Contacts of the strand formed by residues 469 - 479 (chain A) in PDB entry 5I4A
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 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A ALA* 5.6 0.2 - - + -
462A ALA 3.6 11.2 - - - +
463A VAL* 4.1 1.8 - - + -
467A GLY 4.1 1.3 - - - +
468A ASP* 1.3 74.3 - - - +
470A LEU* 1.3 64.0 + - - +
471A TYR 3.9 2.2 - - - +
472A ILE* 3.7 18.4 - - + -
618A TYR* 3.8 19.3 - - + +
622A ILE* 3.7 26.5 - - + -
637A ILE* 3.5 31.0 - - + -
638A PRO* 3.8 20.9 - - + +
639A TYR* 3.6 28.7 - - + -
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Residues in contact with LEU 470 (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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441A LEU* 3.7 28.5 - - + -
462A ALA* 2.7 19.8 + - + +
463A VAL 4.0 11.4 - - - -
464A ASP* 4.1 15.5 - - + +
468A ASP* 3.4 1.1 + - + +
469A ILE* 1.3 76.2 - - - +
471A TYR* 1.3 60.5 + - - +
496A ALA 5.2 0.4 - - - +
499A LYS* 3.6 29.3 - - + +
500A TYR* 3.8 24.2 - - + +
503A LYS* 3.4 45.1 - - + +
639A TYR* 4.4 5.7 + - - -
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Residues in contact with TYR 471 (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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460A ILE* 3.5 25.4 - - + -
461A ALA* 3.4 0.7 - - - -
462A ALA* 2.9 28.6 + - + +
469A ILE* 3.5 2.2 - - - +
470A LEU* 1.3 82.9 - - + +
472A ILE* 1.3 80.0 + - - +
473A GLY* 3.4 16.5 - - - -
492A GLU* 2.2 39.8 + - - -
495A LYS* 3.1 33.1 + - + -
496A ALA* 3.9 16.2 - - + -
499A LYS* 3.6 35.0 - - + -
639A TYR* 3.6 15.3 - - - -
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Residues in contact with ILE 472 (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 CYS* 4.3 4.0 - - - -
460A ILE 3.3 10.3 - - - +
461A ALA* 4.4 2.2 - - + -
469A ILE* 3.7 12.1 - - + -
471A TYR* 1.3 94.6 + - - +
473A GLY* 1.3 62.9 + - - +
474A LYS* 5.5 0.9 - - + -
622A ILE* 3.6 27.6 - - + -
626A VAL* 3.9 33.2 - - + -
633A TRP* 4.5 4.9 - - + -
637A ILE* 3.9 9.2 - - + -
639A TYR* 3.3 51.4 + - + -
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Residues in contact with GLY 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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458A LEU* 6.1 0.2 - - - -
459A CYS* 3.1 7.0 - - - -
460A ILE* 2.8 39.6 + - - +
471A TYR* 3.4 8.4 - - - -
472A ILE* 1.3 75.6 - - - +
474A LYS* 1.3 61.1 + - - -
475A HIS* 4.9 1.1 - - - -
492A GLU* 3.7 26.0 - - - -
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Residues in contact with LYS 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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458A LEU 3.5 10.5 - - - +
459A CYS* 4.4 4.9 - - + -
472A ILE* 5.5 0.7 - - + -
473A GLY* 1.3 74.6 - - - +
475A HIS* 1.3 82.4 + - - +
476A LYS* 4.0 25.4 - - + +
492A GLU* 5.0 0.2 + - - -
626A VAL* 2.8 35.3 + - + +
627A ALA* 4.0 15.9 + - - +
629A THR 2.4 36.0 + - - -
630A ASP* 3.9 11.7 + - - +
633A TRP* 4.6 3.3 - - - +
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Residues in contact with HIS 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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456A THR 4.5 0.7 - - - +
457A ASN* 4.0 4.3 - - - +
458A LEU* 2.9 37.9 + - + +
473A GLY 4.9 0.2 - - - -
474A LYS* 1.3 84.6 + - - +
476A LYS* 1.3 64.1 + - - +
478A LEU* 3.8 28.8 - - + +
488A ILE* 3.6 31.0 - - + +
492A GLU* 2.1 42.2 + - + +
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Residues in contact with LYS 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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457A ASN* 4.2 6.7 - - - -
474A LYS* 4.0 28.3 - - + +
475A HIS* 1.3 77.6 - - - +
477A ASN* 1.3 87.3 + - - +
478A LEU* 3.5 6.0 + - - +
627A ALA 6.1 0.4 - - - -
630A ASP* 2.8 36.0 + - - +
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Residues in contact with ASN 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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455A LYS* 4.2 31.8 - - + +
456A THR 3.6 3.5 + - - -
457A ASN* 3.4 17.8 + - - +
476A LYS* 1.3 98.0 - - - +
478A LEU* 1.3 64.9 + - - +
479A GLU* 4.0 2.3 + - - +
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Residues in contact with LEU 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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455A LYS* 3.1 5.6 - - - -
456A THR* 2.5 63.0 + - + +
458A LEU* 4.4 12.3 - - + -
475A HIS* 3.8 35.2 - - + +
476A LYS 4.5 4.9 - - - +
477A ASN* 1.3 76.4 - - - +
479A GLU* 1.3 61.7 + - - +
485A ASN* 4.1 11.4 - - - +
488A ILE* 4.4 29.4 - - + -
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Residues in contact with GLU 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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454A ARG 3.9 3.2 - - - +
455A LYS* 2.7 35.3 + - - +
477A ASN 4.0 2.1 + - - +
478A LEU* 1.3 71.3 - - - +
480A LEU* 1.3 59.9 + - - +
481A ASN* 2.9 10.6 + - + -
484A MET* 3.5 28.1 - - + +
485A ASN* 3.3 13.2 - - - +
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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