Contacts of the strand formed by residues 285 - 289 (chain A) in PDB entry 6BM0
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 SER 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A PRO* 3.8 9.8 - - - +
282A ALA* 3.1 44.5 + - - +
284A ASN* 1.3 80.5 - - - +
286A LEU* 1.3 63.4 + - - +
287A LEU* 3.4 12.6 - - - +
298A VAL 3.3 13.5 - - - -
299A ALA* 4.0 3.4 - - - +
300A LEU* 4.1 5.2 - - - +
304A THR* 4.7 2.2 - - - -
312A LEU* 3.7 27.6 - - - -
322A LEU* 4.6 0.9 - - - +
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Residues in contact with LEU 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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279A VAL* 4.8 6.3 - - + -
280A VAL 4.0 5.8 - - - +
281A PHE* 3.6 35.7 - - + -
285A SER* 1.3 75.7 - - - +
287A LEU* 1.3 69.3 + - - +
297A GLY* 3.3 0.9 - - - -
298A VAL* 2.7 42.9 + - + +
300A LEU* 4.1 16.4 - - + -
322A LEU* 4.4 4.7 - - + -
347A LEU* 3.7 11.9 - - + -
360A PHE* 3.7 27.4 - - + -
362A PHE* 3.6 34.3 - - + -
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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
----------------------------------------------------------
261A LEU* 3.9 28.0 - - + -
262A PRO* 4.1 15.5 - - + -
265A CYS* 5.7 0.2 - - - -
279A VAL* 3.3 9.7 - - - +
280A VAL* 3.1 45.3 + - + +
282A ALA* 4.8 3.4 - - + -
285A SER* 3.4 26.5 - - - +
286A LEU* 1.3 79.0 - - - +
288A TYR* 1.3 60.4 + - - +
289A LEU* 4.0 16.4 - - + -
296A TYR 3.6 4.0 - - - +
297A GLY* 4.2 3.8 - - - -
310A PHE* 3.7 33.2 - - + -
312A LEU* 4.4 5.4 - - + -
360A PHE* 4.5 3.8 - - - -
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Residues in contact with TYR 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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271A VAL* 3.6 19.5 - - + -
275A ILE* 3.4 11.2 - - + +
276A GLY 2.3 35.4 + - - -
277A GLY* 3.8 5.4 - - - -
278A VAL 3.4 14.6 - - - -
279A VAL* 3.6 14.1 - - + -
287A LEU* 1.3 74.3 - - - +
289A LEU* 1.3 64.8 + - - +
290A ASN* 4.0 25.4 + - + -
293A VAL* 5.3 10.1 - - + -
294A PRO 4.9 1.1 - - - +
295A PRO* 4.1 0.9 - - - +
296A TYR* 2.7 44.3 + - + +
349A LEU* 5.0 4.3 - - + -
355A ARG 5.3 0.7 + - - -
356A SER* 5.5 1.1 - - - -
357A VAL* 3.6 38.4 - - + -
360A PHE* 3.7 21.2 - - + -
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Residues in contact with LEU 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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240A ILE* 3.7 27.1 - - + -
256A TRP* 3.6 10.7 - - + -
258A LEU* 3.7 19.1 - - + -
261A LEU* 4.0 15.0 - - + -
277A GLY* 3.5 3.1 - - - -
278A VAL* 2.8 46.7 + - + +
280A VAL* 3.9 15.7 - - + -
287A LEU* 4.0 19.5 - - + -
288A TYR* 1.3 84.2 - - - +
290A ASN* 1.3 60.9 + - - +
295A PRO* 3.7 29.4 - - + -
310A PHE* 5.2 0.7 - - + -
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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