Contacts of the strand formed by residues 472 - 480 (chain B) 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 LYS 472 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464B TRP* 3.9 29.8 - - + -
465B TYR 3.4 11.4 - - - +
466B GLU* 2.8 34.8 + - + +
470B GLY 3.4 10.9 + - - +
471B THR* 1.3 75.7 - - - +
473B ILE* 1.3 63.8 + - - +
537B TRP* 3.7 11.6 - - - -
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Residues in contact with ILE 473 (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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464B TRP* 3.4 4.1 - - - -
465B TYR* 2.9 69.6 + - + +
467B SER* 4.3 1.3 - - - -
471B THR* 3.8 20.6 - - + +
472B LYS* 1.3 76.3 - - - +
474B PRO* 1.3 73.8 - - + +
526B SER 3.3 27.1 - - - +
527B ILE* 4.2 1.8 - - - +
528B ARG* 4.3 0.9 - - - +
537B TRP* 3.4 28.7 - - + -
552B ASP* 3.7 28.7 - - - +
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Residues in contact with PRO 474 (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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380B VAL* 4.2 3.8 - - + -
462B GLN* 3.6 25.4 - - + +
463B VAL 3.2 6.7 - - - +
464B TRP* 3.5 28.0 - - + -
472B LYS 4.3 0.7 - - - +
473B ILE* 1.3 93.1 - - + +
475B MET* 1.3 56.7 + - - +
526B SER* 2.8 51.0 + - - +
533B PHE* 3.7 29.8 - - + -
537B TRP* 4.6 1.3 - - + -
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Residues in contact with MET 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLN* 3.3 4.9 - - - -
463B VAL* 2.7 40.3 + - + +
465B TYR* 3.9 16.8 - - + -
474B PRO* 1.3 75.9 - - - +
476B PHE* 1.4 78.2 + - - +
477B ILE* 3.7 6.9 + - + -
493B GLN* 5.0 0.4 - - - +
523B ALA* 3.9 19.3 - - - -
524B VAL 3.6 4.7 - - - +
525B PRO* 3.7 29.6 - - + -
526B SER* 5.1 0.2 - - - -
556B ALA* 3.9 14.1 - - - +
559B PHE* 3.7 33.4 - - + -
560B LEU* 3.8 18.6 - - + -
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Residues in contact with PHE 476 (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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380B VAL* 3.6 41.5 - - + -
381B LYS* 4.1 16.2 - - + -
402B VAL* 6.2 1.3 - - + -
423B PHE* 3.4 37.9 - + + -
460B SER* 5.6 3.6 - - - -
461B THR 3.3 11.4 - - - +
462B GLN* 3.6 31.9 - - + -
475B MET* 1.4 76.5 - - - +
477B ILE* 1.3 58.8 + - - +
478B VAL* 5.2 0.4 - - + -
503B ALA 3.9 8.7 - - - -
505B PRO* 3.8 21.1 - - + -
522B PHE 4.3 1.3 - - - -
523B ALA* 3.3 5.5 - - - -
524B VAL* 2.9 45.0 + - + +
526B SER* 4.8 4.3 - - - -
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Residues in contact with ILE 477 (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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459B GLU* 3.7 1.6 - - - +
460B SER* 3.3 2.6 - - - -
461B THR* 2.8 41.6 + - - +
463B VAL* 3.9 27.4 - - + -
475B MET* 3.8 15.7 - - + +
476B PHE* 1.3 82.4 - - - +
478B VAL* 1.3 63.5 + - - +
479B ARG* 5.6 0.5 - - - +
485B PHE* 3.9 31.5 - - + -
521B ILE* 4.1 17.7 - - + -
522B PHE 3.3 4.0 - - - +
523B ALA* 3.9 7.4 - - + -
560B LEU* 3.6 29.2 - - + -
565B TYR* 4.6 6.1 - - + -
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Residues in contact with VAL 478 (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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423B PHE* 3.4 52.3 - - + +
424B ASN* 6.2 0.4 - - + -
458B PHE* 4.6 4.3 - - + -
459B GLU 3.3 12.8 - - - +
460B SER* 3.9 3.4 - - - -
476B PHE* 5.2 0.4 - - + -
477B ILE* 1.3 78.4 - - - +
479B ARG* 1.3 67.2 + - - +
511B ILE* 6.4 0.2 - - + -
512B LEU* 4.0 18.4 - - + -
515B LEU* 3.6 15.6 - - + +
521B ILE* 3.3 7.6 - - - +
522B PHE* 2.8 52.8 + - + +
524B VAL* 5.8 0.2 - - + -
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Residues in contact with ARG 479 (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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458B PHE* 3.3 8.7 - - - +
459B GLU* 2.9 70.9 + - + +
477B ILE 5.6 0.4 - - - +
478B VAL* 1.3 76.9 - - - +
480B HIS* 1.3 68.8 + - - +
481B LYS* 5.0 6.2 - - - +
483B THR* 2.9 33.4 + - - -
484B LYS* 4.2 1.4 - - - +
485B PHE* 3.6 51.2 - - + +
515B LEU* 4.3 4.3 - - - -
520B ALA 4.4 2.9 - - - +
521B ILE* 4.1 17.3 - - + -
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Residues in contact with HIS 480 (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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457B ASP* 3.5 37.4 + - + +
458B PHE* 3.7 19.3 - + + -
479B ARG* 1.3 77.7 - - - +
481B LYS* 1.3 59.7 + - + +
482B SER* 3.0 45.2 + - - -
483B THR* 2.9 35.2 + - - +
515B LEU* 4.4 8.7 - - - +
516B GLN* 3.7 48.0 + - + -
519B GLY* 5.8 0.2 - - - -
520B ALA 4.6 0.8 + - - -
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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