Contacts of the helix formed by residues 579 - 584 (chain B) in PDB entry 1XR2
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 PRO 579 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468B MET* 4.4 10.1 - - + -
535B THR* 3.2 23.1 - - + +
539B TRP* 4.2 13.9 - - + +
577B ASP* 3.4 15.9 - - + +
578B GLU* 1.3 88.1 - - - +
580B ALA* 1.3 56.6 + - - +
581B PHE 3.1 0.2 - - - -
583B GLU* 3.3 20.8 - - - +
618B HIS 4.6 4.4 - - - +
619B MET* 5.2 4.3 - - + -
620B CYS 6.0 1.8 - - - +
621B TYR* 2.5 28.2 + - + +
1201B C2F 4.0 18.6 - - - +
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Residues in contact with ALA 580 (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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534B VAL* 3.7 5.6 - - - +
535B THR* 3.2 33.1 + - + +
538B SER* 3.5 26.0 - - - +
539B TRP* 4.9 3.3 - - - +
578B GLU 3.2 1.0 - - - -
579B PRO* 1.3 76.6 - - - +
581B PHE* 1.3 65.5 + - - +
582B ARG 3.1 0.7 - - - -
583B GLU* 3.6 11.0 - - + -
584B LYS* 2.7 29.7 + - + +
595B TYR* 3.1 1.7 + - - -
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Residues in contact with PHE 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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534B VAL* 5.0 2.2 - - + -
578B GLU* 3.1 35.0 + - + +
579B PRO 3.1 0.2 - - - -
580B ALA* 1.3 76.1 - - - +
582B ARG* 1.3 59.2 + - - +
595B TYR* 2.8 32.3 + - - -
596B PHE* 3.4 37.4 - + - -
599B ALA* 4.1 22.9 - - + -
600B ILE* 4.2 7.4 - - + -
603B PHE* 5.5 1.3 - + + -
619B MET* 3.9 15.5 - - + -
621B TYR* 3.5 3.6 - - - +
627B ILE* 4.7 3.8 - - + -
630B TYR* 4.0 13.0 - - + -
631B ILE* 3.3 34.8 - - + -
634B LEU* 3.8 35.9 - - + -
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Residues in contact with ARG 582 (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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581B PHE* 1.3 73.0 - - - +
583B GLU* 1.3 70.0 + - + +
584B LYS 3.1 2.0 - - - -
585B ALA* 3.0 22.1 + - - +
586B PRO 5.5 1.0 + - - -
589B LYS* 3.8 13.3 - - - +
592B TRP* 3.5 33.8 - - - -
596B PHE* 4.6 2.5 - - - -
621B TYR* 2.8 42.2 + - + -
626B GLU* 4.8 6.1 + - - -
627B ILE* 3.7 30.6 - - + +
1204B MRY 4.5 11.7 + - - -
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Residues in contact with GLU 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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104B LYS* 3.0 39.3 + - + +
107B ASN* 4.1 24.1 - - - +
538B SER* 5.4 2.2 - - - +
539B TRP* 5.0 1.9 + - - -
579B PRO* 3.3 22.5 - - - +
580B ALA* 3.3 7.1 + - + -
582B ARG* 1.3 84.2 + - + +
584B LYS* 1.3 57.4 + - - +
585B ALA 3.6 0.9 + - - +
621B TYR* 4.3 12.3 - - + -
1201B C2F 2.9 35.2 + - - -
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Residues in contact with LYS 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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107B ASN* 5.0 12.4 + - + +
283B ARG* 5.1 11.0 - - - +
534B VAL* 4.0 11.4 - - + -
537B MET* 5.1 4.7 - - - -
538B SER* 3.9 26.7 + - - +
542B TYR* 2.8 37.6 + - - -
548B GLU* 3.9 13.5 + - - -
580B ALA* 2.7 34.4 + - + +
583B GLU* 1.3 70.7 - - - +
585B ALA* 1.3 66.0 + - - +
586B PRO* 3.7 1.7 - - - +
595B TYR* 3.4 23.7 - - + +
598B TRP* 4.9 6.3 - - + -
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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