Contacts of the strand formed by residues 247 - 253 (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 LEU 247 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241J ILE* 4.5 4.3 - - - -
244J GLY 5.7 0.2 - - - +
245J THR 3.6 13.2 - - - +
246J TYR* 1.3 76.0 - - - +
248J GLN* 1.3 61.5 + - - +
265J ILE* 3.7 41.5 - - + +
273J LYS* 5.6 9.0 - - + +
275J ILE* 4.3 11.2 - - + -
293J ALA* 4.4 1.8 - - - -
294J VAL* 2.8 55.9 + - + +
296J LEU* 4.0 28.9 - - + +
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Residues in contact with GLN 248 (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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241J ILE* 4.0 20.9 - - + +
247J LEU* 1.3 74.5 - - - +
249J GLY* 1.3 61.5 + - - +
263J VAL* 5.3 0.2 - - - -
264J TRP 4.3 0.2 - - - +
265J ILE* 3.3 23.8 - - - +
266J HIS 5.2 1.2 + - - -
291J ILE* 4.4 11.6 - - + +
292J VAL 3.2 13.7 - - - +
293J ALA* 4.1 1.1 - - - +
349J ILE* 3.4 30.1 - - + +
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Residues in contact with GLY 249 (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* 1.3 80.0 - - - +
250J THR* 1.3 66.0 + - - -
263J VAL* 4.3 7.7 - - - +
264J TRP 3.3 14.6 - - - -
265J ILE* 5.1 0.9 - - - -
266J HIS 5.7 0.9 - - - -
291J ILE* 3.4 11.1 - - - +
292J VAL* 2.9 30.6 + - - +
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Residues in contact with THR 250 (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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249J GLY* 1.3 74.6 - - - -
251J PHE* 1.3 65.8 + - - +
252J ARG* 5.2 0.5 - - - +
263J VAL* 3.3 8.9 - - - +
264J TRP* 3.1 49.7 + - - +
289J GLU* 6.3 0.4 - - - -
290J ASP 3.3 7.4 - - - +
291J ILE* 3.7 22.2 - - + -
292J VAL* 4.8 0.4 - - - -
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Residues in contact with PHE 251 (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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249J GLY 4.2 0.2 + - - -
250J THR* 1.3 79.1 + - - +
252J ARG* 1.3 71.5 + - - +
253J ALA* 4.2 15.3 - - + -
261J ALA* 3.6 16.4 - - + -
262J THR 3.9 1.6 - - - -
263J VAL* 4.0 15.9 - - + -
277J LEU* 4.4 9.4 - - + -
283J LEU* 3.6 33.2 - - + -
286J ALA* 3.5 31.6 - - + -
287J VAL 3.3 15.5 - - - +
288J HIS* 2.9 39.9 + - - +
289J GLU* 4.3 4.3 - - - -
290J ASP 3.4 11.5 + - - +
292J VAL* 4.4 19.0 - - + +
345J VAL* 4.9 4.5 - - + -
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Residues in contact with ARG 252 (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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250J THR* 5.2 1.6 - - - +
251J PHE* 1.3 82.5 - - - +
253J ALA* 1.3 67.9 + - - +
261J ALA* 3.4 2.6 - - - +
262J THR* 2.9 54.8 + - - +
264J TRP* 5.0 15.0 - - + +
288J HIS* 4.1 10.8 - - + +
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Residues in contact with ALA 253 (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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251J PHE* 4.2 12.3 - - + -
252J ARG* 1.3 80.1 - - - +
254J SER* 1.3 65.0 + - - +
258J TYR* 6.2 2.7 - - - -
260J GLU 4.6 1.6 - - - +
261J ALA* 4.3 10.1 - - + -
262J THR* 5.6 0.2 + - - -
288J HIS* 3.4 32.7 + - + -
379J ARG* 3.9 24.3 + - + +
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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