Contacts of the strand formed by residues 564 - 568 (chain A) in PDB entry 4X8G
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 564 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A LEU* 3.6 27.1 - - + +
491A LEU* 3.9 21.3 - - + -
550A ARG* 3.7 31.8 + - + +
554A LYS* 3.8 35.0 - - + -
559A LEU* 5.0 4.0 - - + -
560A ALA 3.6 14.4 - - - +
561A GLU* 3.4 26.7 + - - +
562A SER 5.0 1.0 - - - -
563A ASP* 1.3 83.8 - - + +
565A ILE* 1.3 72.4 + - - +
566A ASP* 4.2 3.0 + - - +
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Residues in contact with ILE 565 (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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488A ARG* 3.8 37.5 - - + -
489A LEU 3.0 7.8 + - - +
490A LEU* 3.8 13.0 - - + -
491A LEU 3.2 24.3 + - - -
564A ILE* 1.3 79.6 - - - +
566A ASP* 1.3 69.4 + - - +
567A ILE* 3.4 19.8 - - + +
619A LEU* 4.2 34.5 - - + +
620A LEU* 4.9 1.8 - - + -
623A LEU* 3.8 19.1 - - + -
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Residues in contact with ASP 566 (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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491A LEU* 3.5 5.9 - - - +
492A ALA 5.2 0.3 - - - +
493A SER* 3.7 25.5 + - - +
496A SER* 3.8 12.8 + - - -
550A ARG* 2.6 46.3 + - - -
564A ILE 4.9 1.4 - - - +
565A ILE* 1.3 74.5 - - - +
567A ILE* 1.3 61.2 + - - +
619A LEU* 3.4 23.2 - - - +
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Residues in contact with ILE 567 (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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490A LEU* 3.6 36.3 - - + -
491A LEU 2.8 16.3 + - - +
492A ALA* 3.4 2.1 - - - -
493A SER 2.7 30.5 + - - -
496A SER* 4.1 2.0 - - - -
565A ILE* 3.4 27.1 - - + +
566A ASP* 1.3 76.2 - - - +
568A PRO* 1.3 80.1 - - + +
569A GLN* 5.0 2.0 - - + -
586A MET* 4.4 11.4 - - + -
587A VAL* 4.3 27.6 - - + +
589A MET* 6.1 1.3 - - + -
616A VAL* 4.7 9.6 - - + -
619A LEU* 5.0 4.9 - - + -
620A LEU* 5.4 9.9 - - + -
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Residues in contact with PRO 568 (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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493A SER 3.7 8.1 - - - +
496A SER* 3.6 16.3 - - - +
497A CYS* 3.7 22.9 - - + +
500A LEU* 5.6 0.2 - - + -
566A ASP 4.0 2.2 - - - +
567A ILE* 1.3 90.1 - - + +
569A GLN* 1.3 62.6 + - - +
583A PHE* 3.7 2.7 - - - -
586A MET* 3.2 27.0 - - + +
612A LEU* 4.2 19.3 - - + +
615A LYS* 4.4 17.5 - - + -
616A VAL* 4.0 22.2 - - + -
619A LEU* 4.7 5.4 - - + -
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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