Contacts of the strand formed by residues 343 - 350 (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 GLY 343 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275J ILE* 3.4 14.5 - - - +
276J ILE 3.3 7.9 + - - -
277J LEU* 3.5 20.6 - - - +
282J HIS* 4.2 5.5 - - - +
294J VAL* 3.8 6.3 - - - -
295J GLU 3.3 12.6 - - - -
296J LEU* 4.4 1.6 - - - -
297J LEU* 3.9 12.2 - - - +
342J THR* 1.3 75.1 - - - +
344J ARG* 1.3 62.7 + - - +
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Residues in contact with ARG 344 (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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229J SER* 4.8 15.6 + - - -
277J LEU* 4.6 1.6 - - - -
281J LYS 4.5 5.8 - - - +
282J HIS* 3.5 44.4 - - + +
294J VAL* 3.5 5.4 - - - +
295J GLU* 2.7 71.4 + - + +
297J LEU* 4.4 13.9 - - + +
343J GLY* 1.3 75.4 - - - +
345J VAL* 1.3 71.0 + - - +
346J VAL* 3.5 17.8 + - - +
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Residues in contact with VAL 345 (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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229J SER* 4.7 0.5 + - - -
251J PHE* 4.9 10.1 - - + -
277J LEU* 3.7 22.9 - - + +
281J LYS 5.4 0.3 - - - +
282J HIS 3.3 13.8 + - - +
283J LEU* 5.2 0.2 - - - -
284J ASN* 3.4 39.2 - - + +
286J ALA* 5.1 2.9 - - + -
292J VAL* 4.6 13.9 - - + -
293J ALA 3.9 4.9 - - - +
294J VAL* 4.5 13.2 - - + +
344J ARG* 1.3 82.2 + - - +
346J VAL* 1.3 65.5 + - - +
347J GLY 3.6 21.5 - - - +
348J ILE* 4.2 14.1 - - + -
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Residues in contact with VAL 346 (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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230J GLU 3.7 12.8 - - - +
231J HIS* 3.8 3.8 - - - -
232J LEU* 3.6 27.1 + - + +
237J LEU* 4.5 9.2 - - + -
246J TYR* 4.1 33.4 - - + +
284J ASN* 4.6 3.1 - - - -
293J ALA* 3.4 12.9 + - + +
295J GLU* 3.4 29.4 - - + +
344J ARG* 3.5 31.4 - - - +
345J VAL* 1.3 76.4 - - - +
347J GLY* 1.3 59.8 + - - +
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Residues in contact with GLY 347 (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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231J HIS* 4.4 6.5 + - - -
232J LEU 4.8 3.1 - - - -
237J LEU* 3.9 22.4 - - - -
292J VAL* 3.9 0.3 - - - +
293J ALA* 3.3 24.0 + - - -
345J VAL* 3.6 7.3 - - - +
346J VAL* 1.3 85.7 - - - +
348J ILE* 1.3 72.2 + - - +
349J ILE 4.1 0.4 - - - -
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Residues in contact with ILE 348 (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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231J HIS* 4.0 20.2 + - + +
232J LEU 5.2 1.9 + - - +
234J LEU* 5.2 4.9 - - - +
237J LEU* 4.2 8.9 - - - +
284J ASN 4.4 5.2 - - - +
286J ALA* 3.8 29.4 - - + -
290J ASP* 5.5 1.6 - - + -
291J ILE 4.3 4.5 - - - +
292J VAL* 3.8 9.0 - - + -
345J VAL* 4.2 8.3 - - + -
347J GLY* 1.3 84.1 - - - +
349J ILE* 1.3 66.1 + - - +
350J LYS 4.4 3.1 - - - +
351J ARG* 3.5 55.9 - - + +
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Residues in contact with ILE 349 (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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234J LEU* 5.2 18.1 - - + +
237J LEU* 4.8 11.9 - - + -
238J GLN* 6.2 0.9 - - + +
241J ILE* 3.8 11.2 - - + -
248J GLN* 3.4 41.3 - - + +
291J ILE* 2.9 27.1 + - + +
292J VAL 4.0 3.8 - - - +
293J ALA* 3.8 23.6 - - + -
347J GLY 4.1 0.4 + - - -
348J ILE* 1.3 77.6 - - - +
350J LYS* 1.3 61.8 + - + +
351J ARG 4.2 0.4 - - - -
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Residues in contact with LYS 350 (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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168A GLN* 5.2 10.9 + - - +
171A GLU* 5.1 16.6 + - - +
290J ASP* 3.7 2.8 - - - +
291J ILE* 2.9 56.4 + - + +
348J ILE* 4.5 2.2 - - - -
349J ILE* 1.3 79.6 - - + +
351J ARG* 1.3 78.5 + - - +
352J ASN* 3.6 20.1 + - + +
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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
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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