Contacts of the strand formed by residues 526 - 529 (chain A) in PDB entry 4XK8
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 LYS 526 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A THR 5.2 9.4 - - - +
387A THR* 3.6 34.4 - - + +
389A TYR* 3.9 17.5 - - + +
522A ALA* 3.2 5.4 - - - +
523A VAL 2.9 37.4 + - - +
524A GLY 4.5 4.9 - - - +
525A GLY* 1.3 81.2 - - - +
527A VAL* 1.3 62.5 + - - +
626A GLY 3.8 6.5 - - - +
627A THR* 4.5 16.1 - - + +
628A ILE* 4.4 0.2 - - - -
758A GLY 3.0 30.7 + - - +
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Residues in contact with VAL 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 4.3 1.0 - - - +
389A TYR* 2.6 28.8 + - - +
520A LEU* 4.5 6.5 - - + -
521A VAL 4.1 3.6 - - - +
522A ALA* 4.3 2.5 - - - +
526A LYS* 1.3 72.5 - - - +
528A ALA* 1.3 65.2 + - - +
529A LEU* 3.9 15.5 - - - +
530A LEU* 3.7 19.7 - - + -
624A VAL 3.4 23.8 - - - +
625A TRP* 4.4 1.9 - - - -
626A GLY 3.0 21.7 + - - +
628A ILE* 4.3 15.3 - - + -
634A VAL* 3.8 30.5 - - + -
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Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.8 0.9 - - + -
292A GLY* 4.2 11.0 - - - +
386A ALA* 3.8 32.3 - - + +
387A THR* 4.0 13.2 - - + -
521A VAL* 2.8 33.7 + - + +
522A ALA* 4.5 2.0 - - - -
523A VAL* 4.6 0.9 - - + -
526A LYS 3.4 4.0 + - - -
527A VAL* 1.3 75.9 - - - +
529A LEU* 1.3 74.0 + - + +
624A VAL* 4.5 5.2 - - - +
625A TRP* 4.8 4.2 + - - -
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Residues in contact with LEU 529 (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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287A LEU* 3.8 17.0 - - + -
377A TYR* 4.2 12.8 - - + +
378A SER 3.5 27.4 - - - +
380A PRO* 3.6 25.6 - - + -
386A ALA* 5.1 0.2 - - + -
513A LEU* 3.7 19.6 - - + +
514A THR* 4.0 22.0 - - + -
520A LEU* 3.7 2.6 - - - +
521A VAL* 2.9 32.2 + - + +
527A VAL* 3.7 4.5 - - - -
528A ALA* 1.3 87.2 - - - +
530A LEU* 1.3 67.8 + - - +
532A ILE* 5.5 1.3 - - + -
620A MET* 5.7 2.2 - - - -
624A VAL* 4.1 16.2 - - + -
625A TRP* 5.9 1.1 - - - +
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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