Contacts of the helix formed by residues 345 - 357 (chain A) in PDB entry 6PAU
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 ASP 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ARG* 2.9 38.1 + - - -
341A MET* 3.5 16.4 - - + -
342A GLU* 2.8 32.7 + - - +
344A LYS* 1.3 88.4 - - - +
346A ILE* 1.3 64.5 + - - +
347A LYS 3.4 0.4 - - - -
348A SER* 3.0 8.4 + - - -
349A VAL* 2.8 23.1 + - + -
386A VAL* 3.8 1.9 - - - +
394A LEU* 3.6 25.6 - - + +
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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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341A MET* 4.0 17.3 - - + -
342A GLU 3.9 0.2 + - - -
343A PRO* 3.0 38.6 + - + +
344A LYS 3.4 0.8 - - - -
345A ASP* 1.3 77.8 - - - +
347A LYS* 1.3 70.4 + - + +
349A VAL* 3.0 2.4 + - - +
350A ARG* 2.8 20.8 + - - +
368A GLU* 3.6 38.8 - - + +
371A VAL* 3.8 3.5 - - + +
372A ALA* 3.6 29.8 - - + +
376A LEU* 4.4 6.5 - - + -
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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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344A LYS 4.9 2.5 + - - +
345A ASP 3.4 0.4 - - - -
346A ILE* 1.3 77.8 - - + +
348A SER* 1.3 65.3 + - - +
350A ARG* 3.0 11.3 + - - +
351A GLU* 2.9 23.7 + - - +
368A GLU* 3.6 39.3 + - + +
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Residues in contact with SER 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 LYS 5.3 2.2 + - - -
345A ASP* 3.0 11.3 + - - -
347A LYS* 1.3 77.6 - - - +
349A VAL* 1.3 64.1 + - - +
351A GLU* 3.0 11.2 + - - +
352A LEU* 2.8 27.1 + - - +
393A LYS* 5.9 1.9 - - - +
394A LEU* 3.7 30.4 + - - +
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Residues in contact with VAL 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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341A MET* 3.8 24.5 - - + -
345A ASP* 2.8 22.1 + - + +
346A ILE 3.5 6.3 - - - +
348A SER* 1.3 70.9 - - - +
350A ARG* 1.3 64.3 + - - +
352A LEU* 3.0 10.3 + - + +
353A ILE* 2.9 22.3 + - + +
371A VAL* 3.5 22.0 - - + -
375A PHE* 4.4 10.3 - - + -
386A VAL* 4.1 20.9 - - + -
394A LEU* 4.2 4.3 - - + -
397A PHE* 3.9 28.9 - - + -
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Residues in contact with ARG 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 2.8 15.0 + - - +
347A LYS* 3.2 11.7 - - - +
349A VAL* 1.3 75.3 - - - +
351A GLU* 1.3 66.2 + - - +
353A ILE* 3.0 10.7 + - - +
354A ASN* 3.0 34.1 + - - +
365A VAL* 6.1 2.4 - - - +
366A MET 2.9 24.2 + - - +
367A ASP* 3.5 18.2 - - - +
368A GLU* 3.7 35.7 + - + +
371A VAL* 3.6 23.1 - - + +
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Residues in contact with GLU 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 2.9 12.1 + - - +
348A SER* 3.3 11.9 - - - +
350A ARG* 1.3 79.7 - - - +
352A LEU* 1.3 67.0 + - + +
354A ASN* 5.3 2.6 - - - +
355A THR* 3.1 32.4 + - - -
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Residues in contact with LEU 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 SER* 2.8 17.9 + - - +
349A VAL* 3.0 11.2 + - - +
351A GLU* 1.3 78.5 - - + +
353A ILE* 1.3 62.0 + - - +
355A THR* 4.0 2.9 - - - -
356A TYR* 3.1 24.1 + - - +
394A LEU* 3.9 44.9 - - + +
395A THR* 4.1 2.7 - - - +
396A ASP* 4.2 11.4 - - - +
397A PHE* 4.0 27.1 - - + -
425A ILE* 3.8 9.3 - - + +
427A THR* 4.0 26.7 - - + +
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Residues in contact with ILE 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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349A VAL* 2.9 16.3 + - + +
350A ARG* 3.3 14.6 - - - +
352A LEU* 1.3 75.9 - - - +
354A ASN* 1.3 80.7 + - - +
356A TYR* 3.0 1.9 + - - +
357A LEU* 2.8 59.2 + - + +
366A MET* 4.3 12.3 - - + -
371A VAL* 4.6 11.0 - - + -
375A PHE* 3.5 34.3 - - + -
397A PHE* 4.2 8.5 - - + -
423A TYR* 4.1 15.9 - - + -
425A ILE* 4.0 16.6 - - + -
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Residues in contact with ASN 354 (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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350A ARG* 3.0 32.6 + - - +
351A GLU* 4.6 3.3 - - - +
353A ILE* 1.3 89.0 - - - +
355A THR* 1.3 64.0 + - - +
357A LEU* 3.7 5.3 + - - +
358A LYS* 3.4 21.9 + - - +
364A PRO 4.3 3.5 - - - +
365A VAL* 3.8 16.4 - - + +
366A MET* 2.9 44.2 + - - +
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Residues in contact with THR 355 (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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351A GLU* 3.1 32.1 + - - -
352A LEU* 4.0 2.9 - - - -
353A ILE 3.2 0.6 - - - -
354A ASN* 1.3 76.9 - - - +
356A TYR* 1.3 68.4 + - - +
358A LYS* 3.0 46.6 + - - +
359A GLN 4.6 0.2 + - - -
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Residues in contact with TYR 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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352A LEU 3.1 16.1 + - - +
353A ILE 3.0 2.7 + - - +
355A THR* 1.3 80.9 - - - +
357A LEU* 1.3 66.4 + - + +
358A LYS 3.0 5.4 + - - -
359A GLN* 3.2 43.9 + - - +
360A PHE* 3.5 21.3 - + - -
424A ASN 3.8 19.2 + - - -
425A ILE* 3.5 31.0 - - + -
426A HIS* 3.8 32.7 + + - -
427A THR* 6.2 0.4 - - + -
431A LEU* 5.0 2.1 - - - +
456A MET* 4.2 12.1 - - - +
457A GLU* 2.5 43.0 + - - +
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Residues in contact with LEU 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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234A ARG* 2.7 27.6 + - - +
353A ILE* 2.8 47.2 + - + +
354A ASN* 4.2 5.8 - - - +
355A THR 3.2 0.4 - - - -
356A TYR* 1.3 79.9 - - + +
358A LYS* 1.3 55.5 + - - +
359A GLN 3.1 1.9 + - - -
360A PHE* 3.2 30.8 + - + +
363A ALA* 4.0 7.1 - - + +
364A PRO* 3.5 42.2 - - + +
366A MET* 6.1 0.7 - - + -
423A TYR* 4.4 7.4 - - + -
456A MET* 4.1 9.6 - - - -
492A GLY 3.8 17.3 - - - +
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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