Contacts of the helix formed by residues 342 - 347 (chain A) in PDB entry 4KXY
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 THR 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP* 2.7 19.0 + - - -
340A GLY 3.6 9.1 + - - +
341A ASP* 1.3 84.7 - - - +
343A LYS* 1.3 58.6 + - - +
344A ASN* 3.2 4.0 - - - -
345A SER 2.8 21.2 + - - -
346A THR* 2.9 18.0 + - - +
388A THR* 3.4 28.2 + - - +
389A PHE* 4.1 26.9 - - + -
392A PHE* 5.6 4.7 - - + -
189B GLN* 3.8 14.1 - - - +
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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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339A ASP* 3.1 6.7 + - + -
341A ASP 3.7 0.6 - - - -
342A THR* 1.3 77.6 - - - +
344A ASN* 1.3 60.3 + - + +
346A THR* 3.6 1.6 - - - -
347A PHE* 3.0 21.8 + - - -
348A SER* 3.3 23.6 - - - +
349A GLU* 3.1 32.2 + - + +
352A LYS* 3.8 30.7 - - + +
359A PHE* 3.8 12.1 - - + -
361A GLU* 2.8 22.5 + - - +
190B SER* 2.8 36.0 + - - +
191B ASP* 2.8 31.4 + - - +
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Residues in contact with ASN 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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318A ARG* 4.8 0.3 + - - -
342A THR 3.9 0.9 - - - -
343A LYS* 1.3 76.1 - - + +
345A SER* 1.3 62.1 + - - +
347A PHE* 4.1 19.7 - - - -
349A GLU* 3.3 26.1 - - - +
189B GLN* 2.9 44.5 + - - +
190B SER* 3.6 14.4 - - - -
258B HIS* 5.1 4.6 + - - -
260B LYS* 4.6 19.6 - - - +
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Residues in contact with SER 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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318A ARG* 2.9 39.2 + - - +
342A THR 2.8 6.0 + - - -
344A ASN* 1.3 79.7 + - - +
346A THR* 1.3 64.2 + - - +
347A PHE* 3.3 3.1 - - - -
389A PHE* 3.5 31.5 - - - -
416A HIS* 3.5 11.0 + - - -
189B GLN* 3.0 19.7 + - - -
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Residues in contact with THR 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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318A ARG* 3.2 15.4 - - - +
321A TYR* 3.8 12.9 - - - -
339A ASP* 2.6 24.8 + - - +
342A THR* 2.9 32.1 + - - +
343A LYS* 3.6 0.3 - - - -
345A SER* 1.3 77.6 - - - +
347A PHE* 1.3 68.4 + - - +
348A SER* 3.3 8.6 + - - -
387A SER* 4.2 9.2 - - - -
388A THR* 3.7 19.3 - - - +
389A PHE* 4.4 0.7 - - + +
413A CYS* 6.2 1.1 - - - -
415A SER* 3.6 26.8 - - - +
472A THR* 5.6 0.2 + - - -
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Residues in contact with PHE 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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318A ARG* 3.6 46.2 - - + +
319A LYS* 3.6 56.5 - - + -
322A GLY* 3.2 22.0 - - - -
343A LYS 3.0 11.5 + - - -
344A ASN 4.1 9.9 - - - -
345A SER 3.3 8.0 - - - -
346A THR* 1.3 79.3 - - - +
348A SER* 1.3 59.2 + - - +
349A GLU* 3.0 27.1 + - - +
350A ILE* 3.1 24.5 + - + +
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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