Contacts of the strand formed by residues 289 - 294 (chain C) in PDB entry 3V4P
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 ASP 289 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C PHE* 3.9 1.7 - - - -
279C ALA* 3.5 4.0 - - - -
280C VAL* 2.9 38.5 + - - +
281C ASP* 4.1 1.2 - - - +
282C LEU* 3.4 40.8 + - + +
283C ASN* 3.7 12.9 + - - +
285C ASP* 5.5 0.2 - - - +
287C PHE 4.3 0.6 - - - -
288C SER* 1.3 77.5 + - - +
290C LEU* 1.3 65.7 + - - +
309C TYR 3.3 6.7 - - - +
310C ILE* 2.9 22.2 - - - +
311C ASN* 2.4 34.7 + - - +
318C MET* 4.2 1.6 - - - -
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Residues in contact with LEU 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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227C PHE* 3.9 3.6 - - + -
236C VAL* 3.5 45.8 - - + -
248C ALA* 5.5 0.2 - - + -
250C ILE* 3.6 26.2 - - + -
264C MET* 4.4 10.3 - - + -
277C VAL* 4.7 1.6 - - + -
278C CYS 3.5 10.5 - - - +
289C ASP* 1.3 81.1 - - - +
291C LEU* 1.3 79.5 + - - +
292C VAL* 3.5 22.4 - - + -
309C TYR* 2.9 43.0 + - + +
318C MET* 4.0 9.9 - - + -
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Residues in contact with LEU 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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277C VAL* 3.3 4.7 - - - -
278C CYS* 2.9 46.8 + - + +
280C VAL* 4.0 23.8 - - + -
282C LEU* 4.2 13.5 - - + -
290C LEU* 1.3 80.5 - - - +
292C VAL* 1.3 63.4 + - - +
306C VAL* 4.3 15.5 - - + -
307C PHE 3.4 2.9 - - - +
308C VAL* 3.5 44.9 - - + -
325C LEU* 5.2 6.7 - - + -
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Residues in contact with VAL 292 (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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248C ALA* 4.1 12.1 - - + -
264C MET* 5.2 1.3 - - - -
273C PHE* 3.5 36.6 - - + -
274C GLY* 3.4 33.4 - - - +
276C SER 3.5 5.2 - - - +
277C VAL* 4.4 1.8 - - + -
290C LEU* 3.5 23.8 - - + -
291C LEU* 1.3 74.1 - - - +
293C GLY* 1.3 63.9 + - - +
306C VAL* 3.2 9.4 - - - +
307C PHE* 2.9 31.7 + - + +
309C TYR* 3.8 14.1 - - + -
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Residues in contact with GLY 293 (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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272C TYR 3.4 0.2 - - - +
273C PHE* 5.3 0.9 - - - -
274C GLY 3.1 22.4 + - - -
275C ALA 3.3 10.2 + - - -
276C SER* 2.9 25.6 + - - -
292C VAL* 1.3 76.6 - - - +
294C ALA* 1.3 59.3 + - - -
295C PRO* 3.5 7.6 - - - +
305C ARG 3.5 6.7 - - - -
306C VAL* 4.0 9.0 - - - -
307C PHE* 5.4 0.2 - - - -
335C PHE 5.8 0.4 - - - -
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Residues in contact with ALA 294 (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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271C SER* 3.1 34.1 - - - +
272C TYR 3.7 1.3 - - - -
273C PHE* 3.7 11.0 - - - -
293C GLY* 1.3 74.9 - - - +
295C PRO* 1.3 59.2 - - - +
296C MET 3.1 4.7 - - - -
297C GLN* 3.0 26.6 + - - +
305C ARG 2.8 26.4 + - - +
307C PHE* 4.2 10.0 - - + -
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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