Contacts of the helix formed by residues 472 - 482 (chain A) in PDB entry 1IK2
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 SER 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A PHE* 5.2 2.6 - - - -
470A PHE* 3.4 15.2 + - - -
471A ASN* 1.3 78.3 - - - +
473A PHE* 1.3 68.1 + - - +
474A GLU* 3.1 7.0 - - - -
475A GLN* 3.0 19.2 + - - -
476A LEU* 2.9 22.0 + - - +
588A TYR* 3.9 2.7 - - - -
593A TRP* 3.4 32.2 - - - +
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Residues in contact with PHE 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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267A LEU* 6.1 1.6 - - + -
472A SER* 1.3 74.6 - - - +
474A GLU* 1.3 72.8 + - - +
475A GLN 3.1 0.2 - - - -
476A LEU* 3.2 9.9 + - + +
477A CYS* 2.8 56.6 + - - -
593A TRP* 3.9 37.1 - + + -
594A LEU* 6.1 0.2 - - + -
634A GLY* 3.6 33.9 - - - -
635A LYS* 3.7 11.7 - - + -
639A LYS* 3.6 41.1 - - + -
647A VAL* 4.2 15.3 - - + -
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Residues in contact with GLU 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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267A LEU* 6.4 2.7 - - + -
269A GLU* 4.8 17.6 - - + -
270A LYS 4.4 11.1 + - - -
472A SER* 3.1 3.1 - - - -
473A PHE* 1.3 95.3 + - + +
475A GLN* 1.3 74.2 + - - +
477A CYS* 5.0 3.4 - - - -
478A ILE* 3.8 24.1 - - - +
593A TRP* 4.0 12.3 - - - -
631A ILE* 4.5 6.1 - - - +
635A LYS* 4.0 25.8 - - - +
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Residues in contact with GLN 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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466A GLU* 4.6 16.0 + - + +
468A PHE* 3.9 43.4 - - + +
471A ASN* 3.9 24.9 - - + +
472A SER* 3.0 36.6 + - - +
474A GLU* 1.3 92.9 + - - +
476A LEU* 1.3 57.8 + - - +
477A CYS 3.3 1.1 - - - -
478A ILE* 3.7 5.8 - - + -
479A ASN* 2.8 45.7 + - - +
588A TYR* 4.6 0.7 - - + -
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Residues in contact with LEU 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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472A SER 2.9 10.1 + - - +
473A PHE* 3.5 14.4 - - + +
475A GLN* 1.3 78.1 - - - +
477A CYS* 1.3 63.3 + - - +
479A ASN* 3.9 1.9 - - - +
480A PHE* 3.3 20.1 + - - +
530A ILE* 5.9 0.4 - - + -
531A MET* 4.1 15.2 - - - +
534A LEU* 4.7 1.3 - - + -
577A PHE* 3.9 28.9 - - + -
579A LEU* 3.9 21.8 - - + -
581A HIS* 5.1 2.7 + - - +
588A TYR* 3.5 34.8 - - + +
639A LYS* 3.3 29.6 - - - +
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Residues in contact with CYS 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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267A LEU* 4.8 10.5 - - + -
473A PHE* 2.8 52.8 + - - +
474A GLU* 5.0 3.4 - - - -
476A LEU* 1.3 73.4 - - - +
478A ILE* 1.3 61.6 + - + +
480A PHE* 3.5 4.1 + - - +
481A THR* 2.5 33.7 + - - -
531A MET* 4.7 16.6 - - - -
639A LYS* 4.7 1.6 - - - -
647A VAL* 4.9 7.6 - - - -
651A HIS* 4.0 22.7 + - + -
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Residues in contact with ILE 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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266A TYR* 5.6 8.3 - - + -
267A LEU* 6.4 3.6 - - + -
462A ILE* 4.4 11.7 - - + -
463A ALA* 3.6 33.2 - - + +
464A GLY 4.0 16.2 - - - +
466A GLU* 4.7 9.2 - - + +
474A GLU* 3.8 21.2 + - - +
475A GLN* 3.1 12.3 + - + +
477A CYS* 1.3 80.7 - - + +
479A ASN* 1.3 66.1 + - - +
481A THR* 3.0 8.7 + - + -
482A ASN* 2.7 39.6 + - - +
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Residues in contact with ASN 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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465A PHE* 3.6 30.3 - - + -
466A GLU 3.1 25.5 + - - -
475A GLN* 2.8 26.3 + - - +
476A LEU 3.9 2.7 - - - +
478A ILE* 1.3 77.9 - - - +
480A PHE* 1.3 65.4 + - - +
482A ASN* 3.2 13.9 + - - +
486A GLN* 3.4 17.1 + - - -
581A HIS* 3.9 15.1 - - - +
586A VAL* 3.8 13.2 - - - +
588A TYR* 2.5 27.4 + - - +
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Residues in contact with PHE 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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476A LEU 3.3 14.2 + - - +
477A CYS* 3.8 2.9 - - - +
478A ILE 3.2 0.2 - - - -
479A ASN* 1.3 79.4 - - - +
481A THR* 1.3 52.2 + - - +
483A GLU* 2.7 68.7 + - + +
486A GLN* 5.0 2.1 + - - +
521A ILE* 4.3 8.7 - - + -
524A ILE* 3.7 39.5 - - + -
525A GLU* 3.5 24.7 - - + -
531A MET* 4.3 21.1 - - + -
581A HIS* 4.4 10.0 - - + -
651A HIS* 4.5 9.2 - + - -
652A ARG* 4.2 21.8 - - + -
655A LEU* 4.2 14.8 - - + -
657A LYS* 6.2 0.4 - - - -
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Residues in contact with THR 481 (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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266A TYR* 2.9 41.2 - - + +
462A ILE* 3.3 32.2 - - + +
477A CYS 2.5 24.0 + - - -
478A ILE* 3.0 13.2 + - + +
480A PHE* 1.3 73.9 - - - +
482A ASN* 1.3 56.3 + - - +
483A GLU* 3.0 6.4 + - - +
484A LYS* 3.5 5.4 + - - +
651A HIS* 3.1 21.8 + - + -
655A LEU* 3.7 21.8 - - + +
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Residues in contact with ASN 482 (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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177A THR* 5.3 1.3 - - - +
462A ILE* 3.7 12.9 - - - +
463A ALA 3.0 24.2 + - - -
464A GLY* 3.2 4.7 + - - -
465A PHE* 2.9 47.6 + - + +
478A ILE 2.7 22.6 + - - +
479A ASN 3.4 14.8 - - - +
480A PHE 2.9 1.9 + - - -
481A THR* 1.3 70.1 - - - +
483A GLU* 1.3 54.7 + - - +
484A LYS* 2.9 19.1 - - - +
485A LEU* 4.0 1.2 - - - +
486A GLN* 2.8 25.5 + - - +
582A TYR* 4.4 3.4 + - + -
671A ARG* 4.0 11.1 + - - +
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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