Contacts of the strand formed by residues 472 - 480 (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 LYS 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A TRP* 3.8 29.6 - - + -
465A TYR 3.3 12.1 - - - +
466A GLU* 2.9 35.1 + - + +
470A GLY 4.0 10.8 - - - +
471A THR* 1.3 75.1 - - - +
473A ILE* 1.3 65.4 + - - +
537A TRP* 3.9 10.7 - - - -
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Residues in contact with ILE 473 (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* 3.4 3.6 - - - -
465A TYR* 2.9 69.9 + - + +
467A SER* 4.2 2.7 - - - -
471A THR* 3.8 21.1 - - + +
472A LYS* 1.3 76.5 - - - +
474A PRO* 1.3 75.1 - - + +
526A SER 3.3 28.3 - - - +
527A ILE* 4.2 1.6 - - - +
528A ARG* 4.2 0.9 - - - +
537A TRP* 3.4 27.4 - - + -
552A ASP* 3.6 25.6 - - - +
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Residues in contact with PRO 474 (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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380A VAL* 4.2 4.7 - - + -
462A GLN* 3.7 21.1 - - + +
463A VAL 3.2 6.1 - - - +
464A TRP* 3.4 30.9 - - + -
472A LYS 4.3 0.7 - - - +
473A ILE* 1.3 95.9 - - + +
475A MET* 1.3 63.3 + - - +
526A SER* 2.9 40.2 + - - +
533A PHE* 3.7 34.8 - - + -
537A TRP* 4.6 0.9 - - + -
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Residues in contact with MET 475 (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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462A GLN* 3.4 5.2 - - - +
463A VAL* 2.7 44.8 + - + +
465A TYR* 4.0 15.5 - - + -
474A PRO* 1.3 77.1 - - - +
476A PHE* 1.3 77.6 + - - +
477A ILE* 3.7 3.5 + - + -
493A GLN* 4.9 0.2 - - - +
523A ALA* 3.9 20.0 - - - -
524A VAL 3.6 5.4 - - - +
525A PRO* 3.7 30.5 - - + -
526A SER* 5.1 0.4 - - - -
556A ALA* 3.9 12.6 - - - +
559A PHE* 3.7 33.4 - - + -
560A LEU* 3.8 20.6 - - + -
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Residues in contact with PHE 476 (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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380A VAL* 3.5 34.3 - - + -
381A LYS* 4.0 15.3 - - + -
402A VAL* 6.2 1.3 - - + -
423A PHE* 3.5 37.2 - + + -
460A SER* 5.5 3.4 - - - -
461A THR 3.3 11.7 - - - +
462A GLN* 3.5 34.8 - - + -
475A MET* 1.3 77.0 - - - +
477A ILE* 1.3 60.7 + - - +
478A VAL* 4.2 1.1 - - + -
503A ALA 3.9 8.5 - - - -
505A PRO* 3.7 28.7 - - + -
522A PHE 3.6 0.8 - - - +
523A ALA* 3.2 6.1 - - - -
524A VAL* 2.8 44.9 + - + +
526A SER* 4.9 3.4 - - - -
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Residues in contact with ILE 477 (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* 3.7 2.4 - - - +
460A SER* 3.3 2.1 - - - -
461A THR* 2.9 41.7 + - - +
463A VAL* 3.6 31.2 - - + -
475A MET* 4.3 6.5 - - + +
476A PHE* 1.3 79.2 - - - +
478A VAL* 1.3 62.7 + - - +
479A ARG* 5.5 0.5 - - - +
485A PHE* 3.8 31.1 - - + -
521A ILE* 4.0 19.5 - - + -
522A PHE 3.3 3.8 - - - +
523A ALA* 4.7 2.5 - - + -
560A LEU* 4.0 20.9 - - + -
565A TYR* 3.6 27.1 - - + -
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Residues in contact with VAL 478 (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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423A PHE* 3.5 51.8 - - + +
424A ASN* 6.2 0.4 - - + -
458A PHE* 4.7 4.3 - - + -
459A GLU 3.4 12.8 - - - +
460A SER* 3.9 3.6 - - - -
476A PHE* 5.1 1.1 - - + -
477A ILE* 1.3 77.7 - - - +
479A ARG* 1.3 66.7 + - - +
512A LEU* 4.0 18.8 - - + -
515A LEU* 3.5 19.2 - - + +
521A ILE* 3.3 7.4 - - - +
522A PHE* 2.8 49.2 + - + +
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Residues in contact with ARG 479 (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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458A PHE* 3.3 9.5 - - - +
459A GLU* 2.8 71.8 + - + +
477A ILE 5.5 0.7 - - - +
478A VAL* 1.3 77.9 - - - +
480A HIS* 1.3 69.5 + - - +
481A LYS* 5.0 5.4 - - - +
483A THR* 2.9 32.1 + - - -
484A LYS* 4.2 1.4 - - - +
485A PHE* 3.5 50.5 - - + +
515A LEU* 4.2 4.7 - - - -
520A ALA 4.3 2.5 - - - -
521A ILE* 4.0 18.2 - - + -
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Residues in contact with HIS 480 (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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457A ASP* 3.6 35.2 + - + +
458A PHE* 3.6 17.7 - + + -
479A ARG* 1.3 79.5 - - - +
481A LYS* 1.3 62.0 + - + +
482A SER* 3.1 42.9 + - - -
483A THR* 2.9 34.4 + - - +
515A LEU* 4.4 7.8 - - - +
516A GLN* 3.6 51.5 + - + -
519A GLY* 5.8 0.4 - - - -
520A 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