Contacts of the strand formed by residues 285 - 291 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 3.6 21.3 - - + -
262F ALA* 3.3 30.7 - - + -
263F LEU 3.8 9.6 - - - +
264F LEU* 2.9 42.4 - - + +
280F CYS* 4.2 2.2 - - - -
284F VAL* 1.3 77.7 - - - +
286F HIS* 1.3 65.0 + - - +
287F LEU 3.5 0.5 + - - -
323F PRO* 3.8 0.3 - - - +
324F VAL* 2.9 51.4 + - + +
325F VAL 5.1 1.6 - - - +
327F PHE* 4.4 16.2 - - - -
353F GLN* 5.8 0.2 - - - -
354F VAL* 3.4 27.3 - - + +
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Residues in contact with HIS 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F LEU 4.4 0.2 - - - -
262F ALA* 3.4 3.5 - - - -
263F LEU* 2.8 42.4 + - - +
265F HIS 3.4 19.1 + - - -
266F SER* 4.8 0.4 - - - -
275F ALA* 3.2 33.4 - - + +
277F MET* 4.4 1.6 - - - -
278F GLY 3.7 20.7 + - - -
279F ARG* 5.3 1.1 - - - -
280F CYS* 3.2 29.6 + - - -
284F VAL* 5.5 3.6 - - + -
285F MET* 1.3 75.1 - - - +
287F LEU* 1.3 58.1 + - - +
288F PHE* 3.6 20.3 - - + -
321F TYR* 2.9 31.9 + + + -
322F VAL 3.9 4.0 - - - -
323F PRO* 4.9 0.9 - - + -
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Residues in contact with LEU 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU* 4.6 14.4 - - + -
212F TYR* 3.6 44.4 - - + -
260F VAL* 4.1 20.0 - - + -
261F LEU 3.5 9.6 - - - +
262F ALA* 4.3 9.4 - - + +
285F MET 3.5 0.2 + - - -
286F HIS* 1.3 73.0 - - - +
288F PHE* 1.3 77.2 + - - +
289F TYR* 4.9 4.8 - - + -
320F VAL 3.9 0.3 - - - +
321F TYR* 3.4 3.3 - - - -
322F VAL* 2.8 48.6 + - + +
324F VAL* 3.8 20.6 - - + -
327F PHE* 4.8 9.0 - - + -
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Residues in contact with PHE 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F LEU* 5.3 3.1 - - + -
261F LEU* 2.9 52.6 + - + +
263F LEU* 4.4 10.5 - - + -
274F ALA 3.0 28.7 - - - -
275F ALA* 3.9 15.7 - - + -
277F MET* 4.4 2.0 - - + -
286F HIS* 3.6 23.8 - + + -
287F LEU* 1.3 85.3 - - - +
289F TYR* 1.3 68.6 + - - +
312F MET* 4.0 18.2 - - - -
319F LEU* 4.3 12.6 - - + -
320F VAL 3.2 5.8 - - - +
321F TYR* 3.7 27.6 - + + -
1001F UUL 3.3 21.8 - - + -
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Residues in contact with TYR 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LEU* 3.6 23.1 - - + -
212F TYR* 4.6 10.8 + + - -
252F VAL* 3.3 28.0 - - + +
254F ASP* 5.1 0.2 + - - -
257F PHE* 3.6 21.1 - + + -
259F LEU* 3.3 18.4 - - - +
260F VAL* 4.1 11.4 - - + -
287F LEU* 4.9 7.0 - - + -
288F PHE* 1.3 80.3 - - - +
290F VAL* 1.3 63.8 + - - +
291F ARG* 3.3 32.6 - - + -
318F TYR 3.4 1.0 - - - +
319F LEU* 3.5 3.0 - - - +
320F VAL* 2.7 73.7 + - + +
322F VAL* 5.2 1.1 - - + -
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Residues in contact with VAL 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F PHE* 3.7 5.4 - - - +
258F VAL* 3.0 39.3 + - + -
259F LEU* 3.0 39.7 + - + +
289F TYR* 1.3 77.4 - - - +
291F ARG* 1.3 58.9 + - - +
294F VAL* 3.3 35.0 - - + -
299F LEU* 4.9 4.7 - - + -
302F LEU* 5.1 9.2 - - + -
318F TYR* 3.4 9.4 - - + +
319F LEU* 3.7 24.9 - - + +
1001F UUL 5.9 2.5 - - + -
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Residues in contact with ARG 291 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254F ASP* 2.9 37.7 + - + +
256F ASP 4.3 7.2 - - - +
257F PHE* 4.7 1.6 - - - -
258F VAL* 3.5 9.5 - - - +
289F TYR* 3.3 29.8 - - + -
290F VAL* 1.3 76.2 - - - +
292F ALA* 1.3 69.4 + - - +
294F VAL* 3.5 12.6 - - - +
317F PRO* 2.5 37.2 + - - +
318F TYR* 3.1 28.0 + - + +
320F VAL* 3.5 20.1 - - - +
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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