Contacts of the strand formed by residues 573 - 577 (chain A) 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 ILE 573 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 4.2 13.9 - - + -
401A LEU* 5.4 0.2 - - + -
457A VAL* 3.9 22.0 - - + -
525A PRO* 3.9 26.9 - - + +
526A VAL 4.8 1.5 + - - +
527A LYS* 3.1 24.5 - - + +
528A GLY 2.7 27.7 + - - -
571A ILE* 3.1 10.0 + - - +
572A LYS* 1.3 89.6 - - + +
574A VAL* 1.3 59.8 + - - +
613A THR* 4.8 0.2 - - - -
614A GLN* 3.4 25.1 - - + +
616A HIS* 3.5 34.8 - - + +
699A TRP* 4.9 0.4 - - + -
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Residues in contact with VAL 574 (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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528A GLY 3.7 6.3 - - - +
530A LEU* 3.7 30.7 - - + -
563A VAL* 4.5 14.1 - - + +
566A LEU* 4.0 25.4 - - + -
567A GLU* 5.5 0.7 - - + -
571A ILE* 4.3 8.1 - - + +
573A ILE* 1.3 83.2 - - - +
575A GLN* 1.3 68.3 + - - +
576A ILE* 4.1 8.0 + - + -
613A THR* 4.2 15.9 - - + +
614A GLN 3.0 6.9 + - - -
615A ILE* 3.4 17.2 - - + +
616A HIS 2.9 23.3 + - - +
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Residues in contact with GLN 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ILE* 3.0 42.6 + - - +
527A LYS* 3.3 19.1 + - - +
528A GLY 2.8 16.7 + - - +
529A MET* 3.1 30.1 - - - +
530A LEU* 2.8 28.2 + - - +
574A VAL* 1.3 74.8 - - - +
576A ILE* 1.3 67.1 + - - +
577A ASP* 2.7 29.6 + - - +
616A HIS* 3.3 22.2 - - + +
618A HIS* 4.0 8.3 - - + +
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Residues in contact with ILE 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A LEU* 3.4 11.0 - - + +
531A THR 4.3 2.9 - - - -
532A GLY* 3.7 27.6 - - - +
533A PRO* 5.2 1.8 - - + -
559A ILE* 4.9 2.7 - - + -
563A VAL* 4.5 11.4 - - + -
574A VAL* 4.3 13.0 - - + +
575A GLN* 1.3 77.8 - - - +
577A ASP* 1.3 62.1 + - - +
578A GLU* 3.5 2.8 + - - +
603A PHE* 3.7 26.0 - - + -
606A ALA* 4.1 13.0 - - + +
607A ALA* 3.9 36.3 - - + +
615A ILE* 4.7 6.3 - - + -
616A HIS 2.8 12.5 + - - +
617A ALA* 3.8 5.7 - - - +
618A HIS 3.7 13.1 + - - -
619A MET* 6.0 0.3 - - - +
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Residues in contact with ASP 577 (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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409A ILE 5.3 0.6 - - - +
410A GLY* 6.1 0.5 - - - -
462A GLU* 5.3 1.9 - - - +
468A MET* 4.3 21.0 - - + +
529A MET* 4.6 9.2 - - - +
530A LEU 2.9 18.7 + - - +
531A THR* 3.5 5.9 + - - +
532A GLY 2.7 26.2 + - - -
535A THR* 3.8 0.7 + - - -
575A GLN* 2.7 33.2 + - - -
576A ILE* 1.3 70.1 - - - +
578A GLU* 1.3 57.2 + - - +
579A PRO* 3.4 15.1 - - + +
618A HIS* 3.1 30.0 - - + +
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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