Contacts of the strand formed by residues 285 - 291 (chain B) in PDB entry 3VZC
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 MET 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 3.7 26.2 - - + -
262B ALA* 2.9 42.6 - - + -
263B LEU 3.7 9.4 - - - +
264B LEU* 4.2 15.5 - - + -
280B CYS* 4.0 3.8 - - - -
284B VAL* 1.3 77.0 - - - +
286B HIS* 1.3 64.9 + - - +
287B LEU* 3.6 0.4 + - + -
323B PRO* 3.6 3.6 - - - +
324B VAL* 2.9 50.8 + - + +
325B VAL 5.2 1.6 - - - +
326B ALA* 5.8 0.2 - - - -
327B PHE* 3.8 21.1 - - + -
354B VAL* 3.2 27.6 - - + -
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Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B LEU 3.6 1.6 - - - +
262B ALA* 3.6 2.6 - - - +
263B LEU* 2.7 44.5 + - + +
265B HIS 3.7 10.4 + - - -
275B ALA* 3.3 27.0 - - + +
277B MET* 3.6 12.5 - - + +
278B GLY 3.3 24.2 + - - -
279B ARG 4.8 0.2 - - - -
280B CYS* 3.3 31.3 - - + -
284B VAL* 5.4 3.8 - - + -
285B MET* 1.3 73.1 - - - +
287B LEU* 1.3 60.6 + - - +
288B PHE* 3.8 12.5 - - + -
321B TYR* 2.9 41.0 + + + -
322B VAL 4.1 0.2 - - - -
357D ASN* 5.6 2.4 + - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU* 4.3 15.3 - - + -
212B TYR* 3.7 42.4 - - + -
260B VAL* 4.0 15.7 - - + -
261B LEU 3.3 20.6 - - - +
262B ALA* 4.2 9.9 - - + +
285B MET 3.6 0.8 + - - -
286B HIS* 1.3 73.6 - - - +
288B PHE* 1.3 71.6 + - - +
289B TYR* 4.8 6.0 - - + -
320B VAL 3.9 0.2 - - - +
321B TYR* 3.4 7.1 - - - -
322B VAL* 2.8 47.6 + - + +
324B VAL* 3.9 17.7 - - + -
327B PHE* 5.0 9.4 - - + -
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 4.9 2.5 - - + -
260B VAL* 3.7 0.7 - - - -
261B LEU* 2.8 54.4 + - + +
263B LEU* 4.6 7.2 - - + -
274B ALA 3.4 22.2 - - - -
275B ALA* 4.2 13.2 - - + -
277B MET* 4.5 0.7 - - - -
286B HIS* 3.8 22.9 - - + -
287B LEU* 1.3 79.5 - - - +
289B TYR* 1.3 67.7 + - - +
312B MET* 3.8 27.1 - - + -
319B LEU* 4.2 10.5 - - + -
320B VAL 3.3 13.2 - - - -
321B TYR* 3.6 25.6 - + + -
1001B UUL 3.2 27.8 - - + -
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Residues in contact with TYR 289 (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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210B LEU* 3.6 21.8 - - + -
212B TYR* 4.5 15.6 + + - -
252B VAL* 3.8 27.4 - - + +
253B PRO* 5.8 0.2 - - - +
254B ASP* 5.4 0.2 + - - -
257B PHE* 3.6 27.8 - + + -
259B LEU* 3.3 15.7 - - - +
260B VAL* 4.1 7.2 - - + -
287B LEU* 4.8 7.0 - - + -
288B PHE* 1.3 78.5 - - - +
290B VAL* 1.3 61.9 + - - +
291B ARG* 3.8 28.7 - - + -
318B TYR 3.2 2.1 - - - +
319B LEU* 3.6 2.4 - - - +
320B VAL* 2.8 73.1 + - + +
322B VAL* 4.9 3.1 - - + -
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Residues in contact with VAL 290 (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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257B PHE* 3.5 6.6 - - - +
258B VAL* 3.0 38.5 + - + -
259B LEU* 3.1 40.0 + - + +
289B TYR* 1.3 75.4 - - - +
291B ARG* 1.3 60.4 + - - +
294B VAL* 3.4 31.9 - - + -
299B LEU* 5.1 9.9 - - + -
302B LEU* 5.3 5.2 - - + -
316B CYS* 5.9 0.2 - - - -
318B TYR* 3.3 7.9 - - + +
319B LEU* 3.9 24.2 - - + +
1001B UUL 4.7 6.7 - - + -
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Residues in contact with ARG 291 (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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254B ASP* 2.8 44.9 + - - +
256B ASP 4.0 4.7 - - - +
257B PHE* 4.5 3.8 - - - +
258B VAL* 3.5 10.3 - - - +
289B TYR* 3.8 25.1 - - + -
290B VAL* 1.3 81.2 - - - +
292B ALA* 1.3 66.7 + - - +
293B GLY 3.5 2.1 + - - -
294B VAL* 3.7 6.9 - - - +
317B PRO* 2.8 43.1 + - - +
318B TYR* 2.9 41.1 + - + +
320B VAL* 4.5 4.9 - - + +
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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
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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