Contacts of the helix formed by residues 573 - 587 (chain W) in PDB entry 5IY8
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 ASP 573 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571W THR* 3.4 5.5 - - + +
572W GLN* 1.4 82.0 - - - +
574W GLY* 1.3 64.3 + - - +
575W ALA* 3.1 31.4 + - - +
576W GLU* 3.1 32.2 + - + +
577W THR* 2.8 19.7 + - - -
603W LYS* 5.6 4.5 - - - +
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Residues in contact with GLY 574 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573W ASP* 1.3 76.9 + - - +
575W ALA* 1.3 63.5 + - - +
577W THR* 3.5 12.7 - - - -
578W SER* 3.5 14.0 + - - -
603W LYS* 6.5 0.7 - - - -
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Residues in contact with ALA 575 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573W ASP* 3.1 12.0 + - - +
574W GLY* 1.3 75.9 - - - +
576W GLU* 1.3 63.9 + - + +
578W SER* 3.2 17.3 + - - -
579W VAL* 3.5 14.6 + - - +
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Residues in contact with GLU 576 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571W THR* 4.2 9.5 - - - +
572W GLN 3.5 14.1 - - - +
573W ASP* 3.1 26.7 + - + +
575W ALA* 1.3 77.4 - - + +
577W THR* 1.3 61.8 + - - +
579W VAL* 3.3 20.6 + - + +
580W ALA* 3.5 11.1 + - - +
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Residues in contact with THR 577 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568W PHE* 3.7 26.8 - - + -
572W GLN* 3.6 9.1 + - - +
573W ASP 2.8 22.2 + - - -
574W GLY* 3.5 9.6 - - - +
576W GLU* 1.3 75.3 - - - +
578W SER* 1.3 63.2 - - - +
580W ALA* 3.3 8.1 + - - +
581W LEU* 3.3 18.2 + - - +
592W ARG* 3.3 37.8 - - - +
603W LYS* 5.0 8.2 - - + +
604W VAL* 6.3 0.2 - - - -
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Residues in contact with SER 578 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574W GLY 3.5 12.2 + - - -
575W ALA* 3.2 11.3 + - - -
577W THR* 1.3 77.2 - - - +
579W VAL* 1.4 54.3 + - - +
581W LEU* 3.3 13.2 + - - +
582W GLU* 2.7 47.6 + - - +
592W ARG* 5.8 0.2 - - - +
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Residues in contact with VAL 579 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575W ALA 3.7 14.1 - - - +
576W GLU* 3.7 13.9 - - + +
577W THR 3.2 1.2 - - - -
578W SER* 1.4 77.4 - - - +
580W ALA* 1.4 58.5 + - - +
582W GLU* 3.4 12.3 + - + +
583W LYS* 3.0 49.7 + - + +
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Residues in contact with ALA 580 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566W LEU* 3.6 28.3 - - + -
567W LEU 5.4 1.3 - - - +
568W PHE* 5.1 5.6 - - + -
576W GLU 3.5 6.8 + - - +
577W THR* 3.3 10.0 + - - +
578W SER 3.2 0.2 - - - -
579W VAL* 1.4 79.6 - - - +
581W LEU* 1.3 55.5 + - - +
583W LYS* 3.1 5.4 + - - -
584W TYR 3.0 17.7 + - - -
591W GLY* 3.2 2.9 - - - -
592W ARG* 2.9 28.0 + - + +
596W LEU* 4.8 4.5 - - + -
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Residues in contact with LEU 581 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577W THR 3.3 8.5 + - - +
578W SER* 3.5 14.8 - - - +
580W ALA* 1.3 69.5 - - - +
582W GLU* 1.3 76.0 + - + +
584W TYR* 3.9 16.1 - - + -
585W GLN* 3.0 38.5 + - + +
592W ARG* 3.5 42.0 - - - +
608W ILE* 3.3 47.8 - - + -
610W PHE* 4.7 10.5 - - + -
614W TYR* 5.2 0.2 - - + -
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Residues in contact with GLU 582 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578W SER* 2.7 31.8 + - - +
579W VAL* 3.4 12.1 + - + +
581W LEU* 1.3 77.1 - - + +
583W LYS* 1.4 59.0 + - + +
585W GLN* 2.8 34.8 + - + +
586W GLU* 3.0 16.5 + - - +
610W PHE* 6.1 2.7 - - + -
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Residues in contact with LYS 583 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566W LEU* 4.6 22.2 - - + +
579W VAL* 3.0 36.5 + - + +
580W ALA* 3.1 8.5 + - - +
582W GLU* 1.4 77.3 - - + +
584W TYR* 1.3 58.7 + - - +
586W GLU* 4.0 4.5 - - - +
587W ALA 2.9 28.8 + - - +
590W ASN* 3.6 13.5 - - - +
591W GLY* 4.0 7.9 - - - +
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Residues in contact with TYR 584 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534W GLY* 4.3 12.6 - - - -
580W ALA 3.0 6.4 + - - +
581W LEU* 3.4 11.6 + - + +
583W LYS* 1.3 73.6 - - - +
585W GLN* 1.3 66.9 + - - +
587W ALA* 4.0 8.1 + - - +
588W CYS 4.6 3.6 - - - +
590W ASN 3.7 8.5 - - - -
591W GLY* 3.3 9.4 - - - -
592W ARG 2.8 25.8 - - - +
593W GLY* 3.7 11.2 - - - -
594W ALA* 2.9 40.6 - - + -
608W ILE* 5.4 0.2 - - + -
614W TYR* 1.5 77.2 + + + -
615W GLY* 1.9 13.2 + - - -
616W ARG* 4.5 4.0 + - - -
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Residues in contact with GLN 585 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1830 TYR* 5.8 1.6 + - - -
2060 ARG* 2.8 67.8 + - - +
581W LEU* 3.0 30.7 + - + +
582W GLU* 2.8 30.9 + - + +
584W TYR* 1.3 80.2 - - - +
586W GLU* 1.3 88.3 + - - +
587W ALA* 4.7 0.2 - - - -
610W PHE* 3.6 24.4 - - + -
612W HIS* 4.1 12.1 - - - +
614W TYR* 4.6 11.0 - - + -
616W ARG* 5.4 0.5 + - - -
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Residues in contact with GLU 586 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1820 ILE* 6.0 2.4 - - - +
1830 TYR* 4.5 21.2 + - - +
2050 VAL 4.0 0.2 - - - -
2060 ARG* 3.4 7.0 + - - +
2070 VAL* 2.9 45.0 + - + +
582W GLU* 3.0 20.6 + - - +
583W LYS* 4.0 5.3 - - - +
584W TYR 3.4 0.2 - - - -
585W GLN* 1.3 92.4 + - - +
587W ALA* 1.3 68.0 + - + +
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Residues in contact with ALA 587 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740 LEU 3.8 7.2 - - - +
1750 THR* 3.4 27.6 - - - +
2050 VAL* 4.7 6.7 - - - +
2070 VAL* 4.1 12.3 - - + -
583W LYS 2.9 17.3 + - - +
584W TYR 4.0 4.0 - - - +
585W GLN 3.5 1.8 - - - -
586W GLU* 1.3 90.0 - - + +
588W CYS* 1.3 77.2 - - + +
590W ASN 3.8 3.1 - - - +
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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