Contacts of the strand formed by residues 466 - 472 (chain B) in PDB entry 4J15
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 HIS 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B GLN* 2.7 33.9 + - + +
258B ILE* 3.6 21.9 - - + +
259B CYS* 5.2 2.2 - - - -
292B GLU* 3.4 25.8 - - + -
293B MET 3.2 17.3 - - - +
294B ALA* 3.6 9.0 - - - +
295B PHE* 3.5 7.2 - - - -
430B GLN* 3.5 3.5 + - - +
431B ARG* 2.8 47.7 + - + +
433B HIS* 3.9 11.4 - - + +
459B PHE* 3.6 24.2 - + - -
463B ALA* 5.3 0.2 - - + -
464B PRO 2.8 23.0 + - - -
465B PRO* 1.3 74.8 - - - +
467B ALA* 1.3 55.1 + - - +
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Residues in contact with ALA 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B GLU* 3.4 9.7 - - - +
293B MET 2.7 35.3 + - - +
295B PHE* 3.9 5.8 - - + -
299B TYR* 4.2 7.0 - - + +
302B VAL* 3.6 25.6 - - + +
416B TYR* 3.6 9.9 - - - +
429B ALA 3.3 17.0 - - - +
430B GLN* 3.8 9.0 - - - +
431B ARG* 4.4 0.2 - - - +
466B HIS* 1.3 75.1 - - - +
468B GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE 3.2 16.2 - - - -
292B GLU* 3.6 1.3 - - - -
302B VAL* 4.3 0.9 - - - -
306B ILE* 3.8 12.3 - - - -
416B TYR* 2.8 20.7 + - - -
428B GLY* 3.2 14.2 - - - -
429B ALA 3.4 4.7 + - - -
431B ARG* 3.1 14.3 + - - +
467B ALA* 1.3 77.9 - - - +
469B GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LYS* 4.9 0.7 - - - -
290B ASP* 4.5 3.1 - - - -
291B ILE* 3.1 33.0 + - - +
306B ILE* 4.0 2.5 - - - +
426B LEU* 3.7 23.2 - - - +
427B SER 4.3 3.4 - - - -
428B GLY* 4.2 8.5 - - - -
431B ARG* 3.4 8.1 - - - +
468B GLY* 1.3 74.1 - - - -
470B GLY* 1.3 58.5 + - - -
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Residues in contact with GLY 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU 3.3 11.7 - - - -
290B ASP* 4.1 15.4 + - - -
425B ILE 3.2 12.5 - - - +
426B LEU* 3.5 14.1 - - - +
427B SER 4.3 4.3 + - - -
469B GLY* 1.3 73.3 - - - -
471B ILE* 1.3 63.2 + - - -
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 5.5 2.5 - - + -
206B PHE* 4.6 9.0 - - + -
286B PHE* 4.6 3.0 - - - -
288B GLY* 3.4 5.4 - - - -
289B LEU* 2.9 66.7 + - + +
290B ASP* 5.5 0.2 - - - +
310B MET* 4.0 33.7 - - + -
313B ILE* 5.0 3.1 - - + -
425B ILE* 3.4 26.7 - - + +
426B LEU* 4.2 10.8 - - + -
470B GLY* 1.3 76.0 - - - +
472B GLY* 1.3 61.3 + - - +
473B LEU* 5.6 0.9 - - - -
476B VAL* 3.8 20.6 - - + -
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Residues in contact with GLY 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B PHE* 3.8 21.7 - - - -
287B VAL 3.4 7.4 - - - -
425B ILE* 4.2 4.4 + - - +
471B ILE* 1.3 73.5 - - - +
473B LEU* 1.3 65.1 + - - -
474B GLU 3.4 2.2 - - - -
475B ARG* 3.4 13.5 + - - +
476B VAL* 3.0 27.4 + - - +
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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