Contacts of the helix formed by residues 355 - 362 (chain A) in PDB entry 4XZC
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 LYS 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A PRO 3.5 4.6 + - - +
354A LEU* 1.3 72.8 - - - +
356A TRP* 1.3 62.2 + - - +
357A GLY 3.2 0.7 + - - -
358A LYS* 3.6 5.9 + - - +
359A LYS* 3.5 44.1 + - + +
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Residues in contact with TRP 356 (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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318A ALA* 3.9 25.7 - - + +
319A GLY 5.2 1.6 - - - -
320A ILE* 3.4 31.6 - - + +
324A THR* 3.9 14.8 + - + -
327A THR* 2.7 42.2 + - - -
328A LEU* 3.8 22.9 - - + -
331A PHE* 3.8 31.2 - + + -
349A LEU* 3.7 22.7 - - + -
352A THR* 5.6 4.3 - - + -
354A LEU* 3.8 25.7 - - + +
355A LYS* 1.3 77.1 - - - +
357A GLY* 1.3 61.9 + - - +
359A LYS* 3.5 0.8 - - - +
360A ILE* 2.7 50.6 + - + +
386A MET* 5.8 0.7 - - + -
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Residues in contact with GLY 357 (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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349A LEU* 3.4 21.7 - - - +
352A THR* 3.7 14.3 - - - +
354A LEU 3.3 3.6 + - - -
355A LYS 3.1 2.0 - - - -
356A TRP* 1.3 97.4 - - - +
358A LYS* 1.3 61.3 + - - +
360A ILE* 3.4 3.8 + - - +
361A ILE* 3.3 22.7 + - - +
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Residues in contact with LYS 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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349A LEU 4.1 9.9 - - - +
350A THR* 3.5 36.4 + - + -
352A THR 4.8 9.0 + - - +
354A LEU 4.5 2.0 + - - +
355A LYS 3.6 6.8 + - - +
357A GLY* 1.3 73.6 - - - +
359A LYS* 1.3 60.3 + - - +
361A ILE* 3.3 11.6 + - + +
362A SER* 3.1 27.5 + - - -
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Residues in contact with LYS 359 (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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317A LYS 5.0 4.0 - - - +
318A ALA* 3.2 32.1 + - - +
319A GLY* 5.6 2.8 - - - -
355A LYS* 3.5 38.9 + - + +
356A TRP* 3.2 7.8 + - - +
358A LYS* 1.3 76.4 - - - +
360A ILE* 1.3 62.6 + - - +
362A SER* 3.0 21.7 + - - +
363A LEU* 3.5 15.1 - - - +
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Residues in contact with ILE 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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314A TRP 4.6 4.9 - - - +
315A ALA* 5.7 0.2 - - - -
318A ALA* 3.6 22.7 - - + -
328A LEU* 5.1 3.1 - - + -
349A LEU* 4.0 17.0 - - + -
356A TRP* 2.7 32.4 + - + +
357A GLY 3.6 3.6 - - - +
358A LYS 3.3 0.2 - - - -
359A LYS* 1.3 68.9 - - - +
361A ILE* 1.3 67.1 + - - +
363A LEU* 3.0 24.7 + - + +
364A PHE* 3.3 29.1 - - + -
381A LEU* 3.6 21.8 - - + -
386A MET* 4.2 11.4 - - + -
389A MET* 4.0 24.0 - - + -
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Residues in contact with ILE 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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346A ILE* 3.5 17.7 - - + +
349A LEU* 3.6 19.7 - - + +
350A THR* 3.1 46.4 - - - +
357A GLY 3.3 12.1 + - - +
358A LYS* 3.3 13.4 + - + +
360A ILE* 1.3 77.6 - - - +
362A SER* 1.3 57.5 + - - +
364A PHE* 2.9 41.7 + - + +
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Residues in contact with SER 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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110A TYR* 5.2 0.2 - - - -
114A MET* 4.0 17.0 - - - +
358A LYS 3.1 12.6 + - - -
359A LYS* 3.0 20.3 + - - +
361A ILE* 1.3 78.0 - - - +
363A LEU* 1.3 62.9 + - - +
364A PHE 3.2 1.7 + - - +
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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