Contacts of the helix formed by residues 524 - 534 (chain A) in PDB entry 2WXL
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 TYR 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522A GLU 5.9 1.3 - - - -
523A LEU* 1.3 77.7 - - - +
525A GLU* 1.3 55.9 + - - +
526A HIS* 3.3 29.4 - + + +
527A GLU* 2.8 35.5 + - - +
528A LYS* 2.7 33.1 + - - +
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Residues in contact with GLU 525 (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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524A TYR* 1.3 73.8 - - - +
526A HIS* 1.3 57.2 + - - +
528A LYS* 3.2 33.1 + - - +
529A ASP* 2.8 51.4 + - - +
554A LYS* 4.8 15.9 + - - -
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Residues in contact with HIS 526 (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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511A LEU* 5.8 7.0 - - + +
524A TYR* 3.6 28.9 - + + +
525A GLU* 1.3 75.6 - - - +
527A GLU* 1.3 85.2 + - + +
529A ASP* 3.1 10.4 + - - +
530A LEU* 3.1 23.0 + - - +
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Residues in contact with GLU 527 (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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511A LEU* 5.7 3.9 - - + +
515A LEU* 3.9 37.7 - - + +
522A GLU 4.8 0.7 - - - +
523A LEU* 3.5 18.1 - - + +
524A TYR* 2.8 51.4 + - + +
526A HIS* 1.3 97.5 - - + +
528A LYS* 1.3 62.3 + - - +
529A ASP 3.4 0.2 + - - -
530A LEU* 3.4 4.4 + - - +
531A VAL* 3.3 28.2 + - - +
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Residues in contact with LYS 528 (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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523A LEU* 3.5 41.3 - - + +
524A TYR 2.7 18.8 + - - +
525A GLU* 3.3 38.7 + - - +
527A GLU* 1.3 73.7 - - - +
529A ASP* 1.3 62.3 + - - +
531A VAL* 3.5 3.0 + - - +
532A TRP* 3.2 23.0 + - - +
551A LEU 5.4 6.1 + - - -
552A VAL* 3.8 32.0 - - + +
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Residues in contact with ASP 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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525A GLU* 2.8 43.8 + - - +
526A HIS* 3.1 12.5 + - - +
528A LYS* 1.3 75.0 - - - +
530A LEU* 1.3 59.8 + - - +
532A TRP* 3.5 6.1 + - - +
533A LYS* 2.9 30.0 + - - +
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Residues in contact with LEU 530 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510A GLN* 5.0 5.2 - - + -
511A LEU* 3.8 38.8 - - + +
512A ARG* 3.7 40.8 - - + +
515A LEU* 4.8 4.7 - - + -
526A HIS 3.1 14.9 + - - +
527A GLU* 3.4 5.1 + - - +
529A ASP* 1.3 75.3 - - - +
531A VAL* 1.3 57.3 + - - +
533A LYS* 3.3 8.3 + - + +
534A MET* 2.8 45.1 + - + +
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Residues in contact with VAL 531 (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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512A ARG* 4.2 11.4 - - + +
515A LEU* 4.1 20.0 - - + -
516A GLU* 4.0 22.2 - - - +
523A LEU* 4.4 9.2 - - + -
527A GLU 3.3 15.7 + - - +
528A LYS 3.7 7.6 - - - +
529A ASP 3.3 0.2 - - - -
530A LEU* 1.3 75.8 - - - +
532A TRP* 1.3 62.2 + - - +
534A MET 3.2 4.5 + - - +
535A ARG* 3.2 21.0 + - - -
538A VAL* 4.1 4.4 - - + +
548A ARG* 4.6 5.6 - - + +
549A LEU* 4.0 21.7 - - + +
552A VAL* 3.7 21.1 - - + -
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Residues in contact with TRP 532 (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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528A LYS 3.2 14.5 + - - +
529A ASP* 3.9 5.2 - - - +
531A VAL* 1.3 75.7 - - - +
533A LYS* 1.3 69.6 + - - +
534A MET 3.2 0.7 + - - -
535A ARG* 3.1 57.4 + - - +
549A LEU* 4.0 17.5 - - + -
552A VAL* 4.1 9.2 - - + +
553A THR* 3.7 36.1 - - + -
554A LYS* 6.6 0.2 - - + -
560A ASP* 3.2 50.6 + - + -
563A GLN* 3.5 29.8 + - + -
564A MET* 4.0 10.8 - - + -
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Residues in contact with LYS 533 (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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529A ASP 2.9 18.4 + - - +
530A LEU* 3.4 12.3 - - + +
532A TRP* 1.3 80.4 - - - +
534A MET* 1.3 85.5 + - + +
535A ARG* 3.5 12.9 + - - +
536A HIS* 4.9 5.5 + - - -
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Residues in contact with MET 534 (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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512A ARG* 3.0 41.1 - - - +
530A LEU* 2.8 27.2 + - + +
531A VAL 3.4 4.5 - - - -
532A TRP 3.1 0.2 - - - -
533A LYS* 1.3 116.3 - - + +
535A ARG* 1.3 61.7 + - - +
536A HIS* 3.2 4.3 - - - +
537A GLU* 2.8 34.8 + - - +
538A VAL* 3.1 21.5 + - - +
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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