Contacts of the strand formed by residues 568 - 572 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390E THR* 3.8 10.8 - - + -
392E VAL* 3.6 35.0 - - + -
471E ILE* 3.6 30.3 - - + -
484E HIS* 4.3 8.1 - - + -
485E SER 5.6 0.7 - - - +
487E ARG 3.2 4.4 + - - +
488E ILE* 3.3 19.4 - - + +
489E SER 2.9 25.3 + - - +
566E ALA* 3.9 1.6 - - - +
567E ASP* 1.3 79.3 - - + +
569E TYR* 1.3 70.0 + - - +
570E LEU* 3.7 17.9 - - + -
599E THR* 3.7 22.4 - - + +
601E ILE* 4.3 9.6 - - + -
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Residues in contact with TYR 569 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489E SER* 3.5 18.8 - - - +
516E ARG* 3.8 6.2 + - - -
561E ALA 3.3 16.6 - - - -
562E VAL* 3.9 9.0 + - - -
564E LYS 2.6 29.3 + - - -
565E ASP* 3.6 2.9 - - - -
566E ALA* 3.2 32.7 + - + -
568E LEU* 1.3 76.4 - - - +
570E LEU* 1.3 64.2 + - - +
571E LEU* 3.9 7.5 + - + +
595E MET* 3.6 31.2 - - + -
598E LYS* 3.6 40.8 - - + -
599E THR 3.0 12.9 + - - +
600E ARG* 3.3 5.3 - - + +
601E ILE 2.9 28.4 + - - +
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Residues in contact with LEU 570 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468E LEU* 3.6 43.7 - - + +
471E ILE* 4.0 13.7 - - + -
472E MET* 3.7 21.5 - - + -
488E ILE* 3.8 16.2 - - + -
489E SER 2.7 11.8 + - - +
490E PHE* 3.4 11.2 - - + -
491E CYS 2.8 26.5 + - - -
568E LEU* 3.7 25.8 - - + -
569E TYR* 1.3 72.9 - - - +
571E LEU* 1.3 62.6 + - - +
572E ASP 4.0 0.7 - - - -
601E ILE* 3.7 29.4 - - + -
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Residues in contact with LEU 571 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468E LEU* 4.5 2.6 - - - +
489E SER 5.1 0.9 - - - +
491E CYS* 3.7 21.5 - - + +
558E LEU* 4.4 18.6 - - + -
561E ALA* 4.7 7.2 - - + -
562E VAL* 5.5 0.2 - - + -
569E TYR* 4.5 9.0 - - + +
570E LEU* 1.3 83.8 - - - +
572E ASP* 1.3 59.4 + - - +
573E SER 3.4 3.3 + - - -
574E PRO* 4.3 7.2 - - + -
591E VAL* 4.4 20.2 - - + -
595E MET* 3.9 25.1 - - + -
600E ARG* 4.3 17.0 - - + -
601E ILE 2.9 13.8 + - - +
602E LEU* 3.4 18.5 - - + +
603E VAL* 2.9 26.5 + - - +
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Residues in contact with ASP 572 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E MG 4.1 0.2 - - - -
465E THR* 2.6 41.6 + - - +
468E LEU* 3.7 18.9 - - + +
490E PHE* 4.1 8.6 - - + -
491E CYS 2.8 17.9 + - - +
492E SER 3.5 2.8 - - - +
493E GLN* 3.3 43.4 + - + +
570E LEU 4.0 0.4 + - - -
571E LEU* 1.3 68.1 - - - +
573E SER* 1.3 67.7 + - - +
574E PRO* 3.3 1.9 - - - +
603E VAL* 3.4 23.6 - - - +
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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
------------------------------------------------------------
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