Contacts of the helix formed by residues 397 - 409 (chain A) in PDB entry 4X4W
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 GLU 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A PRO* 4.2 6.1 - - + -
395A GLN* 3.9 15.9 + - - +
396A MET* 1.3 77.0 - - - +
398A LYS* 1.3 68.1 + - - +
399A ASP 3.2 3.5 + - - +
400A GLU* 3.1 19.8 + - + +
401A LEU* 3.1 25.1 + - - +
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Residues in contact with LYS 398 (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 PRO* 3.6 27.0 + - + +
362A VAL* 4.2 12.6 - - + -
366A ASP* 3.4 33.9 - - - +
397A GLU* 1.3 75.3 - - - +
399A ASP* 1.3 61.5 + - - +
401A LEU* 3.1 2.4 + - - +
402A LEU* 2.8 48.9 + - + +
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Residues in contact with ASP 399 (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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397A GLU* 3.3 2.4 - - + +
398A LYS* 1.3 81.3 - - - +
400A GLU* 1.3 53.9 + - + +
402A LEU* 3.7 13.1 - - - +
403A SER* 2.7 37.4 + - - -
406A LYS* 5.8 1.0 + - - -
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Residues in contact with GLU 400 (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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395A GLN* 4.3 8.3 + - - +
396A MET* 3.4 32.2 - - + +
397A GLU* 3.1 35.8 + - + +
399A ASP* 1.3 77.8 - - + +
401A LEU* 1.3 57.0 + - - +
403A SER* 3.3 8.0 + - - -
404A TYR* 2.9 27.5 + - - +
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Residues in contact with LEU 401 (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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360A PHE* 4.3 3.1 - - + -
361A PRO* 3.5 36.6 - - + -
362A VAL* 3.8 17.9 - - + -
385A LEU* 3.1 44.1 - - + +
388A GLN* 4.1 7.0 - - + -
389A TRP* 4.0 16.4 - - + +
396A MET* 3.7 33.7 - - + +
397A GLU 3.1 12.0 + - - +
398A LYS 3.6 6.1 - - - +
400A GLU* 1.3 79.7 - - - +
402A LEU* 1.3 57.2 + - - +
404A TYR* 3.2 4.9 + - + +
405A ILE 3.0 21.8 + - - -
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Residues in contact with LEU 402 (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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362A VAL* 4.1 14.4 - - + -
366A ASP* 4.1 32.1 - - + +
367A ILE* 4.2 14.8 - - + -
370A VAL* 4.4 6.7 - - + -
385A LEU* 4.8 0.9 - - + -
398A LYS* 2.8 49.6 + - + +
399A ASP* 3.8 13.0 - - - +
401A LEU* 1.3 71.0 - - - +
403A SER* 1.3 66.4 + - - +
405A ILE* 3.3 10.0 - - + +
406A LYS* 3.1 43.6 + - - +
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Residues in contact with SER 403 (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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399A ASP 2.7 22.3 + - - -
400A GLU* 3.3 9.9 - - - -
402A LEU* 1.3 74.0 - - - +
404A TYR* 1.3 63.4 + - - +
406A LYS* 3.3 18.6 + - - +
407A LYS* 3.4 26.3 + - - +
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Residues in contact with TYR 404 (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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384A GLN* 5.2 7.4 - - + -
385A LEU* 3.8 16.6 - - + -
388A GLN* 3.3 49.6 + - + +
396A MET* 5.6 6.5 - - - -
400A GLU 2.9 13.5 + - - +
401A LEU* 3.3 11.4 - - + +
403A SER* 1.3 77.9 - - - +
405A ILE* 1.3 68.0 + - + +
407A LYS* 3.4 15.2 + - + +
408A THR* 3.3 32.2 + - - -
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Residues in contact with ILE 405 (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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367A ILE* 4.4 6.7 - - + -
370A VAL* 5.1 5.2 - - + -
381A LEU* 3.5 46.9 - - + +
384A GLN* 4.1 15.9 - - + +
385A LEU* 3.9 30.5 - - + -
401A LEU 3.0 9.7 + - - +
402A LEU* 3.3 28.9 - - + +
404A TYR* 1.3 77.9 - - + +
406A LYS* 1.3 74.1 + - + +
408A THR* 3.3 12.5 + - - +
409A LEU* 3.0 30.4 + - + +
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Residues in contact with LYS 406 (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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370A VAL* 4.0 28.9 - - + +
399A ASP* 5.8 1.0 + - - -
402A LEU* 3.1 39.7 + - - +
403A SER* 3.3 11.7 + - - +
405A ILE* 1.3 81.2 - - + +
407A LYS* 1.3 64.1 + - + +
409A LEU* 3.3 26.0 + - + +
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Residues in contact with LYS 407 (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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403A SER* 3.4 24.2 + - - +
404A TYR* 3.5 14.4 - - + +
405A ILE 3.2 0.4 - - - -
406A LYS* 1.3 76.8 - - + +
408A THR* 1.3 68.2 + - - +
409A LEU 3.0 7.3 + - - -
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Residues in contact with THR 408 (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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381A LEU* 4.9 2.2 - - + -
384A GLN* 3.6 23.9 + - - +
404A TYR* 3.3 28.5 + - - -
405A ILE* 3.3 17.7 + - + +
407A LYS* 1.3 77.2 - - - +
409A LEU* 1.3 70.4 + - + +
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Residues in contact with LEU 409 (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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370A VAL* 4.3 23.8 - - + +
372A ILE* 4.6 13.2 - - + -
377A GLU* 4.8 7.9 - - - +
381A LEU* 4.1 26.7 - - + -
405A ILE* 3.0 33.2 + - + +
406A LYS* 3.4 19.5 - - + +
407A LYS 3.0 11.3 - - - -
408A THR* 1.3 86.6 - - + +
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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