Contacts of the strand formed by residues 458 - 466 (chain A) in PDB entry 5N4D
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 PHE 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ASN* 3.0 26.2 + - + -
453A LEU* 3.9 17.7 - - + -
454A ASP 3.5 22.7 - - - -
455A PRO* 3.1 15.8 + - + +
456A ASP* 3.1 1.1 - - - +
457A ASP* 1.3 86.7 - - + +
459A GLU* 1.3 60.7 + - - +
478A VAL* 4.7 4.3 - - + -
479A ARG 3.3 7.2 - - - +
480A HIS* 3.6 34.1 - + + -
481A LYS* 3.7 10.7 - - - -
512A LEU* 3.3 63.9 - - + -
515A LEU* 4.3 3.1 - - + -
516A GLN* 3.6 22.9 - - + -
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Residues in contact with GLU 459 (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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424A ASN* 4.2 2.0 - - - +
458A PHE* 1.3 76.0 - - - +
460A SER* 1.3 60.7 - - - +
461A THR* 3.5 27.0 + - - +
477A ILE 3.7 1.1 - - - +
478A VAL* 3.4 5.0 - - - +
479A ARG* 2.8 78.2 + - + +
481A LYS* 3.9 21.3 - - + +
485A PHE* 4.4 4.9 - - - -
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Residues in contact with SER 460 (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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402A VAL* 5.2 9.7 - - - +
423A PHE* 3.8 37.2 + - - +
424A ASN* 4.1 11.8 + - - +
459A GLU* 1.3 73.3 - - - +
461A THR* 1.3 71.4 + - - +
476A PHE* 5.5 3.0 - - - -
477A ILE 3.3 8.5 - - - -
478A VAL* 3.9 8.1 - - - -
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Residues in contact with THR 461 (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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459A GLU* 3.5 29.8 + - - +
460A SER* 1.3 79.9 - - - +
462A GLN* 1.3 63.0 + - - +
463A VAL* 4.2 10.2 - - - +
476A PHE* 3.3 9.7 - - - -
477A ILE* 2.9 42.4 + - - +
485A PHE* 5.1 6.5 - - + -
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Residues in contact with GLN 462 (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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379A ASN* 2.9 33.2 + - - +
380A VAL* 4.0 3.6 - - - +
381A LYS* 3.4 26.0 + - + +
461A THR* 1.3 76.9 - - - +
463A VAL* 1.3 68.0 + - - +
464A TRP* 4.4 15.1 + - - +
474A PRO* 3.7 30.5 - - + +
475A MET 3.4 11.4 - - - +
476A PHE* 3.5 28.1 - - + +
526A SER* 5.0 0.6 + - - -
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Residues in contact with VAL 463 (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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461A THR* 4.3 12.6 - - - +
462A GLN* 1.3 79.2 - - - +
464A TRP* 1.3 65.0 + - - +
473A ILE 3.9 0.2 - - - +
474A PRO* 3.2 3.1 - - - +
475A MET* 2.7 50.7 + - + +
477A ILE* 3.6 31.0 - - + -
559A PHE* 3.9 22.0 - - + -
565A TYR* 3.6 23.8 - - + +
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Residues in contact with TRP 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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379A ASN* 3.6 24.2 - - - -
462A GLN* 4.4 16.5 + - - +
463A VAL* 1.3 83.2 - - - +
465A TYR* 1.3 62.6 + - - +
472A LYS* 3.8 25.4 - - + -
473A ILE 3.4 11.7 - - - -
474A PRO* 3.4 48.9 - - + +
533A PHE* 3.9 16.4 - + - -
537A TRP* 6.1 0.2 - + - -
559A PHE* 3.8 15.5 - - - -
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Residues in contact with TYR 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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464A TRP* 1.3 75.3 - - - +
466A GLU* 1.3 73.3 + - - +
467A SER 4.6 0.4 - - - -
472A LYS* 3.3 9.3 - - - +
473A ILE* 2.9 75.6 + - + +
475A MET* 4.0 23.1 - - + -
525A PRO* 3.6 9.0 - - + +
527A ILE* 3.6 9.0 - - - +
552A ASP* 2.7 34.8 + - - +
555A ALA* 3.8 10.5 - - + -
556A ALA* 3.5 29.5 - - + +
559A PHE* 3.5 34.1 - + + -
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Residues in contact with GLU 466 (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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465A TYR* 1.3 84.7 - - - +
467A SER* 1.3 73.0 + - - +
468A LYS 5.5 0.2 - - - +
470A GLY* 3.4 30.1 + - - +
471A THR 3.5 2.7 - - - -
472A LYS* 2.9 31.0 + - - +
555A ALA* 3.9 6.6 - - - +
559A PHE* 5.3 0.6 - - - -
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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