Contacts of the helix formed by residues 342 - 352 (chain B) 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 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B ARG 3.0 6.5 + - - -
341B GLY* 1.3 77.2 - - - +
343B LYS* 1.3 57.8 + - - -
344B LYS* 3.0 5.0 - - - +
345B MET* 3.2 2.6 + - - +
346B ILE* 3.1 36.1 + - - +
383B ALA* 5.6 3.4 - - - -
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLY* 1.3 69.9 - - - -
344B LYS* 1.3 58.2 + - - +
346B ILE* 4.0 13.0 - - + +
347B LYS* 3.2 27.2 + - - +
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B PRO 4.7 5.4 - - - +
340B ARG* 3.4 20.9 - - + +
342B GLY* 3.0 1.0 - - - +
343B LYS* 1.3 78.0 - - - +
345B MET* 1.3 59.9 + - - +
347B LYS* 3.3 5.2 + - - +
348B ALA* 3.0 28.9 + - - +
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Residues in contact with MET 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B PHE* 3.6 27.8 - - + -
335B MET* 3.8 21.3 - - + +
340B ARG 3.0 20.3 + - - +
341B GLY 3.6 19.1 - - - +
342B GLY 3.2 5.3 + - - +
344B LYS* 1.3 77.0 - - - +
346B ILE* 1.3 80.9 + - + +
348B ALA* 3.0 5.4 + - - +
349B LEU* 2.9 37.5 + - + +
364B PHE* 4.0 12.3 - - + -
383B ALA* 4.2 6.1 - - - +
386B MET* 3.7 38.8 - - + -
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Residues in contact with ILE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B GLY 3.1 19.4 + - - +
343B LYS* 4.3 8.5 - - - +
345B MET* 1.3 90.0 - - + +
347B LYS* 1.3 60.5 + - - +
349B LEU* 3.4 7.1 + - - -
350B THR* 2.8 31.2 + - - +
361B ILE* 3.4 24.5 - - + +
364B PHE* 4.1 12.1 - - + -
383B ALA* 4.1 20.0 - - + -
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Residues in contact with LYS 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LYS 3.2 20.5 + - - +
344B LYS* 3.7 5.6 - - - +
345B MET 3.2 0.2 - - - -
346B ILE* 1.3 76.7 - - - +
348B ALA* 1.3 64.1 + - - +
350B THR* 3.3 6.4 + - - -
351B ASN* 2.9 46.6 + - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B PHE* 3.6 24.4 - - + -
344B LYS 3.0 13.9 + - - +
345B MET* 3.0 9.6 + - - +
347B LYS* 1.3 76.6 - - - +
349B LEU* 1.3 58.3 + - - +
351B ASN* 4.0 6.5 - - - +
352B THR* 3.1 28.6 + - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B PHE* 3.6 27.6 - - + -
345B MET* 2.9 45.1 + - + +
346B ILE* 4.3 0.2 - - - -
347B LYS 3.2 0.2 - - - -
348B ALA* 1.3 77.0 - - - +
350B THR* 1.3 59.2 + - - +
352B THR* 3.1 23.6 - - + +
356B TRP* 4.1 15.7 - - + -
357B GLY* 3.7 22.7 - - - +
358B LYS* 3.5 16.1 + - - +
360B ILE* 4.4 7.0 - - + -
361B ILE* 3.5 31.2 - - + -
364B PHE* 4.5 0.9 - - + -
386B MET* 4.4 13.7 - - + -
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Residues in contact with THR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ILE* 2.8 23.7 + - - +
347B LYS* 3.3 8.7 + - - -
349B LEU* 1.3 77.1 - - - +
351B ASN* 1.3 64.5 + - - +
352B THR 3.6 2.5 - - - +
358B LYS* 3.6 37.5 + - - +
361B ILE* 3.2 14.2 - - + +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B LYS* 2.9 40.5 + - - +
348B ALA* 4.0 6.5 - - - +
349B LEU 3.2 0.2 - - - -
350B THR* 1.3 84.1 - - - +
352B THR* 1.3 69.0 + - - +
353B PRO* 3.5 3.8 - - - +
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Residues in contact with THR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B PHE* 6.2 3.1 - - - -
348B ALA 3.1 14.5 + - - +
349B LEU* 3.1 25.5 - - + +
350B THR 4.4 4.2 - - - +
351B ASN* 1.3 80.5 - - - +
353B PRO* 1.3 74.3 - - - +
354B LEU* 3.5 36.0 + - + +
356B TRP* 5.9 3.3 - - + -
357B GLY* 3.9 12.1 - - - +
358B LYS* 5.1 4.9 - - - +
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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