Contacts of the strand formed by residues 463 - 469 (chain A) in PDB entry 4OE4
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 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A THR* 4.5 4.2 - - - +
344A PHE* 4.3 0.2 - - - -
355A SER* 3.9 20.3 - - - +
411A LEU* 3.6 29.8 - - + +
414A VAL* 3.6 27.1 - - + -
415A ILE* 4.1 18.4 - - + -
440A VAL* 5.3 1.6 - - + -
443A THR* 3.4 15.0 - - - +
445A ILE* 3.9 26.9 - - + -
459A PHE* 4.2 25.4 - - + +
461A GLY 2.8 13.7 + - - +
462A PRO* 1.3 82.8 - - + +
464A LEU* 1.3 63.9 + - - +
465A THR* 4.7 2.4 + - - +
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Residues in contact with LEU 464 (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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324A HIS* 6.5 0.2 - - + -
339A THR* 3.9 17.3 - - + -
343A THR* 3.7 24.2 - - + +
344A PHE* 4.2 5.2 - - + -
354A ALA* 4.6 1.6 - - + -
355A SER* 3.5 29.4 - - - +
356A ARG 3.8 14.1 - - - +
357A LEU* 3.9 28.0 - - + -
371A MET* 4.3 16.4 - - + -
443A THR 2.8 14.3 + - - +
444A VAL* 3.4 12.5 - - + +
445A ILE* 2.8 29.5 + - - +
462A PRO 4.2 0.2 - - - -
463A ILE* 1.3 73.5 - - - +
465A THR* 1.3 65.8 + - - +
466A VAL 4.0 0.2 + - - -
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Residues in contact with THR 465 (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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321A LYS* 4.5 0.5 + - - -
355A SER 2.9 13.1 + - - -
356A ARG* 3.3 4.2 - - - +
357A LEU* 2.9 25.1 + - - +
424A LEU* 5.1 0.7 - - + -
445A ILE* 3.1 12.1 - - + +
446A LYS 5.0 0.2 - - - -
447A ALA* 3.9 15.7 - - + +
454A TYR* 3.0 46.7 + - + +
455A MET* 3.4 23.3 - - - +
459A PHE* 4.3 9.2 - - - -
463A ILE* 4.7 3.6 + - - +
464A LEU* 1.3 74.6 - - - +
466A VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.4 35.7 - - + +
359A LEU* 3.9 21.8 - - + -
368A LEU* 4.8 4.0 - - + -
427A LEU* 4.1 11.7 - - + -
444A VAL* 3.9 22.9 - - + -
445A ILE 2.7 20.7 + - - +
446A LYS* 3.3 17.9 - - + +
447A ALA 2.8 31.5 + - - +
455A MET* 4.5 2.0 - - - -
464A LEU* 5.1 0.9 - - + -
465A THR* 1.3 75.0 - - - +
467A TYR* 1.3 67.3 + - - +
468A GLU* 4.3 6.1 - - + +
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Residues in contact with TYR 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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357A LEU 2.9 7.8 + - - +
358A TYR* 3.3 13.1 - + + +
359A LEU 3.0 22.5 + - - -
447A ALA 3.4 16.6 - - - +
448A LYS* 3.9 9.0 + - - -
449A ARG* 3.7 17.5 - - - +
450A PRO* 3.6 38.1 - - + +
455A MET* 3.8 24.6 - - + -
465A THR 4.3 0.4 + - - -
466A VAL* 1.3 75.6 - - - +
468A GLU* 1.3 84.0 + - - +
469A TYR* 3.8 9.5 + - + -
470A PRO* 4.9 5.5 - - - +
473A GLU* 5.7 0.5 + - - -
477A ILE* 3.8 27.6 - - + -
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Residues in contact with GLU 468 (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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359A LEU* 3.2 14.1 - - + +
361A GLU* 4.0 19.9 - - + +
364A SER* 3.5 28.6 + - - +
368A LEU* 3.4 27.2 - - - +
427A LEU* 4.8 0.2 - - - +
446A LYS* 3.3 42.3 + - + +
447A ALA 4.8 1.2 + - - -
466A VAL* 4.5 7.1 - - + +
467A TYR* 1.3 94.9 + - - +
469A TYR* 1.3 60.2 + - - +
470A PRO* 4.2 0.7 - - - +
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Residues in contact with TYR 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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325A LEU* 4.3 4.0 - - + -
326A VAL 2.6 25.1 + - - -
328A PRO* 3.6 11.0 - - + +
358A TYR* 3.9 16.2 - - + -
359A LEU 2.9 46.2 + - - -
360A PRO* 3.3 11.3 - - + +
361A GLU* 2.8 24.1 + - - -
467A TYR* 3.8 16.2 - + + -
468A GLU* 1.3 74.6 - - - +
470A PRO* 1.3 92.4 - - + +
471A ASP 4.1 4.7 - - - -
473A GLU* 4.1 6.7 - - + +
474A PHE* 3.4 47.3 - + + -
477A ILE* 4.0 17.3 - - + -
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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