Contacts of the strand formed by residues 466 - 472 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLN* 2.8 32.3 + - + +
258A ILE* 3.6 25.2 - - + +
259A CYS* 5.0 2.2 - - - -
292A GLU* 3.4 25.6 - - + +
293A MET 3.3 15.3 - - - +
294A ALA* 3.7 7.6 - - - -
295A PHE* 3.4 9.5 - - - -
430A GLN* 3.5 3.7 - - - +
431A ARG* 2.9 40.7 + - + +
433A HIS* 4.0 11.2 + - + +
459A PHE* 3.6 25.5 - + - -
463A ALA* 5.3 0.4 - - + -
464A PRO 2.8 22.2 + - - -
465A PRO* 1.3 76.9 - - - +
467A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 467 (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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292A GLU* 3.1 10.7 - - - +
293A MET 2.7 35.3 + - - +
295A PHE* 3.8 7.5 - - + -
299A TYR* 4.2 6.3 - - + -
302A VAL* 3.6 20.8 - - + +
416A TYR* 3.7 11.0 - - - +
429A ALA 3.3 18.2 - - - +
430A GLN* 3.6 10.3 - - - +
431A ARG 4.3 0.2 - - - +
466A HIS* 1.3 74.9 - - - +
468A GLY* 1.3 56.1 + - - +
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Residues in contact with GLY 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE 3.1 13.9 - - - -
292A GLU* 3.5 3.3 + - - -
302A VAL* 4.1 1.3 - - - -
306A ILE* 3.8 13.7 - - - -
416A TYR* 2.9 20.5 + - - -
428A GLY* 3.2 15.1 - - - -
429A ALA 3.4 6.0 + - - -
431A ARG* 3.3 10.7 - - - +
467A ALA* 1.3 78.1 - - - +
469A GLY* 1.3 56.5 + - - -
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Residues in contact with GLY 469 (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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254A LYS* 4.1 1.3 - - - +
290A ASP* 4.1 5.6 - - - -
291A ILE* 2.9 35.3 + - - +
306A ILE* 4.5 0.6 - - - +
426A LEU* 4.1 15.6 - - - +
427A SER 4.6 3.1 - - - -
428A GLY* 4.3 11.9 - - - -
431A ARG* 3.3 10.9 - - - +
468A GLY* 1.3 73.5 - - - -
470A GLY* 1.3 57.8 + - - -
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Residues in contact with GLY 470 (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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289A LEU 3.3 12.8 - - - -
290A ASP* 3.7 14.2 + - - -
425A ILE 3.2 13.3 - - - +
426A LEU* 3.5 15.8 - - - +
427A SER 4.4 3.5 + - - +
469A GLY* 1.3 74.9 - - - -
471A ILE* 1.3 63.8 + - - -
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Residues in contact with ILE 471 (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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202A ILE* 5.3 4.0 - - + -
206A PHE* 4.8 6.7 - - + -
286A PHE* 4.6 3.0 - - - -
288A GLY* 3.1 6.8 - - - -
289A LEU* 2.8 61.6 + - + +
310A MET* 4.1 23.6 - - + -
313A ILE* 5.3 3.4 - - + -
425A ILE* 3.5 34.1 - - + +
426A LEU* 4.2 11.7 - - + -
470A GLY* 1.3 77.1 - - - +
472A GLY* 1.3 62.4 + - - +
473A LEU* 5.4 1.3 - - - -
476A VAL* 3.8 26.0 - - + -
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Residues in contact with GLY 472 (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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286A PHE* 3.8 19.2 - - - -
287A VAL 3.2 7.9 - - - -
425A ILE* 4.5 2.8 + - - +
471A ILE* 1.3 75.9 - - - +
473A LEU* 1.3 66.2 + - - -
474A GLU* 3.4 2.5 - - - -
475A ARG* 3.4 15.5 + - - +
476A VAL* 3.0 25.0 + - - +
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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