Contacts of the strand formed by residues 291 - 296 (chain J) in PDB entry 6H25
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 ILE 291 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248J GLN* 4.4 14.1 - - - +
249J GLY* 3.4 8.7 - - - +
250J THR* 3.7 22.9 - - + -
290J ASP* 1.3 84.5 - - - +
292J VAL* 1.3 64.4 + - - +
348J ILE* 4.0 1.0 - - - +
349J ILE* 2.9 42.8 + - + +
350J LYS* 2.9 39.2 + - + +
352J ASN* 5.8 4.5 - - + +
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Residues in contact with VAL 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248J GLN* 3.2 6.9 - - - +
249J GLY 2.9 37.9 + - - +
251J PHE* 4.4 13.5 - - + -
263J VAL* 4.2 16.8 - - + -
286J ALA* 3.9 17.0 - - + -
290J ASP* 4.3 11.9 - - + -
291J ILE* 1.3 77.6 - - - +
293J ALA* 1.3 59.8 + - - +
294J VAL* 4.1 19.3 - - + -
345J VAL* 4.6 10.5 - - + -
347J GLY 3.9 9.2 - - - +
348J ILE* 3.8 24.5 - - + -
349J ILE* 4.0 5.1 - - - +
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Residues in contact with ALA 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237J LEU* 4.7 16.2 - - + -
241J ILE* 4.4 13.5 - - + -
246J TYR* 5.2 5.2 - - + -
247J LEU 3.7 5.8 - - - +
248J GLN* 4.1 0.4 - - - +
292J VAL* 1.3 76.6 - - - +
294J VAL* 1.3 63.7 + - - +
345J VAL* 3.9 2.4 - - - -
346J VAL* 3.4 27.6 + - + +
347J GLY 3.3 14.1 + - - +
349J ILE* 3.8 22.2 - - + +
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Residues in contact with VAL 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J TYR* 3.7 5.2 - - - -
247J LEU* 2.8 45.8 + - + +
263J VAL* 3.8 40.4 - - + -
265J ILE* 5.5 0.4 - - + -
275J ILE* 4.6 18.2 - - + -
277J LEU* 5.5 2.0 - - + -
292J VAL* 4.1 8.7 - - + -
293J ALA* 1.3 77.3 - - - +
295J GLU* 1.3 74.9 + - - +
343J GLY* 3.8 9.6 - - - -
344J ARG 3.5 19.3 - - - +
345J VAL* 4.5 7.6 - - + -
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Residues in contact with GLU 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J THR* 5.0 6.3 - - - +
246J TYR* 3.6 35.8 + - + -
293J ALA 4.1 1.0 + - - -
294J VAL* 1.3 74.5 - - - +
296J LEU* 1.3 74.4 + - - +
297J LEU* 5.3 0.4 - - - +
343J GLY* 3.3 2.4 - - - -
344J ARG* 2.7 71.4 + - + +
346J VAL* 3.4 13.2 - - + +
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Residues in contact with LEU 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J THR* 4.9 11.3 + - - +
247J LEU* 4.0 20.1 - - + +
273J LYS* 5.7 10.3 - - - +
275J ILE* 4.1 27.6 - - + -
294J VAL 4.2 0.4 + - - -
295J GLU* 1.3 91.5 - - - +
297J LEU* 1.3 71.8 + - - +
298J PRO* 4.6 1.4 - - - +
302J TRP* 5.6 11.4 - - + -
341J PRO* 6.0 2.0 - - + -
342J THR 4.1 9.6 - - - +
343J GLY* 4.4 0.4 - - - -
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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