Contacts of the helix formed by residues 344 - 365 (chain A) in PDB entry 4N78
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 ASN 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A TYR* 1.3 71.8 - - - +
345A ILE* 1.3 64.2 + - - +
346A CYS* 3.0 19.8 - - - +
347A GLU* 2.8 58.5 + - + +
348A GLN* 3.2 11.3 + - - +
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TYR 3.6 6.4 + - - +
344A ASN* 1.3 75.7 - - - +
346A CYS* 1.3 76.5 + - + +
348A GLN* 3.5 12.4 - - - +
349A MET* 2.6 46.3 + - + +
407A HIS* 4.1 24.5 - - + +
411A VAL* 4.8 12.3 - - + -
446A GLU* 4.8 12.8 - - + +
447A GLU* 4.3 30.1 - - + +
450A ALA* 4.6 18.6 - - + -
451A LEU* 6.2 1.8 - - + -
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Residues in contact with CYS 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ASN* 2.9 20.3 + - - +
345A ILE* 1.3 91.4 - - + +
347A GLU* 1.3 57.9 + - - +
349A MET* 3.5 6.4 + - - +
350A ILE* 3.3 37.9 + - - +
353A ARG* 4.8 3.5 + - - -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TYR* 5.6 8.5 - - - +
344A ASN* 2.8 29.2 + - + +
346A CYS* 1.3 75.8 - - - +
348A GLN* 1.3 68.5 + - - +
350A ILE* 3.7 14.6 + - - +
351A GLN* 3.7 12.6 + - - +
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Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A TYR* 3.3 38.0 - - + +
344A ASN 3.3 14.6 - - - +
345A ILE* 3.1 14.1 + - - +
347A GLU* 1.3 84.9 - - + +
349A MET* 1.3 60.9 + - - +
351A GLN* 3.4 6.2 + - - +
352A ILE* 3.0 36.8 + - + +
407A HIS* 3.8 35.3 + - + +
411A VAL* 5.4 3.4 - - - +
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Residues in contact with MET 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 2.6 30.9 + - + +
346A CYS* 4.0 6.1 - - - +
347A GLU 3.4 0.2 - - - -
348A GLN* 1.3 71.0 - - - +
350A ILE* 1.3 60.2 + - - +
352A ILE* 3.8 6.9 - - + +
353A ARG* 2.9 56.7 + - + +
407A HIS* 4.8 6.7 - - - -
450A ALA* 3.8 26.5 - - + +
453A GLU* 3.6 45.8 - - + +
454A VAL* 3.6 20.9 - - + -
457A MET* 3.9 16.2 - - + -
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A CYS* 3.3 24.5 + - - +
347A GLU* 3.9 10.8 - - - +
348A GLN 3.3 0.2 - - - -
349A MET* 1.3 79.2 - - - +
351A GLN* 1.3 62.2 + - - +
353A ARG* 3.9 18.5 - - - +
354A GLU* 3.0 47.6 + - + +
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Residues in contact with GLN 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 GLU 3.7 8.7 + - - +
348A GLN* 3.4 9.3 + - - +
349A MET 3.3 0.2 - - - -
350A ILE* 1.3 78.1 - - - +
352A ILE* 1.3 61.8 + - + +
354A GLU* 3.0 24.1 + - - +
355A ASP* 2.9 67.0 + - - +
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Residues in contact with ILE 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 GLN* 3.0 26.2 + - + +
349A MET* 3.8 8.1 - - + +
351A GLN* 1.3 77.1 - - + +
353A ARG* 1.3 58.6 + - - +
355A ASP* 3.3 5.9 + - - +
356A HIS* 2.9 27.7 + - - +
404A TRP* 3.6 41.9 - - + +
407A HIS* 4.3 22.4 - - + +
454A VAL* 4.1 22.7 - - + -
457A MET* 3.6 26.0 - - + -
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Residues in contact with ARG 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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346A CYS* 4.8 4.8 + - - +
349A MET* 2.9 43.4 + - + +
350A ILE* 3.9 23.5 - - - +
352A ILE* 1.3 74.6 - - - +
354A GLU* 1.3 62.6 + - + +
356A HIS* 3.5 8.4 + - - +
357A MET* 3.1 22.5 + - - +
453A GLU* 3.0 40.1 + - - +
457A MET* 4.2 17.5 - - + -
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Residues in contact with GLU 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 ILE* 3.0 41.6 + - + +
351A GLN* 3.0 26.0 + - - +
353A ARG* 1.3 77.2 - - + +
355A ASP* 1.3 60.3 + - - +
357A MET* 3.2 8.1 + - - +
358A ARG* 2.9 33.0 + - - +
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Residues in contact with ASP 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 GLN* 2.9 51.0 + - - +
352A ILE* 3.8 6.3 - - - +
354A GLU* 1.3 74.0 - - - +
356A HIS* 1.3 65.7 + - - +
358A ARG* 4.1 11.3 + - - +
359A PHE* 3.0 29.6 + - - +
400A LEU* 3.9 29.0 - - + +
403A GLN* 4.9 5.5 - - - +
404A TRP* 4.6 1.0 + - + -
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Residues in contact with HIS 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 ILE 2.9 17.7 + - - +
