Contacts of the strand formed by residues 568 - 572 (chain D) in PDB entry 1XMI
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 LEU 568 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D THR* 3.8 7.6 - - + -
392D VAL* 3.7 33.4 - - + -
471D ILE* 3.7 29.8 - - + -
484D HIS* 4.5 11.2 - - + -
485D SER 5.2 0.7 - - - +
487D ARG 3.1 8.0 + - - +
488D ILE* 3.4 13.5 - - + +
489D SER* 2.8 32.4 + - - +
566D ALA* 3.4 2.2 - - - +
567D ASP* 1.3 81.7 - - - +
569D TYR* 1.3 66.2 + - - +
570D LEU* 3.9 11.7 - - + -
599D THR* 3.6 22.4 - - + +
601D ILE* 3.8 16.8 - - + -
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Residues in contact with TYR 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489D SER* 3.4 19.1 - - - -
516D ARG* 3.6 12.3 + - - -
561D ALA 3.2 23.8 - - - -
562D VAL* 4.0 7.4 - - - -
564D LYS 2.4 24.9 + - - -
565D ASP* 3.7 0.3 - - - -
566D ALA* 3.2 29.9 + - + -
568D LEU* 1.3 75.7 - - - +
570D LEU* 1.3 64.3 + - - +
571D LEU* 4.0 8.3 - - + -
595D MET* 3.4 30.7 - - + -
598D LYS* 3.7 33.0 - - + -
599D THR 2.9 19.0 + - - +
600D ARG* 3.2 6.4 - - + +
601D ILE 2.8 28.8 + - - +
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Residues in contact with LEU 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D LEU* 4.0 24.9 - - + +
471D ILE* 4.1 15.9 - - + -
472D MET* 3.7 24.7 - - + -
488D ILE* 3.7 25.1 - - + -
489D SER 2.7 14.8 + - - +
490D PHE* 3.4 13.6 - - + -
491D CYS 2.8 30.8 + - - -
568D LEU* 3.9 13.5 - - + -
569D TYR* 1.3 77.8 - - - +
571D LEU* 1.3 57.8 + - - +
572D ASP 3.9 0.7 - - - -
601D ILE* 3.6 36.8 - - + -
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Residues in contact with LEU 571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D LEU* 4.5 2.2 - - - +
489D SER 5.4 0.4 - - - +
491D CYS* 3.7 20.6 - - + +
558D LEU* 4.4 18.4 - - + -
561D ALA* 4.8 6.7 - - + -
562D VAL* 5.3 0.2 - - + -
569D TYR* 4.0 14.6 - - + +
570D LEU* 1.3 81.0 - - - +
572D ASP* 1.3 60.3 + - - +
573D SER 3.3 3.4 + - - -
574D PRO* 4.1 8.3 - - + -
591D VAL* 5.0 12.8 - - + -
595D MET* 4.4 12.8 - - + -
600D ARG* 3.9 27.8 - - + -
601D ILE 2.9 16.4 + - - +
602D LEU* 3.4 23.4 - - + +
603D VAL* 2.9 26.3 + - - +
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Residues in contact with ASP 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D MG 4.1 0.5 - - - -
465D THR* 2.5 43.0 + - - +
468D LEU* 3.8 18.6 - - + +
490D PHE* 4.1 6.7 - - + -
491D CYS 2.8 18.4 + - - +
492D SER* 3.6 3.3 + - - +
493D GLN* 3.4 41.8 + - - +
570D LEU 3.9 0.4 + - - -
571D LEU* 1.3 68.4 - - - +
573D SER* 1.3 70.2 + - - +
574D PRO* 3.3 1.8 - - - +
603D VAL* 3.6 22.3 - - - +
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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