Contacts of the helix formed by residues 342 - 360 (chain A) in PDB entry 2ZZ0
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 LEU 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A TYR* 4.6 9.9 - - + +
334A ASP* 4.0 0.4 + - - -
340A VAL* 2.9 35.3 + - + -
341A GLU* 1.3 76.3 - - - +
343A THR* 1.3 67.6 + - - +
344A PRO* 4.6 6.3 - - + -
345A VAL* 2.8 20.9 + - + +
346A ALA* 2.9 11.2 + - - +
370A VAL* 4.4 2.9 - - + -
371A PRO 4.2 14.6 - - - +
372A THR* 4.0 24.9 - - - +
900A FAD 3.0 42.8 + - + +
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Residues in contact with THR 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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22A SER* 3.1 23.3 - - - +
59A CYS* 3.4 22.1 - - + +
64A CYS* 3.5 0.7 - - - -
342A LEU* 1.3 69.0 - - - +
344A PRO* 1.3 74.7 - - + +
346A ALA* 2.9 4.3 + - - +
347A ILE* 2.9 34.4 + - + +
900A FAD 3.0 42.6 + - - -
472B HIS* 3.9 17.0 - - + -
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Residues in contact with PRO 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.5 6.3 - - + -
343A THR* 1.3 93.7 - - + +
345A VAL* 1.3 51.5 + - - +
347A ILE* 3.3 10.2 + - + +
348A GLN* 2.7 35.3 + - - +
900A FAD 3.6 6.7 - - - +
469B ILE* 3.5 13.7 - - + +
470B GLY* 3.2 33.4 - - - +
471B ILE* 4.6 0.4 - - - -
472B HIS* 3.3 32.5 - - + +
477B GLU* 4.9 3.1 - - - +
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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
----------------------------------------------------------
340A VAL* 3.7 29.8 - - + +
342A LEU* 2.8 17.3 + - + +
344A PRO* 1.3 69.6 - - + +
346A ALA* 1.3 71.7 + - - +
348A GLN* 3.7 3.7 - - - +
349A ALA* 3.0 19.8 + - - +
365A CYS* 4.6 3.8 - - - -
367A TYR* 3.3 37.0 - - + -
370A VAL* 3.7 33.2 - - + -
469B ILE* 4.0 12.3 - - + -
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Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 4.0 1.3 - - - -
23A GLY* 3.5 28.7 - - - +
332A ILE* 4.1 1.0 - - - +
333A GLY* 4.2 16.4 - - - +
340A VAL 5.3 0.4 + - - -
342A LEU 2.9 10.2 + - - +
343A THR* 3.5 7.4 - - - +
345A VAL* 1.3 78.9 - - - +
347A ILE* 1.3 60.0 + - - +
349A ALA* 3.1 3.5 + - - +
350A GLY* 2.8 27.4 + - - -
900A FAD 4.0 24.0 - - - +
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Residues in contact with ILE 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER* 3.6 23.8 - - - +
26A ALA* 3.8 18.8 - - + +
343A THR* 2.9 31.5 + - + +
344A PRO* 3.5 10.8 - - + +
346A ALA* 1.3 76.5 - - - +
348A GLN* 1.3 65.4 + - - +
351A ARG* 3.0 33.9 + - + +
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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
----------------------------------------------------------
344A PRO 2.7 20.0 + - - +
345A VAL 3.7 4.3 - - - +
347A ILE* 1.3 75.4 - - - +
349A ALA* 1.3 58.9 + - - +
351A ARG* 3.7 22.2 + - - +
352A LEU* 2.9 53.0 + - + +
365A CYS* 3.8 14.6 - - - -
366A ASP 5.5 0.7 - - - +
466B ASP 3.1 26.1 + - - -
467B SER* 4.4 5.3 + - - +
468B THR 4.9 2.1 + - - -
469B ILE* 3.7 30.2 - - + +
481B THR* 5.3 5.5 - - - +
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Residues in contact with ALA 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 4.4 5.6 - - + +
332A ILE* 3.7 22.0 - - + -
333A GLY 5.4 1.1 - - - +
345A VAL 3.0 10.6 + - - +
346A ALA* 3.4 8.5 - - - +
348A GLN* 1.3 79.2 - - - +
350A GLY* 1.3 64.4 + - - +
352A LEU* 3.8 1.0 - - - +
353A LEU* 2.8 27.0 + - - +
356A ARG* 5.0 0.7 + - - -
365A CYS* 4.0 12.5 - - + -
367A TYR* 3.5 23.3 - - - +
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 4.3 1.1 - - - -
26A ALA* 4.7 0.2 - - - -
27A ALA* 3.6 29.6 - - - +
332A ILE* 3.6 24.2 - - - +
346A ALA 2.8 16.4 + - - -
347A ILE 3.9 1.1 - - - -
349A ALA* 1.3 75.2 - - - +
351A ARG* 1.3 61.1 + - - +
353A LEU* 3.5 3.8 - - - +
354A ALA* 3.2 17.2 + - - +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA* 4.5 11.0 - - + +
27A ALA 4.4 1.6 - - - +
30A GLU* 2.9 46.7 + - + +
347A ILE* 3.0 26.2 + - + +
