Contacts of the helix formed by residues 532 - 539 (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 GLY 532 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531B THR* 1.3 77.5 - - - +
533B PRO* 1.3 66.0 - - - +
536B ILE* 3.1 25.3 + - - +
559B ILE* 3.7 0.4 - - - -
576B ILE* 3.6 16.2 - - - +
577B ASP 2.6 16.4 + - - -
578B GLU* 3.0 21.7 - - - +
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Residues in contact with PRO 533 (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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532B GLY* 1.3 81.5 - - - +
534B VAL* 1.3 66.7 + - - +
536B ILE* 3.3 2.8 + - - +
537B MET* 3.1 24.8 + - - +
552B ALA* 3.6 24.9 - - - +
555B ILE* 3.9 16.5 - - + +
556B ALA* 3.8 14.6 - - + +
559B ILE* 3.5 8.9 - - + -
576B ILE* 5.0 1.1 - - + -
578B GLU* 3.4 9.2 - - - +
602B ALA* 3.6 33.7 - - + +
603B PHE* 4.6 4.3 - - - -
606B ALA* 4.0 12.1 - - + -
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Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B PRO* 1.3 73.7 - - - +
535B THR* 1.3 57.1 + - - +
537B MET* 3.8 8.0 - - + +
538B SER* 2.8 32.4 + - - -
552B ALA* 4.9 1.1 - - + -
578B GLU* 2.9 28.0 + - + +
580B ALA* 3.8 9.2 - - + +
581B PHE* 4.8 0.9 - - - +
584B LYS* 4.0 17.3 - - + -
595B TYR* 3.7 21.8 - - - +
598B TRP* 4.1 18.8 - - + -
599B ALA* 4.0 29.8 - - + +
602B ALA* 4.2 12.6 - - + -
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Residues in contact with THR 535 (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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468B MET* 5.0 0.4 - - - -
469B VAL* 3.8 3.8 - - + +
531B THR* 3.9 17.3 - - + -
532B GLY 3.7 4.5 - - - -
533B PRO 3.2 0.2 - - - -
534B VAL* 1.3 75.1 - - - +
536B ILE* 1.3 65.8 + - - +
538B SER 3.1 0.5 + - - -
539B TRP* 3.1 48.9 + - + +
578B GLU* 2.6 23.2 + - - -
579B PRO* 3.2 39.2 - - + +
580B ALA* 3.2 16.6 + - - +
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Residues in contact with ILE 536 (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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469B VAL* 3.8 20.9 - - + +
472B PHE* 4.2 27.6 - - + -
473B ALA* 5.8 2.2 - - + +
476B LEU* 4.4 8.5 - - + -
479B ILE* 4.5 17.7 - - + -
500B ILE* 4.5 1.1 - - + +
510B MET* 6.5 0.2 - - + -
531B THR* 3.8 29.4 - - + +
532B GLY 3.1 9.1 + - - +
533B PRO 3.8 7.0 - - - +
535B THR* 1.3 79.4 - - - +
537B MET* 1.3 60.3 + - - +
539B TRP 3.8 0.3 + - - -
540B SER* 2.9 26.8 + - - +
555B ILE* 3.9 33.2 - - + -
559B ILE* 3.9 9.0 - - + -
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Residues in contact with MET 537 (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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500B ILE* 3.8 12.3 - - + -
533B PRO 3.1 9.8 + - - +
534B VAL* 3.8 11.0 - - + +
536B ILE* 1.3 75.2 - - - +
538B SER* 1.3 65.2 + - - +
540B SER 3.0 24.3 + - - +
542B TYR* 3.4 57.2 - - + +
548B GLU* 3.8 23.6 - - + +
551B ILE* 3.7 18.6 - - + -
552B ALA* 4.0 19.7 - - - -
555B ILE* 3.7 18.4 - - + -
584B LYS* 5.1 5.2 - - - -
598B TRP* 4.7 11.0 - - - -
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Residues in contact with SER 538 (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 2.8 21.4 + - - -
535B THR 3.1 2.6 + - - -
537B MET* 1.3 79.8 - - - +
539B TRP* 1.3 65.5 + - - +
540B SER 3.2 3.8 + - - +
542B TYR* 5.7 0.2 - - - -
580B ALA* 3.5 22.4 - - - +
583B GLU* 5.4 1.9 - - - +
584B LYS* 3.9 33.7 + - - +
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Residues in contact with TRP 539 (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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467B ASP* 3.3 21.3 - - - -
468B MET* 3.7 35.0 - - + -
469B VAL* 3.3 24.2 - - + -
495B TYR* 3.4 32.9 - + + +
497B PRO* 3.2 21.1 - - - +
498B PRO* 3.7 0.7 - - - +
535B THR* 3.1 33.5 + - + +
537B MET 3.3 0.2 - - - -
538B SER* 1.3 89.5 + - - +
540B SER* 1.3 59.2 + - - +
579B PRO* 4.2 7.6 - - + +
580B ALA* 4.9 3.8 - - - +
583B GLU* 5.0 2.2 + - - -
1201B C2F 3.2 75.2 + + - -
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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