Contacts of the helix formed by residues 339 - 353 (chain A) in PDB entry 3PEY
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 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A VAL* 3.4 8.4 - - - +
338A ALA* 1.3 90.7 - - + +
340A LYS* 1.3 60.7 + - - +
341A LYS* 3.7 9.5 + - - +
342A THR* 3.0 31.3 + - - +
343A ALA 3.0 22.3 + - - -
387A THR* 4.2 5.6 - - - -
1B U 3.5 21.5 - - + +
2B U 3.4 9.4 - - - -
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A THR* 1.3 69.2 - - - +
341A LYS* 1.3 66.3 + - - +
343A ALA* 3.2 8.0 + - - +
344A ASN* 2.9 31.7 + - - +
361A HIS* 3.7 34.3 - - + +
362A GLY 4.8 0.4 - - - -
363A ASP* 2.9 44.8 + - - +
387A THR* 3.9 8.7 - - + -
2B U 2.8 34.6 + - - +
3B U 3.0 28.6 + - - +
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Residues in contact with LYS 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A THR* 3.2 9.2 + - - +
340A LYS* 1.3 78.5 - - - +
342A THR* 1.3 63.4 + - - +
344A ASN* 3.3 9.2 + - + +
345A VAL* 2.9 35.6 + - + +
2B U 4.5 0.8 + - - -
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 3.9 15.0 - - + -
338A ALA* 5.9 0.2 - - - +
339A THR* 3.0 23.0 + - - +
341A LYS* 1.3 77.0 - - - +
343A ALA* 1.3 58.4 + - - +
345A VAL* 4.4 6.5 - - + +
346A LEU* 2.8 33.5 + - + +
405A TYR* 4.5 14.8 - - + -
406A ASP* 3.9 22.9 + - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 3.6 24.0 - - + +
339A THR 3.0 9.9 + - - +
340A LYS* 3.2 10.5 + - - +
342A THR* 1.3 73.5 - - - +
344A ASN* 1.3 59.3 + - - +
346A LEU* 3.9 1.3 - - - +
347A TYR* 2.9 31.2 + - - +
359A ILE* 3.4 19.4 - - + +
361A HIS* 4.1 9.9 - - + -
385A ILE* 3.9 14.7 - - + +
386A THR* 5.2 2.5 - - - -
387A THR* 4.7 4.9 - - + -
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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
----------------------------------------------------------
340A LYS* 2.9 23.6 + - - +
341A LYS* 3.8 6.4 - - - +
343A ALA* 1.3 75.2 - - - +
345A VAL* 1.3 65.1 + - + +
347A TYR* 3.5 5.4 - - - +
348A GLY* 3.0 20.4 + - - -
359A ILE* 3.3 11.7 - - - +
361A HIS* 2.9 29.7 + - - -
364A LEU* 5.6 0.7 - - - +
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Residues in contact with VAL 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LYS* 2.9 34.6 + - + +
342A THR* 3.2 6.9 + - + +
344A ASN* 1.3 77.4 - - + +
346A LEU* 1.3 59.2 + - - +
348A GLY* 3.2 2.6 + - - -
349A LYS* 2.9 51.6 + - + +
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Residues in contact with LEU 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 PHE* 3.6 31.9 - - + -
321A LEU* 3.8 28.5 - - + -
335A ILE* 4.3 8.7 - - + -
337A VAL* 3.8 27.4 - - + -
342A THR* 2.8 19.4 + - + +
343A ALA 3.9 2.5 - - - +
345A VAL* 1.3 75.9 - - - +
347A TYR* 1.3 60.4 + - - +
349A LYS* 3.8 5.2 - - + +
350A LEU* 2.9 42.4 + - + +
385A ILE* 4.1 10.3 - - + -
405A TYR* 4.1 21.1 - - + +
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Residues in contact with TYR 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 ALA 2.9 19.3 + - - +
344A ASN* 3.5 7.6 - - - +
346A LEU* 1.3 76.8 - - - +
348A GLY* 1.3 67.1 + - - +
350A LEU* 3.3 1.4 + - - +
351A LYS* 3.0 54.1 + - + +
357A VAL* 3.2 37.4 + - + -
358A SER* 4.1 5.2 - - - -
359A ILE* 3.8 39.9 - - + -
385A ILE* 3.5 11.0 - - + +
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Residues in contact with GLY 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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344A ASN 3.0 12.1 + - - -
345A VAL 3.2 3.3 + - - -
347A TYR* 1.3 85.8 - - - +
349A LYS* 1.3 59.5 + - - +
351A LYS* 3.5 4.3 + - - +
352A SER* 3.0 25.8 + - - -
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Residues in contact with LYS 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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318A PHE* 3.5 54.1 - - + +
345A VAL* 2.9 43.2 + - + +
346A LEU* 3.8 4.2 - - + +
348A GLY* 1.3 72.1 - - - +
350A LEU* 1.3 64.1 + - - +
352A SER* 3.1 19.4 + - - -
353A GLU* 3.3 16.3 + - - +
405A TYR* 5.6 0.6 + - - -
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Residues in contact with LEU 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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318A PHE* 3.8 20.9 - - + -
321A LEU* 4.2 16.8 - - + +
322A THR* 3.9 15.9 - - + -
325A TYR* 5.1 9.4 - - + -
335A ILE* 4.6 7.4 - - + -
346A LEU* 2.9 28.8 + - + +
347A TYR 3.9 2.5 - - - +
349A LYS* 1.3 77.6 - - - +
351A LYS* 1.3 61.5 + - - +
353A GLU 3.1 8.0 + - - -
355A HIS* 3.1 51.3 + - + -
357A VAL* 4.0 17.9 - - + -
385A ILE* 3.9 21.1 - - + -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A TYR* 3.0 48.7 + - + +
348A GLY* 3.8 5.4 - - - +
350A LEU* 1.3 76.2 - - - +
352A SER* 1.3 58.2 + - - +
354A GLY* 3.0 18.9 + - - -
355A HIS 3.6 16.4 - - - +
356A GLU* 4.6 13.1 + - - +
357A VAL* 3.9 25.1 + - + +
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Residues in contact with SER 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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348A GLY 3.0 16.2 + - - -
349A LYS* 3.1 15.8 + - - -
350A LEU 3.3 0.2 - - - -
351A LYS* 1.3 77.1 - - - +
353A GLU* 1.3 60.2 + - - +
354A GLY 3.3 2.7 + - - -
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Residues in contact with GLU 353 (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 PHE* 3.3 29.3 - - - -
322A THR* 4.0 14.6 + - - +
349A LYS 3.3 12.0 + - - +
350A LEU* 3.1 9.0 + - - +
351A LYS 3.1 1.0 - - - -
352A SER* 1.3 80.1 - - - +
354A GLY* 1.3 60.8 + - - +
355A HIS* 3.3 25.4 + - + +
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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