341B SER 4.3 9.2 - - - +
342B ALA* 5.3 6.3 - - - +
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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