Contacts of the strand formed by residues 285 - 291 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.5 28.0 - - + -
262A ALA* 3.7 24.2 - - + -
263A LEU 3.9 7.0 - - - +
264A LEU* 2.8 46.9 - - + +
280A CYS* 3.9 8.7 - - - -
284A VAL* 1.3 75.4 - - - +
286A HIS* 1.3 65.6 + - - +
323A PRO* 3.5 4.9 - - - +
324A VAL* 2.9 52.5 + - + +
325A VAL 5.4 1.3 - - - -
326A ALA* 5.8 0.4 - - - -
327A PHE* 4.6 8.3 - - - -
354A VAL* 3.5 23.5 - - + +
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU 3.8 0.4 - - - +
262A ALA* 3.4 3.6 - - - -
263A LEU* 2.8 47.1 + - - +
265A HIS 3.6 13.9 + - - -
266A SER* 5.0 0.7 - - - -
275A ALA* 3.4 28.4 - - + +
277A MET* 3.9 6.4 - - - -
278A GLY 3.5 21.9 + - - -
279A ARG* 5.3 1.1 - - - -
280A CYS* 3.2 26.8 + - - -
284A VAL* 6.3 0.7 - - + -
285A MET* 1.3 76.2 - - - +
287A LEU* 1.3 59.8 + - - +
288A PHE* 3.6 19.3 - - + -
321A TYR* 2.7 39.5 + + + -
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Residues in contact with LEU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.4 14.1 - - + -
212A TYR* 3.6 45.5 - - + -
260A VAL* 4.0 21.5 - - + -
261A LEU 3.4 16.2 - - - +
262A ALA* 4.2 12.1 - - + +
286A HIS* 1.3 74.6 - - - +
288A PHE* 1.3 65.2 + - - +
289A TYR* 4.9 5.4 - - + -
320A VAL 3.6 0.9 - - - +
321A TYR* 3.3 5.6 - - - -
322A VAL* 2.9 50.1 + - + +
324A VAL* 3.9 13.9 - - + -
327A PHE* 4.8 13.0 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 4.8 3.1 - - + -
260A VAL* 3.4 2.8 - - - +
261A LEU* 2.7 66.1 + - + +
263A LEU* 4.3 13.5 - - + -
274A ALA 3.4 22.7 - - - -
275A ALA* 4.1 4.3 - - + -
277A MET* 4.0 8.3 - - + -
286A HIS* 3.6 24.5 - + + -
287A LEU* 1.3 76.1 - - - +
289A TYR* 1.3 65.7 + - - +
312A MET* 4.0 17.7 - - - -
319A LEU* 4.3 10.5 - - + -
320A VAL 3.2 7.0 - - - +
321A TYR* 3.6 30.7 - + + -
1001A UUL 3.2 28.9 - - + -
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 3.6 17.7 - - + -
212A TYR* 4.5 12.7 + + - -
252A VAL* 3.5 35.4 - - + +
253A PRO* 5.6 0.5 - - - +
254A ASP* 4.1 3.8 + - - -
257A PHE* 3.3 22.2 - + + -
259A LEU* 3.2 13.0 - - - +
260A VAL* 3.8 16.8 - - + -
287A LEU* 4.9 7.9 - - + -
288A PHE* 1.3 78.1 - - - +
290A VAL* 1.3 64.2 + - - +
291A ARG* 4.1 16.7 - - + -
318A TYR 3.5 0.9 - - - +
319A LEU* 3.5 4.3 - - - +
320A VAL* 2.8 76.8 + - + +
322A VAL* 5.3 2.0 - - + -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PHE* 3.4 8.4 - - - +
258A VAL* 2.8 56.8 + - + -
259A LEU* 2.8 32.2 + - + -
289A TYR* 1.3 74.7 - - - +
291A ARG* 1.3 66.2 + - - +
294A VAL* 3.8 22.4 - - + -
299A LEU* 5.0 5.8 - - + -
302A LEU* 5.1 5.4 - - + -
318A TYR 3.1 9.9 - - - +
319A LEU* 3.6 24.7 - - + -
1001A UUL 5.0 6.5 - - + -
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ASP* 3.2 36.6 + - + +
256A ASP 3.8 7.4 - - - +
257A PHE* 4.5 4.0 - - - +
258A VAL* 3.8 3.2 - - - +
289A TYR* 4.1 16.2 - - + -
290A VAL* 1.3 86.5 - - - +
292A ALA* 1.3 71.5 + - - +
293A GLY 3.5 1.7 + - - -
294A VAL 4.1 1.2 + - - -
317A PRO 3.1 27.7 + - - -
318A TYR* 2.8 46.6 + - + +
320A VAL* 4.5 8.3 - - + -
315D GLU* 5.3 5.9 + - - -
317D PRO* 4.7 15.2 - - - +
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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