Contacts of the strand formed by residues 285 - 291 (chain C) in PDB entry 3VZD
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C LEU* 3.8 25.8 - - + -
262C ALA* 4.1 13.0 - - - -
263C LEU 3.9 1.8 - - - +
264C LEU* 3.8 24.7 - - + -
280C CYS* 4.0 6.1 - - - -
284C VAL* 1.3 77.6 - - - +
286C HIS* 1.3 67.8 + - - +
323C PRO* 3.5 3.5 - - - +
324C VAL* 2.8 55.1 + - + +
325C VAL 4.1 9.6 - - - +
326C ALA* 4.1 1.6 - - - +
327C PHE* 3.6 30.3 - - + -
352C GLY 4.4 0.2 - - - +
354C VAL* 3.4 27.8 - - + +
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU 3.5 0.3 - - - +
262C ALA* 3.0 8.3 - - - +
263C LEU* 2.8 50.3 + - + +
265C HIS 3.5 14.4 + - - -
266C SER* 5.0 0.7 - - - -
275C ALA* 3.3 27.9 - - + +
277C MET* 3.7 12.1 - - - +
278C GLY 3.8 15.9 + - - -
279C ARG* 5.6 0.2 - - - -
280C CYS* 3.3 26.2 - - - -
284C VAL* 5.9 1.3 - - + -
285C MET* 1.3 73.0 - - - +
287C LEU* 1.3 59.7 + - - +
288C PHE* 3.9 13.0 - - + -
321C TYR* 2.6 42.3 + + + -
322C VAL 4.3 0.9 - - - -
323C PRO* 5.5 0.9 - - + -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C LEU* 4.1 15.9 - - + -
212C TYR* 3.5 47.1 - - + -
260C VAL* 3.7 29.6 - - + -
261C LEU 3.3 11.0 - - - +
262C ALA* 4.4 10.1 - - + -
285C MET 3.8 0.4 + - - -
286C HIS* 1.3 72.6 - - - +
288C PHE* 1.3 64.7 + - - +
289C TYR* 4.7 6.0 - - + -
320C VAL 3.9 0.3 - - - +
321C TYR* 3.5 5.4 - - - -
322C VAL* 3.0 45.3 + - + +
324C VAL* 3.8 12.3 - - + -
327C PHE* 4.7 11.7 - - + -
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Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU* 4.7 3.8 - - + -
260C VAL* 3.7 3.1 - - - +
261C LEU* 2.8 54.8 + - + +
263C LEU* 4.5 10.8 - - + -
274C ALA* 3.4 23.1 - - + -
275C ALA* 4.2 7.2 - - + -
277C MET* 3.8 14.6 - - + -
286C HIS* 3.9 20.4 - - + -
287C LEU* 1.3 75.3 - - - +
289C TYR* 1.3 66.6 + - - +
312C MET* 4.0 11.9 - - - -
319C LEU* 4.2 13.5 - - + -
320C VAL 3.3 6.3 - - - +
321C TYR* 3.6 30.1 - + + -
401C UUL 3.1 30.3 - - + -
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Residues in contact with TYR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C LEU* 3.4 27.4 - - + -
212C TYR* 4.3 12.3 + + - -
252C VAL* 3.3 36.1 - - + +
253C PRO* 5.3 1.2 - - - +
257C PHE* 3.9 14.1 - + + -
259C LEU* 3.2 15.5 - - - +
260C VAL* 3.9 13.2 - - + -
287C LEU* 4.7 7.6 - - + -
288C PHE* 1.3 78.1 - - - +
290C VAL* 1.3 63.3 + - - +
291C ARG* 4.0 21.0 - - + -
318C TYR 3.3 1.2 - - - +
319C LEU* 3.6 4.2 - - - +
320C VAL* 3.0 74.6 + - + +
322C VAL* 5.7 0.9 - - + -
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C PHE* 3.4 5.9 - - - +
258C VAL* 2.7 48.8 + - + -
259C LEU* 3.1 31.2 + - + -
289C TYR* 1.3 79.8 - - - +
291C ARG* 1.3 55.7 + - - +
294C VAL* 3.1 36.3 - - + -
299C LEU* 4.6 11.2 - - + -
302C LEU* 5.4 2.9 - - + -
316C CYS* 5.8 0.4 - - - -
318C TYR* 3.2 9.2 - - + +
319C LEU* 3.8 22.4 - - + +
401C UUL 5.0 5.4 - - + -
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C VAL* 5.9 0.2 - - - -
253C PRO* 6.4 0.4 - - - -
254C ASP* 2.7 41.6 + - + +
256C ASP 3.7 4.9 - - - -
257C PHE* 4.4 2.9 - - + +
258C VAL* 3.7 0.6 - - - +
289C TYR* 4.0 22.9 - - + -
290C VAL* 1.3 73.7 - - - +
292C ALA* 1.3 69.4 + - - +
293C GLY 3.4 2.1 + - - -
294C VAL* 3.5 17.2 - - - +
317C PRO* 3.5 34.3 + - - +
318C TYR* 2.8 49.0 + - + +
320C VAL* 4.9 4.1 - - + +
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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
------------------------------------------------------------
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