353A ARG 3.6 6.4 + - - +
355A ASP* 1.3 77.1 - - - +
357A MET* 1.3 64.9 + - - +
360A ILE* 3.1 65.5 + - + +
400A LEU* 4.9 0.4 - - - -
404A TRP* 3.8 21.5 - + + -
457A MET* 3.4 48.0 + - + +
460A GLY* 6.0 1.2 - - - -
461A LEU 5.5 0.8 + - - -
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Residues in contact with MET 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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353A ARG 3.1 10.9 + - - +
354A GLU* 3.4 10.8 - - - +
356A HIS* 1.3 83.5 + - - +
358A ARG* 1.3 64.2 + - + +
360A ILE* 5.3 0.4 - - - -
361A SER* 2.6 46.6 + - - +
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Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A GLU* 2.9 21.5 + - - +
355A ASP* 3.5 12.6 + - - +
357A MET* 1.3 78.0 - - + +
359A PHE* 1.3 60.6 + - - +
361A SER* 3.9 4.4 - - - -
362A GLU* 3.6 19.2 + - - +
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Residues in contact with PHE 359 (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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355A ASP 3.0 16.9 + - - +
356A HIS 4.5 0.2 - - - +
358A ARG* 1.3 77.3 - - - +
360A ILE* 1.3 64.6 + - + +
362A GLU* 3.1 9.7 + - - +
363A LEU* 2.8 41.6 + - + +
393A LEU* 3.5 36.8 - - + -
396A GLN* 3.6 40.8 - - + +
397A GLY* 3.3 27.6 - - - -
400A LEU* 3.9 22.7 - - + -
461A LEU* 3.9 27.1 - - + -
465A MET* 4.2 4.9 - - - -
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Residues in contact with ILE 360 (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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356A HIS* 3.1 60.0 + - + +
357A MET* 4.5 1.1 - - - +
359A PHE* 1.3 74.9 - - + +
361A SER* 1.3 60.7 + - - +
363A LEU* 4.2 7.0 - - + -
364A ALA* 2.9 33.3 + - + +
404A TRP* 5.7 0.4 - - + -
460A GLY 5.7 0.2 - - - -
461A LEU* 4.2 30.5 - - + +
464A LEU* 3.6 31.4 - - + -
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Residues in contact with SER 361 (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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357A MET* 2.6 39.0 + - - +
358A ARG* 3.9 5.8 - - - -
360A ILE* 1.3 79.2 - - - +
362A GLU* 1.3 60.8 + - - +
364A ALA* 3.8 4.7 + - - +
365A ARG* 3.2 25.5 + - - +
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Residues in contact with GLU 362 (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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358A ARG 3.6 11.3 + - - +
359A PHE* 3.1 12.8 + - - +
361A SER* 1.3 78.0 - - - +
363A LEU* 1.3 66.7 + - - +
365A ARG* 3.0 26.4 + - - +
366A TYR* 3.0 36.1 + - + +
389A LYS* 3.0 30.4 + - - -
393A LEU* 3.9 19.0 - - + +
396A GLN* 4.8 7.4 + - - +
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Residues in contact with LEU 363 (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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359A PHE* 2.8 27.8 + - + +
360A ILE* 3.9 5.8 - - + +
362A GLU* 1.3 77.5 - - - +
364A ALA* 1.3 56.8 + - - +
366A TYR* 2.8 34.0 + - + +
367A SER* 3.8 3.3 + - - +
390A LEU* 6.2 0.2 - - + -
393A LEU* 4.5 19.7 - - + +
461A LEU* 4.0 27.1 - - + -
464A LEU* 4.2 22.2 - - + +
465A MET* 4.0 14.4 - - - +
468A MET* 4.5 14.1 - - + -
472A PHE* 3.9 26.7 - - + -
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Residues in contact with ALA 364 (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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360A ILE* 2.9 24.0 + - + +
361A SER* 3.9 7.2 - - - +
362A GLU 3.3 0.2 - - - -
363A LEU* 1.3 76.3 - - - +
365A ARG* 1.3 61.0 + - + +
366A TYR 3.1 0.9 + - - -
367A SER* 3.8 19.2 + - - -
464A LEU* 6.1 2.4 - - + +
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Residues in contact with ARG 365 (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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361A SER 3.2 20.2 - - - +
362A GLU* 3.3 23.5 - - - +
363A LEU 3.0 1.0 + - - -
364A ALA* 1.3 76.0 - - + +
366A TYR* 1.3 68.6 + - + +
367A SER 3.4 3.7 + - - -
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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