Contacts of the helix formed by residues 507 - 516 (chain A) in PDB entry 1XB7
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 HIS 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A CYS 4.8 1.8 + - - -
326A ASP* 3.5 32.6 - - + -
329A ASP* 3.3 37.1 + - + +
505A PRO 5.8 1.8 - - - -
506A MET* 1.3 79.4 - - - +
508A LYS* 1.3 67.8 + - - +
509A LEU 3.4 0.7 - - - +
510A PHE* 3.3 6.5 + - - +
511A LEU* 3.2 18.6 + - - +
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Residues in contact with LYS 508 (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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507A HIS* 1.3 73.2 - - - +
509A LEU* 1.3 58.3 + - - +
511A LEU* 3.2 12.6 + - + +
512A GLU* 2.9 30.2 + - - +
209P GLU* 4.0 25.4 - - + +
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Residues in contact with LEU 509 (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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329A ASP* 3.7 12.8 + - - +
332A ILE* 3.5 35.7 - - + -
333A VAL* 3.8 29.4 - - + +
336A ILE* 4.4 4.9 - - + -
507A HIS* 3.4 0.6 - - - +
508A LYS* 1.3 78.9 - - - +
510A PHE* 1.3 58.3 + - - +
512A GLU* 3.3 7.7 + - - +
513A MET* 3.0 43.4 + - + +
209P GLU* 4.0 26.4 - - + +
210P LEU* 4.0 17.5 - - + +
213P TYR* 4.0 16.4 - - + +
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Residues in contact with PHE 510 (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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325A CYS* 4.0 29.6 - - + -
328A PHE* 3.5 33.7 - + + -
329A ASP* 3.3 22.0 + - + +
332A ILE* 3.7 21.1 - - + -
361A TRP* 3.7 21.1 - + - -
362A MET* 5.4 0.9 - - + -
495A PHE* 3.8 25.6 - + + -
506A MET* 3.9 22.2 - - + -
507A HIS 3.7 9.2 - - - +
508A LYS 3.3 0.4 - - - -
509A LEU* 1.3 78.6 - - - +
511A LEU* 1.3 61.3 + - - +
513A MET* 3.4 2.1 + - - +
514A LEU* 3.1 50.2 + - + +
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Residues in contact with LEU 511 (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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499A LYS* 3.7 42.3 - - + -
506A MET* 3.9 35.0 - - + +
507A HIS 3.2 13.9 + - - +
508A LYS* 3.2 12.0 + - + +
510A PHE* 1.3 73.5 - - - +
512A GLU* 1.3 68.1 + - - +
514A LEU* 3.2 7.3 + - - +
515A GLU* 3.0 23.9 + - - +
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Residues in contact with GLU 512 (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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508A LYS* 2.9 12.8 + - - +
509A LEU* 3.4 10.9 - - - +
511A LEU* 1.3 77.5 - - - +
513A MET* 1.3 63.4 + - + +
515A GLU* 3.5 7.1 + - - +
516A ALA* 3.3 21.3 + - - +
208P SER* 3.3 18.4 + - - -
209P GLU* 2.9 35.1 + - - +
210P LEU* 3.0 32.9 + - - +
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Residues in contact with MET 513 (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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332A ILE* 4.1 28.3 - - + -
336A ILE* 5.5 1.1 - - + -
357A LEU* 3.9 13.2 - - + +
358A GLN* 4.0 11.6 - - - +
361A TRP* 3.5 61.2 + - + +
492A LEU* 5.1 1.7 - - - +
509A LEU* 3.0 30.9 + - + +
510A PHE 3.9 2.7 - - - +
511A LEU 3.2 0.2 - - - -
512A GLU* 1.3 77.9 - - - +
514A LEU* 1.3 64.4 + - - +
516A ALA* 3.6 18.1 + - - +
210P LEU* 3.7 34.1 - - + -
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Residues in contact with LEU 514 (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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361A TRP* 4.6 6.3 - - + -
362A MET* 5.9 0.2 - - + -
492A LEU* 3.9 41.2 - - + +
495A PHE* 4.1 20.2 - - + +
496A TYR* 3.6 36.0 - - + +
499A LYS* 4.6 8.3 - - + -
506A MET* 4.2 9.6 - - - -
510A PHE* 3.1 51.6 + - + +
511A LEU* 3.6 7.6 - - - +
513A MET* 1.3 76.2 - - - +
515A GLU* 1.3 65.1 + - - +
516A ALA 3.9 4.9 - - - +
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Residues in contact with GLU 515 (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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496A TYR* 4.4 11.5 + - - -
499A LYS* 5.4 8.7 - - - +
511A LEU 3.0 13.4 + - - +
512A GLU* 3.6 11.2 - - - +
514A LEU* 1.3 77.4 - - - +
516A ALA* 1.3 64.3 + - - +
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Residues in contact with ALA 516 (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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358A GLN* 3.8 52.5 - - + +
512A GLU 3.3 14.3 + - - +
513A MET* 3.9 12.8 - - - +
514A LEU 3.3 5.8 - - - +
515A GLU* 1.3 85.7 - - - +
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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