Contacts of the helix formed by residues 357 - 363 (chain A) in PDB entry 2X7Z
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 GLY 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A LYS* 4.6 9.6 - - - -
328A GLY 3.9 9.2 - - - -
330A GLY* 4.4 11.4 - - - -
354A ILE* 3.2 15.3 + - - +
355A GLU 3.3 2.4 + - - -
356A GLY* 1.3 79.8 - - - +
358A ALA* 1.3 65.4 + - - -
359A ALA 3.3 2.9 - - - -
360A HIS 3.3 3.0 + - - -
361A LYS* 3.0 21.2 + - - +
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Residues in contact with ALA 358 (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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322A LEU* 3.8 14.0 - - + +
323A ILE 3.3 29.2 - - - +
324A LYS* 4.5 2.5 - - - -
325A GLY 4.8 1.8 - - - +
327A LYS* 5.6 0.2 - - - +
328A GLY 3.1 20.3 + - - +
329A LEU* 3.6 8.9 + - + -
357A GLY* 1.3 71.9 - - - -
359A ALA* 1.3 62.4 + - - +
361A LYS* 3.9 6.5 - - - +
362A ASP* 3.0 25.8 + - - +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 4.1 15.1 - - + +
329A LEU 3.0 20.0 + - - +
330A GLY 4.2 6.3 - - - +
331A PHE* 4.0 8.1 - - + -
353A ILE* 4.2 8.6 - - + +
358A ALA* 1.3 76.8 - - - +
360A HIS* 1.3 58.0 + - - +
362A ASP* 3.5 2.3 + - - +
363A GLY* 3.0 24.6 + - - -
364A LYS 4.2 3.6 + - - -
365A LEU* 3.9 36.0 + - + +
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Residues in contact with HIS 360 (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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353A ILE* 3.5 21.7 - - + +
354A ILE 3.2 20.4 + - - +
355A GLU* 3.5 22.1 - - + +
356A GLY* 2.9 25.2 + - - -
357A GLY 3.3 5.1 + - - +
359A ALA* 1.3 74.4 - - - +
361A LYS* 1.3 71.4 + - + +
363A GLY* 3.0 16.3 + - - -
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Residues in contact with LYS 361 (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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327A LYS* 5.9 2.5 - - - +
356A GLY* 3.8 27.4 - - - +
357A GLY 3.0 19.7 + - - +
358A ALA* 3.9 7.0 - - - +
360A HIS* 1.3 80.8 - - - +
362A ASP* 1.3 60.9 + - - +
363A GLY* 4.4 0.3 - - - -
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Residues in contact with ASP 362 (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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320A ILE* 3.9 12.3 - - - +
321A LYS 4.5 6.1 - - - +
322A LEU* 3.6 20.2 - - + +
358A ALA 3.0 19.4 + - - +
359A ALA* 3.8 2.4 - - - +
361A LYS* 1.3 77.1 - - - +
363A GLY* 1.3 60.2 + - - +
364A LYS* 3.0 53.6 + - - +
365A LEU 4.4 0.5 + - - -
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Residues in contact with GLY 363 (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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359A ALA 3.0 10.4 + - - -
360A HIS* 3.0 14.5 + - - -
361A LYS 4.4 0.7 - - - -
362A ASP* 1.3 76.7 - - - +
364A LYS* 1.3 70.2 + - - +
365A LEU 3.7 3.1 - - - -
366A GLN* 3.4 16.0 - - - +
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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