Contacts of the helix formed by residues 534 - 542 (chain A) in PDB entry 2WXJ
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 MET 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A ARG* 3.1 46.0 - - + +
530A LEU* 2.9 27.1 - - + +
531A VAL 2.9 9.2 + - - +
533A LYS* 1.3 91.1 - - + +
535A ARG* 1.3 65.5 + - - +
536A HIS 3.1 3.4 - - - -
537A GLU* 2.8 33.0 + - + +
538A VAL* 2.8 21.2 + - - +
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Residues in contact with ARG 535 (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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531A VAL 3.1 7.4 + - - -
532A TRP* 3.0 67.6 + - - +
533A LYS* 3.3 12.1 + - - +
534A MET* 1.3 75.0 - - - +
536A HIS* 1.3 84.3 + - + +
538A VAL* 3.4 10.0 + - - +
539A GLN* 3.0 26.5 + - - +
549A LEU* 3.8 20.9 - - + +
563A GLN* 3.2 42.4 + - - +
564A MET* 5.2 0.7 - - - -
567A LEU* 3.5 27.2 - - + +
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Residues in contact with HIS 536 (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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533A LYS 4.5 6.5 + - - -
534A MET 2.9 1.2 + - - -
535A ARG* 1.3 108.4 + - + +
537A GLU* 1.3 71.0 + - - +
539A GLN* 3.2 9.8 + - - +
540A GLU* 3.0 43.6 + - - +
566A TYR* 5.9 4.2 - + - -
567A LEU* 3.7 25.3 - - + +
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Residues in contact with GLU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ARG* 4.6 4.0 - - - +
533A LYS 4.2 3.8 - - - +
534A MET* 2.8 55.3 + - + +
536A HIS* 1.3 84.8 + - - +
538A VAL* 1.3 59.6 + - - +
540A GLU* 3.9 11.2 - - - +
541A HIS* 3.0 41.2 + - + +
542A PHE* 3.7 7.7 + - + -
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ARG* 3.1 28.3 - - - +
516A GLU* 4.1 3.8 - - - +
531A VAL* 4.2 12.6 - - + +
534A MET 2.8 21.9 + - - +
535A ARG* 3.4 12.3 - - - +
537A GLU* 1.3 76.3 - - - +
539A GLN* 1.3 58.9 + - - +
542A PHE* 2.9 53.3 + - + +
543A PRO* 3.7 0.2 - - - +
545A ALA* 4.3 15.3 - - + -
549A LEU* 4.0 14.6 - - + -
571A TRP* 3.7 17.5 - - + -
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Residues in contact with GLN 539 (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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535A ARG 3.0 10.7 + - - +
536A HIS* 3.3 9.5 - - - +
538A VAL* 1.3 78.7 - - - +
540A GLU* 1.3 73.4 + - - +
543A PRO* 3.8 18.2 - - - +
567A LEU* 2.8 49.3 + - + +
570A SER* 3.0 24.9 + - - -
571A TRP* 3.5 32.0 - - + -
572A PRO* 4.3 15.1 - - + +
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Residues in contact with GLU 540 (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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536A HIS* 3.0 30.3 + - - +
537A GLU* 4.2 6.1 - - - +
539A GLN* 1.3 89.5 - - + +
541A HIS* 1.3 90.9 + - + +
542A PHE 3.8 0.2 - - - -
543A PRO* 4.5 3.9 - - - +
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Residues in contact with HIS 541 (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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537A GLU* 3.0 22.0 + - + +
540A GLU* 1.3 108.3 + - + +
542A PHE* 1.3 84.4 + - + +
543A PRO* 3.6 5.7 - - - +
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Residues in contact with PHE 542 (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* 3.9 24.9 - - + -
513A GLU* 3.0 46.2 - - + -
516A GLU* 3.7 20.2 - - + +
517A ARG* 5.3 8.3 - - - -
537A GLU* 3.7 13.7 - - + -
538A VAL* 2.9 18.6 + - - +
541A HIS* 1.3 105.4 - - + +
543A PRO* 1.3 69.5 - - - +
544A GLU* 3.0 3.1 - - - -
545A ALA* 2.7 23.4 + - + +
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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