Contacts of the strand formed by residues 314 - 319 (chain B) in PDB entry 3VF1
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 LEU 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B PRO* 4.3 11.2 - - + -
260B ASN* 4.6 6.7 - - - +
261B PHE* 3.6 41.8 - - + -
289B ILE* 4.3 5.4 - - + -
290B THR 3.4 6.5 - - - +
291B ASP* 3.7 26.0 - - - +
312B THR 3.9 3.4 - - - +
313B PRO* 1.3 78.1 - - - +
315B GLY* 1.3 60.4 + - - +
330B ILE* 3.3 7.1 - - - +
331B GLN* 2.8 51.6 + - + +
334B GLN* 3.3 38.4 - - - +
360B LEU* 4.3 3.1 - - - -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 4.4 1.6 - - - -
289B ILE* 3.2 9.6 - - - +
290B THR* 2.9 44.0 + - - -
314B LEU* 1.3 74.6 - - - +
316B LEU* 1.3 60.6 + - - -
317B PHE* 3.8 5.7 - - - -
329B ALA 3.6 5.4 - - - -
330B ILE* 4.4 0.2 - - - -
360B LEU* 4.0 18.9 - - - +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B CYS* 4.8 1.3 - - - -
257B LEU* 3.9 30.3 - - + -
261B PHE* 4.1 8.7 - - + -
263B VAL* 4.3 17.5 - - + -
278B LEU* 4.3 12.3 - - + -
287B ILE* 3.6 23.6 - - + -
288B PHE 3.5 13.5 - - - +
289B ILE* 4.1 16.4 - - + -
315B GLY* 1.3 72.1 - - - -
317B PHE* 1.3 64.3 - - - +
327B PRO* 3.5 5.4 - - - +
328B ILE* 2.8 46.2 + - + -
329B ALA* 2.9 22.6 + - + +
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Residues in contact with PHE 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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238B PHE* 4.3 0.9 - + - -
239B GLY* 4.1 9.4 - - - -
242B PHE* 3.9 42.8 - + - -
251B ILE* 4.2 10.5 - - + -
287B ILE* 3.5 11.1 - - - +
288B PHE* 2.8 43.7 + - + +
290B THR* 3.5 28.3 - - + -
315B GLY* 3.8 15.3 - - - -
316B LEU* 1.3 75.8 - - - +
318B TYR* 1.3 62.2 + - - +
325B ILE* 4.0 25.4 - - + -
326B ILE 3.1 7.6 - - - +
327B PRO* 3.7 29.8 - - + -
328B ILE* 4.4 3.8 - - - -
360B LEU* 4.2 9.9 - - + -
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Residues in contact with TYR 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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271B LEU 4.5 8.1 - - - -
272B LEU* 3.6 28.0 - - + +
273B ASP* 2.3 53.9 + - - +
276B TYR* 4.2 5.5 - - - -
281B ALA* 3.9 19.1 - - + -
286B LEU* 3.4 28.6 - - + +
287B ILE* 3.8 9.0 - - + -
288B PHE* 5.3 0.4 - - - -
317B PHE* 1.3 75.2 - - - +
319B LEU* 1.3 75.0 + - - +
320B LYS* 3.4 18.8 + - + -
325B ILE* 3.1 7.6 - - - -
326B ILE* 2.8 35.7 + - + +
328B ILE* 3.8 23.1 - - + +
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ASP* 4.8 0.7 - - - +
285B GLY 4.5 3.4 - - - +
286B LEU* 2.8 47.7 + - + +
288B PHE* 4.0 15.0 - - + -
318B TYR* 1.3 82.6 + - - +
320B LYS* 1.3 67.8 + - - +
323B ASP* 3.9 34.5 - - + +
324B ASP 3.9 0.9 - - - -
325B ILE* 3.8 20.4 - - + +
468B LEU* 4.0 24.5 - - + -
469B ARG 6.2 0.9 - - - +
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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
------------------------------------------------------------
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