Contacts of the strand formed by residues 521 - 525 (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 ILE 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A ILE* 4.0 17.0 - - + -
478A VAL 3.3 10.3 - - - +
479A ARG* 4.0 17.9 - - + -
483A THR* 4.0 11.4 - - + -
485A PHE* 4.0 12.3 - - + -
489A ALA* 4.1 8.5 - - + -
490A ALA 2.8 10.2 + - - +
491A ALA* 3.6 24.2 - - + -
492A ILE* 2.9 26.3 + - - +
515A LEU* 3.5 7.1 - - - +
520A ALA* 1.3 80.7 - - - +
522A PHE* 1.3 60.6 + - - +
523A ALA* 5.4 0.9 - - + -
560A LEU* 4.3 9.4 - - + -
565A TYR* 3.6 37.7 - - + +
566A ALA* 4.5 0.7 - - + -
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Residues in contact with PHE 522 (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* 4.1 8.7 - + - -
476A PHE 3.6 1.0 - - - +
477A ILE* 3.3 3.8 - - - -
478A VAL* 2.8 51.7 + - + +
492A ILE* 3.4 29.6 - - + -
494A TYR* 3.7 35.2 - + + -
506A PHE* 3.9 22.7 - + - -
511A ILE* 3.7 39.7 - - + -
515A LEU* 3.7 21.1 - - + +
521A ILE* 1.3 75.0 - - - +
523A ALA* 1.3 59.2 + - - +
524A VAL* 3.4 22.9 - - + -
715A TRP* 5.2 0.9 - + - -
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Residues in contact with ALA 523 (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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475A MET* 3.9 15.5 - - + -
476A PHE 3.2 5.4 - - - +
477A ILE* 4.6 2.5 - - + +
491A ALA* 5.2 2.9 - - + -
492A ILE 2.9 11.6 + - - +
493A GLN* 3.3 6.7 - - + -
494A TYR* 3.0 26.7 + - - +
521A ILE* 4.2 2.0 - - + -
522A PHE* 1.3 73.6 - - - +
524A VAL* 1.3 64.6 + - - +
525A PRO* 3.5 2.9 - - - +
560A LEU* 3.8 33.7 - - + -
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Residues in contact with VAL 524 (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* 4.1 14.4 - - + -
475A MET* 3.6 3.8 - - - +
476A PHE* 2.8 41.0 + - + +
494A TYR* 4.0 8.7 - - + +
503A ALA* 3.9 35.2 - - + +
506A PHE* 5.1 1.8 - - + -
522A PHE* 3.4 37.2 - - + +
523A ALA* 1.3 78.3 - - - +
525A PRO* 1.3 61.5 - - - +
526A SER* 3.7 2.4 + - - -
9C TRP* 4.0 16.2 - - + -
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Residues in contact with PRO 525 (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* 3.6 24.5 - - + +
474A PRO 3.6 7.0 - - - +
475A MET* 3.7 12.8 - - + -
493A GLN* 4.0 7.9 - - + -
494A TYR 3.5 13.7 - - - +
495A GLY* 5.5 2.4 - - - -
503A ALA* 4.5 8.8 - - - +
523A ALA 3.5 5.8 - - - +
524A VAL* 1.3 90.2 - - - +
526A SER* 1.3 58.9 + - - +
527A ILE* 3.0 14.5 + - + +
553A PHE* 3.8 28.3 - - + -
556A ALA* 3.8 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