348A GLN* 3.7 17.4 + - - +
350A GLY* 1.3 76.7 - - - +
352A LEU* 1.3 74.1 + - - +
354A ALA 3.3 0.2 + - - -
355A GLN* 3.2 38.4 + - - +
466B ASP* 5.7 3.6 + - - -
481B THR* 4.1 25.9 + - - +
483B SER* 6.0 4.0 - - - -
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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
----------------------------------------------------------
348A GLN* 2.9 40.5 + - + +
349A ALA* 4.0 2.7 - - - +
351A ARG* 1.3 82.3 - - - +
353A LEU* 1.3 52.3 + - - +
355A GLN* 3.0 24.0 + - - +
356A ARG* 2.8 45.9 + - - +
361A SER* 4.5 0.7 - - - +
363A VAL* 3.4 36.8 - - + +
364A LYS 3.5 5.2 - - - +
365A CYS* 3.4 38.6 - - + +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 6.4 0.7 - - + -
27A ALA* 5.1 0.4 - - + -
158A LEU* 3.7 43.1 - - + -
321A GLU 3.7 10.5 - - - +
322A GLU* 4.6 2.0 - - + -
330A TYR* 3.9 29.2 - - + -
332A ILE* 4.3 10.1 - - + -
349A ALA 2.8 22.3 + - - +
350A GLY 3.5 3.4 - - - +
352A LEU* 1.3 70.2 - - - +
354A ALA* 1.3 67.3 + - - +
356A ARG* 2.9 42.7 + - - +
357A LEU* 3.0 29.5 + - + +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 6.1 0.9 - - + -
27A ALA* 4.2 5.8 - - + +
30A GLU* 3.8 10.8 - - + -
31A ALA* 3.7 37.2 - - + +
34A TYR* 4.1 2.5 - - - -
350A GLY 3.2 7.3 + - - +
351A ARG 3.7 7.9 - - - +
353A LEU* 1.3 82.3 - - - +
355A GLN* 1.3 61.2 + - - +
357A LEU* 4.6 0.9 - - - +
358A TYR* 3.0 38.3 + - + +
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Residues in contact with GLN 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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30A GLU* 3.0 34.1 + - + +
34A TYR* 3.0 28.2 + - + +
351A ARG* 3.2 27.9 + - - +
352A LEU* 3.0 27.2 + - - +
354A ALA* 1.3 73.8 - - - +
356A ARG* 1.3 67.7 - - - +
359A ALA* 2.9 23.9 + - + -
360A GLY 3.3 6.4 + - - -
361A SER* 3.3 21.6 + - - +
363A VAL* 5.7 0.3 - - - +
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Residues in contact with ARG 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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321A GLU* 2.8 67.4 + - - +
322A GLU* 3.5 9.6 + - - -
349A ALA 5.0 0.2 + - - -
352A LEU* 2.8 30.1 + - - +
353A LEU* 2.9 29.4 + - - +
355A GLN* 1.3 79.7 - - - +
357A LEU* 1.3 70.7 + - + +
360A GLY* 3.7 9.7 + - - -
361A SER* 3.4 28.0 - - - +
362A THR* 4.6 4.0 - - - +
363A VAL 3.2 32.8 + - - +
364A LYS* 4.2 9.5 - - - +
365A CYS* 4.6 0.4 - - - +
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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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15A LEU* 5.6 3.4 - - + -
156A ARG* 3.5 39.5 - - + +
321A GLU* 6.0 1.1 - - - +
330A TYR* 4.2 31.0 - - + +
353A LEU* 3.0 30.3 + - + +
354A ALA* 3.9 3.6 - - - +
356A ARG* 1.3 85.4 - - + +
358A TYR* 1.3 89.6 + - + +
359A ALA 3.3 4.1 + - - -
360A GLY 4.1 2.6 + - - -
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Residues in contact with TYR 358 (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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14A ASP* 3.7 11.7 + - + -
15A LEU* 3.7 32.9 - - + +
31A ALA* 3.9 33.0 - - + -
34A TYR* 3.1 34.6 - - + +
36A LYS* 3.8 33.2 - - + -
156A ARG* 3.9 19.7 + - - -
354A ALA* 3.0 18.2 + - - -
357A LEU* 1.3 102.6 - - + +
359A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.3 31.2 - - + +
355A GLN* 2.9 18.4 + - + +
357A LEU 3.3 1.0 + - - -
358A TYR* 1.3 78.5 - - - +
360A GLY* 1.3 66.8 + - - +
361A SER* 3.2 3.2 + - - +
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Residues in contact with GLY 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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355A GLN 3.3 1.8 + - - -
356A ARG 3.7 8.3 + - - -
357A LEU 4.1 2.6 + - - -
359A ALA* 1.3 77.2 - - - +
361A SER* 1.3 65.5 + - - +
362A THR* 3.7 10.4 + - - +
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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
------------------------------------------------------------
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