Contacts of the strand formed by residues 568 - 572 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B THR* 3.9 7.2 - - + -
392B VAL* 3.6 33.4 - - + -
471B ILE* 3.7 29.8 - - + -
484B HIS* 4.5 10.8 - - + -
485B SER 5.3 0.7 - - - +
487B ARG 3.1 7.8 + - - +
488B ILE* 3.4 14.9 - - + +
489B SER 2.8 26.7 + - - +
566B ALA* 3.3 2.5 - - - +
567B ASP* 1.3 80.7 - - - +
569B TYR* 1.3 65.6 + - - +
570B LEU* 3.8 19.1 - - + -
599B THR* 3.6 26.7 - - + +
601B ILE* 4.4 10.8 - - + -
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Residues in contact with TYR 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B SER* 3.3 15.9 - - - +
516B ARG* 3.5 13.0 + - - -
561B ALA 3.3 22.2 - - - -
562B VAL* 4.0 7.4 - - - -
564B LYS 2.5 29.7 + - - -
565B ASP* 3.6 0.2 - - - -
566B ALA* 3.0 33.3 + - + -
567B ASP 4.9 0.2 - - - -
568B LEU* 1.3 77.0 - - - +
570B LEU* 1.3 60.2 + - - +
571B LEU* 4.0 12.6 - - + -
595B MET* 3.4 33.2 - - + -
598B LYS* 3.7 28.1 + - + +
599B THR 3.0 18.1 + - - +
600B ARG* 3.3 2.0 - - + +
601B ILE 2.8 32.1 + - - +
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 3.8 31.6 - - + +
471B ILE* 3.8 15.7 - - + -
472B MET* 3.7 32.8 - - + -
488B ILE* 3.8 18.2 - - + -
489B SER 2.8 10.3 + - - +
490B PHE* 3.4 9.2 - - + -
491B CYS 2.8 26.5 + - - -
568B LEU* 3.8 22.4 - - + -
569B TYR* 1.3 78.3 - - - +
571B LEU* 1.3 62.6 + - - +
572B ASP 3.9 0.4 - - - -
601B ILE* 3.6 28.7 - - + -
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Residues in contact with LEU 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 4.7 2.8 - - - +
489B SER 5.2 0.7 - - - +
491B CYS* 3.6 24.2 - - + -
558B LEU* 4.2 18.4 - - + -
561B ALA* 4.4 9.0 - - + -
562B VAL* 5.1 1.8 - - + -
569B TYR* 4.0 26.5 - - + +
570B LEU* 1.3 76.1 - - - +
572B ASP* 1.3 60.4 + - - +
573B SER 3.3 3.3 + - - -
574B PRO* 4.3 9.0 - - + -
591B VAL* 5.1 11.2 - - + -
595B MET* 4.3 13.9 - - + -
600B ARG* 4.1 13.5 - - + -
601B ILE 2.8 19.1 + - - +
602B LEU* 3.4 21.6 - - + +
603B VAL 2.9 26.5 + - - -
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Residues in contact with ASP 572 (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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6B MG 4.0 0.3 - - - -
465B THR* 2.5 40.5 + - - +
468B LEU* 3.7 17.8 - - + +
490B PHE* 4.1 7.9 - - + -
491B CYS 2.8 18.1 + - - +
492B SER* 3.6 2.8 + - - +
493B GLN* 3.3 41.5 + - + +
570B LEU 3.9 0.8 + - - -
571B LEU* 1.3 69.6 - - - +
573B SER* 1.3 71.4 + - - +
574B PRO* 3.3 1.8 - - - +
603B VAL* 3.4 25.6 - - - +
662E LEU* 6.0 0.2 - - - +
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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
------------------------------------------------------------
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