Contacts of the strand formed by residues 575 - 582 (chain A) in PDB entry 5IZL
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 VAL 575 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A HIS* 3.6 2.8 + - - +
477A GLY* 2.9 53.9 + - - +
478A LEU 4.0 4.7 - - - +
479A VAL* 3.6 20.0 - - + -
493A LEU* 3.8 18.8 - - + -
508A VAL* 4.4 11.0 - - + -
509A HIS 3.2 6.7 - - - +
510A LEU* 3.6 28.9 - - + -
511A SER 5.6 0.2 - - - -
528A PHE* 5.6 2.2 - - + -
530A ILE* 4.8 13.2 - - + -
574A HIS* 1.3 72.5 - - - +
576A VAL* 1.3 71.9 + - - +
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Residues in contact with VAL 576 (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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474A HIS* 3.2 39.5 - - + +
475A LYS 3.3 11.2 - - - +
476A HIS* 3.2 19.7 - - + +
493A LEU* 6.4 0.4 - - - -
508A VAL* 3.3 4.7 - - - +
509A HIS* 2.8 41.7 + - + +
574A HIS* 5.5 2.5 - - + -
575A VAL* 1.3 81.8 - - - +
577A LEU* 1.3 63.4 + - - +
578A SER* 4.4 1.2 + - - +
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Residues in contact with LEU 577 (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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473A LYS 3.9 0.3 - - - +
474A HIS* 3.2 9.2 + - - -
475A LYS* 3.1 40.0 + - + +
493A LEU* 5.1 11.4 - - + +
494A PHE* 4.6 15.3 - - + -
503A PHE* 4.4 16.2 - - + -
506A LEU* 4.6 9.6 - - + -
507A LYS 3.3 27.6 - - - +
508A VAL* 4.2 9.6 - - + -
518A ILE* 4.5 13.7 - - + -
576A VAL* 1.3 72.8 - - - +
578A SER* 1.3 71.5 + - - +
579A LEU* 4.1 23.6 - - + +
594A GLN* 3.6 12.3 - - - +
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Residues in contact with SER 578 (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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472A LEU* 6.3 1.6 - - - -
473A LYS 3.7 6.5 - - - -
474A HIS* 3.1 26.9 + - - -
507A LYS 4.9 1.4 + - - -
576A VAL* 4.7 1.6 + - - +
577A LEU* 1.3 76.7 - - - +
579A LEU* 1.3 59.8 + - - +
594A GLN* 3.6 28.8 + - - +
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Residues in contact with LEU 579 (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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472A LEU* 3.9 3.7 - - - +
473A LYS* 2.9 59.6 + - + +
475A LYS* 6.4 2.0 - - + -
503A PHE* 3.8 29.8 - - + -
506A LEU* 5.0 8.7 - - + -
577A LEU* 4.3 18.4 - - + +
578A SER* 1.3 74.1 - - - +
580A THR* 1.3 64.5 + - - +
581A PHE* 4.0 10.3 - - + -
592A MET* 3.7 28.3 - - + -
593A VAL 3.5 10.8 - - - +
594A GLN* 5.0 0.9 - - - +
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Residues in contact with THR 580 (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 TYR* 3.8 29.8 - - + -
471A LYS 3.4 3.1 - - - -
472A LEU* 3.6 26.0 - - + -
579A LEU* 1.3 74.3 - - - +
581A PHE* 1.3 61.4 + - - +
582A LYS* 3.8 8.5 + - - -
592A MET* 3.7 2.1 - - - +
593A VAL* 2.8 57.0 + - - +
594A GLN* 4.9 7.1 + - - +
595A SER* 5.6 2.1 + - - +
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Residues in contact with PHE 581 (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 TYR* 3.9 0.7 - - - -
471A LYS* 2.6 50.7 + - + +
473A LYS* 4.4 14.8 - - + -
579A LEU* 4.0 15.4 - - + +
580A THR* 1.3 69.4 - - - +
582A LYS* 1.3 67.4 + - - +
583A ARG* 3.4 19.5 + - + -
587A ASP* 6.0 4.9 - - + -
590A LYS 6.1 1.1 - - - -
592A MET* 4.1 19.7 - - + +
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Residues in contact with LYS 582 (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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372A GLU* 2.3 45.1 + - - +
468A LYS* 4.6 8.6 - - + +
469A VAL 3.3 10.1 - - - +
470A TYR* 3.6 25.1 - - + +
580A THR* 3.8 11.6 + - - +
581A PHE* 1.3 80.1 - - - +
583A ARG* 1.3 65.4 + - - +
584A TYR 3.3 1.4 + - - -
585A VAL* 3.7 16.6 - - + -
586A PHE* 3.4 35.5 - - + +
587A ASP* 3.6 14.4 + - - +
592A MET* 6.1 0.2 - - - +
593A VAL* 4.6 17.5 - - + -
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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