Contacts of the helix formed by residues 570 - 584 (chain B) in PDB entry 2XOY
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 THR 570 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564B LEU* 4.7 3.3 - - - +
568B GLY 5.2 2.5 - - - +
569B LEU* 1.3 79.5 - - - +
571B TRP* 1.3 68.4 + - - +
572B LYS* 2.9 20.0 + - - +
573B ASN* 3.0 31.1 + - - +
574B MET* 3.2 9.4 + - - +
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Residues in contact with TRP 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539B LEU 3.6 12.6 - - - -
540B ASN* 4.6 1.8 - - + -
541B LEU* 3.5 36.6 - - + -
542B GLY 3.6 18.7 + - - -
543B ASP* 5.1 8.6 + - - +
545B CYS* 3.5 24.5 - - - -
546B LEU* 3.9 37.3 - - + +
564B LEU* 4.6 3.4 - - - -
570B THR* 1.3 76.5 - - - +
572B LYS* 1.3 93.2 + - + +
574B MET* 3.4 11.2 + - - +
575B LEU* 3.0 42.8 + - + +
609B PHE* 4.2 15.4 - + + -
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Residues in contact with LYS 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B CYS 4.7 3.2 + - - -
538B GLU* 3.5 23.0 + - - +
539B LEU 3.7 4.6 + - - -
540B ASN* 3.0 29.0 + - - -
570B THR* 2.9 11.3 + - - +
571B TRP* 1.3 116.3 - - + +
573B ASN* 1.3 62.6 + - - +
575B LEU* 3.3 4.9 + - + +
576B THR* 2.8 35.0 + - - +
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Residues in contact with ASN 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLY 4.2 3.3 - - - +
569B LEU* 3.6 30.0 - - + +
570B THR* 3.0 35.3 + - - +
572B LYS* 1.3 77.9 - - - +
574B MET* 1.3 63.8 + - - +
576B THR* 3.5 7.5 + - - -
577B GLU* 3.1 31.9 + - + +
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Residues in contact with MET 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LEU* 4.0 15.7 - - + -
560B LEU* 3.9 8.3 - - - -
564B LEU* 3.8 24.2 - - + -
569B LEU* 5.3 2.1 - - - +
570B THR 3.2 6.3 + - - +
571B TRP* 3.5 10.5 - - - +
572B LYS 3.2 0.4 - - - -
573B ASN* 1.3 75.3 - - - +
575B LEU* 1.3 65.8 + - - +
577B GLU* 3.3 3.5 + - - +
578B SER* 2.9 28.6 + - - +
609B PHE* 3.5 24.5 - - + -
613B THR* 3.3 43.5 - - + +
616B TYR* 3.7 42.9 - - + -
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.9 36.6 - - + +
537B CYS 4.7 8.3 - - - +
539B LEU* 4.9 4.9 - - + +
541B LEU* 4.9 2.7 - - + -
571B TRP* 3.0 36.8 + - + +
572B LYS* 3.5 7.6 - - + +
574B MET* 1.3 76.6 - - - +
576B THR* 1.3 53.0 + - - +
578B SER* 2.9 6.7 + - - -
579B LEU* 2.7 47.6 + - + +
609B PHE* 3.5 29.4 - - + -
612B LEU* 4.0 23.3 - - + -
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Residues in contact with THR 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B CYS* 5.3 6.4 + - - +
572B LYS* 2.8 27.2 + - - +
573B ASN* 3.5 11.3 + - - -
575B LEU* 1.3 73.5 - - - +
577B GLU* 1.3 76.9 + - - +
579B LEU* 3.2 11.9 + - - +
580B VAL* 3.0 26.5 + - + +
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Residues in contact with GLU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LEU* 6.3 2.9 - - + -
573B ASN* 3.1 19.2 + - + +
574B MET 3.9 3.4 - - - +
576B THR* 1.3 95.4 - - - +
578B SER* 1.3 63.2 + - - +
580B VAL* 3.3 15.9 + - - +
581B ALA* 3.2 20.6 + - - +
616B TYR* 4.7 15.5 - - + -
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Residues in contact with SER 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B MET* 2.9 19.3 + - - +
575B LEU* 3.3 10.5 - - - -
577B GLU* 1.3 77.2 - - - +
579B LEU* 1.3 58.8 + - - +
581B ALA* 3.0 5.5 + - - +
582B LEU* 2.9 27.8 + - - +
587B PHE* 3.7 27.2 - - - -
612B LEU* 3.8 30.1 + - - +
613B THR 4.9 0.2 + - - -
616B TYR* 3.8 17.4 - - - +
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Residues in contact with LEU 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B PHE* 3.9 13.7 - - + -
537B CYS* 3.5 40.8 - - + +
575B LEU* 2.7 31.8 + - + +
576B THR* 3.4 12.1 - - - +
578B SER* 1.3 73.8 - - - +
580B VAL* 1.3 61.8 + - + +
582B LEU* 3.2 14.4 + - + +
583B GLN* 3.0 23.2 + - - +
596B GLY* 3.7 29.3 + - - +
612B LEU* 3.8 21.3 - - + -
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Residues in contact with VAL 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B THR* 3.0 19.6 + - + +
577B GLU* 3.5 20.9 - - - +
578B SER 3.2 0.2 - - - -
579B LEU* 1.3 75.5 - - + +
581B ALA* 1.3 59.5 + - + +
583B GLN* 3.3 14.8 + - - +
584B ARG* 3.0 59.5 + - + +
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Residues in contact with ALA 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577B GLU 3.2 10.5 + - - +
578B SER 3.0 8.3 + - - +
580B VAL* 1.3 76.5 - - + +
582B LEU* 1.3 62.2 + - - +
584B ARG* 3.8 4.3 - - - +
585B GLY 3.2 1.9 + - - -
586B VAL* 2.7 43.6 + - + +
587B PHE* 3.0 34.4 + - + -
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Residues in contact with LEU 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578B SER 2.9 11.9 + - - +
579B LEU* 3.2 25.8 + - + +
581B ALA* 1.3 74.9 - - - +
583B GLN* 1.3 61.7 + - - +
585B GLY* 2.9 19.8 + - - -
587B PHE* 3.2 28.2 - - - +
588B LEU* 4.0 11.0 - - - -
589B LEU* 3.6 33.7 - - + +
594B VAL* 3.7 17.0 - - + +
595B THR* 4.2 13.7 - - + -
596B GLY 4.8 0.4 - - - +
612B LEU* 4.4 9.0 - - + -
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Residues in contact with GLN 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579B LEU 3.0 11.7 + - - +
580B VAL* 3.6 20.0 - - - +
582B LEU* 1.3 78.3 - - - +
584B ARG* 1.3 69.2 + - + +
585B GLY* 3.2 1.0 + - - -
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Residues in contact with ARG 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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580B VAL* 3.0 42.2 + - + +
581B ALA* 3.5 5.8 + - - +
582B LEU 3.2 0.2 - - - -
583B GLN* 1.3 87.3 + - + +
585B GLY* 1.3 59.0 + - - +
586B VAL* 3.5 16.7 + - + +
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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