Contacts of the strand formed by residues 484 - 489 (chain A) in PDB entry 5ZE3
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 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLY* 3.5 29.6 - - - -
332A ALA* 3.5 22.9 - - + -
474A MET* 4.1 17.7 - - - -
477A CYS* 3.7 3.6 - - - -
483A GLY* 1.3 74.1 - - - -
485A ALA* 1.3 69.9 + - - +
543A CYS* 3.1 11.4 - - - +
544A SER 2.6 31.9 + - - +
545A GLU 3.9 6.7 - - - -
546A THR* 3.1 43.7 - - - +
547A ALA* 3.4 12.3 - - + -
608A GLN* 4.1 9.2 - - - -
723A SER* 3.5 35.4 - - - -
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Residues in contact with ALA 485 (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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470A ILE* 4.0 7.2 - - + +
473A ALA* 3.6 18.2 - - + -
474A MET* 3.3 47.2 - - + +
477A CYS* 3.7 6.4 - - - +
484A PHE* 1.3 84.2 - - - +
486A SER* 1.3 59.4 + - - +
487A ASN 4.5 2.2 - - - +
542A ALA 3.6 5.4 - - - +
544A SER 4.6 0.4 - - - -
546A THR 5.0 0.7 - - - +
547A ALA* 4.8 2.4 - - - +
721A ALA* 3.2 17.6 - - - +
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Residues in contact with SER 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 4.1 2.7 - - - +
484A PHE 3.9 0.6 + - - -
485A ALA* 1.3 73.7 - - - +
487A ASN* 1.3 70.6 + - - +
542A ALA* 2.6 43.0 + - - +
543A CYS 3.3 8.8 + - - -
544A SER* 4.3 15.6 - - - -
546A THR 5.8 0.4 - - - -
721A ALA* 3.7 19.8 + - - +
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Residues in contact with ASN 487 (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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470A ILE* 3.7 10.7 - - - +
473A ALA* 3.8 7.6 - - - +
486A SER* 1.3 100.2 + - - +
488A ALA* 1.3 62.2 + - - +
489A PHE* 3.7 31.8 - - + -
541A VAL* 3.6 3.3 - - - -
542A ALA* 3.1 33.2 + - + +
614A LYS* 5.9 6.7 + - - +
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Residues in contact with ALA 488 (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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468A TRP* 3.6 16.9 - - + +
469A GLY* 3.2 38.8 - - - +
470A ILE* 3.6 7.4 - - + +
473A ALA* 3.7 7.4 - - + -
487A ASN* 1.3 75.7 - - - +
489A PHE* 1.3 71.5 + - - +
490A GLN* 4.5 0.5 + - - +
540A GLY 3.7 4.7 - - - -
614A LYS* 5.7 4.5 + - - -
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Residues in contact with PHE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU* 5.5 2.0 - - - -
468A TRP* 3.2 8.8 - - - -
487A ASN* 3.7 33.0 - - + -
488A ALA* 1.3 78.9 - - - +
490A GLN* 1.3 61.2 + - - +
491A GLU 4.6 2.5 - - - +
492A THR* 3.9 9.2 - - + -
494A TYR* 3.6 24.7 - - - +
495A TRP* 3.9 24.9 - + - -
539A ALA* 3.1 24.6 - - - -
540A GLY 3.0 25.4 + - - +
541A VAL 3.9 15.5 - - - -
542A ALA* 4.2 5.4 - - + -
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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