Contacts of the helix formed by residues 341 - 352 (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 GLY 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A MET* 4.4 11.6 + - - +
339A PRO* 3.5 3.3 - - - +
340A ARG* 1.3 82.7 - - - +
342A GLY* 1.3 66.6 + - - -
343A LYS 3.4 0.2 + - - -
344A LYS* 3.2 7.8 + - - +
345A MET* 3.2 18.2 + - - -
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Residues in contact with GLY 342 (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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341A GLY* 1.3 69.4 - - - -
343A LYS* 1.3 60.0 + - - -
345A MET* 3.3 14.3 + - - +
346A ILE* 3.1 36.2 + - - +
383A ALA* 5.2 6.5 + - - -
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Residues in contact with LYS 343 (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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341A GLY 3.4 0.6 + - - -
342A GLY* 1.3 71.3 - - - -
344A LYS* 1.3 60.1 + - - +
346A ILE* 3.9 14.2 - - + +
347A LYS* 3.0 32.1 + - - +
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Residues in contact with LYS 344 (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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339A PRO 4.2 7.2 + - - +
340A ARG* 3.5 57.0 - - + +
341A GLY 3.2 9.9 + - - +
343A LYS* 1.3 77.4 - - - +
345A MET* 1.3 58.6 + - - +
347A LYS* 3.6 6.1 + - - +
348A ALA* 3.0 27.8 + - + +
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Residues in contact with MET 345 (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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331A PHE* 3.8 17.9 - - + -
335A MET* 4.0 12.8 - - - +
340A ARG 3.4 18.6 + - - +
341A GLY* 3.2 8.4 + - - -
342A GLY 3.5 24.7 - - - +
343A LYS 3.2 0.2 - - - -
344A LYS* 1.3 76.2 - - - +
346A ILE* 1.3 57.3 + - + +
348A ALA* 3.0 7.4 + - - +
349A LEU* 2.8 51.4 + - + +
364A PHE* 4.1 10.1 - - + -
383A ALA* 3.5 37.0 - - + +
386A MET* 3.8 28.7 - - - -
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Residues in contact with ILE 346 (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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342A GLY 3.1 22.5 + - - +
343A LYS* 3.9 15.5 - - + +
344A LYS 3.5 0.2 - - - -
345A MET* 1.3 84.9 - - + +
347A LYS* 1.3 55.3 + - - +
349A LEU* 3.2 7.9 + - - -
350A THR* 2.7 48.3 + - - +
361A ILE* 3.5 16.3 - - + +
364A PHE* 4.1 15.0 - - + -
383A ALA* 4.3 13.9 - - + -
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Residues in contact with LYS 347 (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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343A LYS 3.0 18.9 + - - +
344A LYS* 3.8 6.1 - - - +
346A ILE* 1.3 79.2 - - - +
348A ALA* 1.3 57.1 + - - +
350A THR* 3.3 9.1 + - + +
351A ASN* 3.0 51.3 + - - +
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Residues in contact with ALA 348 (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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331A PHE* 3.7 22.8 - - + -
344A LYS* 3.0 19.4 + - + +
345A MET* 3.0 5.6 + - - +
347A LYS* 1.3 75.6 - - - +
349A LEU* 1.3 57.4 + - - +
351A ASN* 3.1 7.0 + - - +
352A THR* 2.9 30.8 + - - -
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Residues in contact with LEU 349 (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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331A PHE* 3.4 28.9 - - + -
345A MET* 2.8 45.7 + - + +
346A ILE* 4.1 2.2 - - - -
348A ALA* 1.3 72.2 - - - +
350A THR* 1.3 61.4 + - - +
352A THR* 3.2 21.8 - - - +
356A TRP* 3.7 27.4 - - + -
357A GLY* 3.4 16.7 - - - +
358A LYS* 3.6 3.6 + - - +
360A ILE* 4.0 20.0 - - + -
361A ILE* 3.6 27.8 - - + -
364A PHE* 4.0 11.9 - - + -
386A MET* 4.8 3.6 - - + -
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Residues in contact with THR 350 (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* 2.7 32.1 + - - +
347A LYS* 3.5 11.4 - - + +
348A ALA 3.3 0.2 - - - -
349A LEU* 1.3 74.1 - - - +
351A ASN* 1.3 68.9 + - - +
352A THR 4.9 0.2 - - - -
358A LYS* 3.5 34.0 + - + +
361A ILE* 3.1 16.9 - - - +
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Residues in contact with ASN 351 (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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347A LYS* 3.0 39.1 + - - +
348A ALA* 3.1 7.0 + - - +
350A THR* 1.3 88.0 - - - +
352A THR* 1.3 69.3 + - - +
353A PRO* 3.4 5.2 - - - +
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Residues in contact with THR 352 (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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331A PHE* 6.0 4.9 - - + -
348A ALA 2.9 13.1 + - - +
349A LEU* 3.2 24.7 - - + +
350A THR 4.6 2.1 - - - +
351A ASN* 1.3 78.5 - - - +
353A PRO* 1.3 75.9 - - - +
354A LEU* 3.2 36.3 + - + +
356A TRP* 5.6 4.9 - - + -
357A GLY* 3.7 20.2 - - - +
358A LYS* 4.8 8.8 + - - +
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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