Contacts of the helix formed by residues 327 - 343 (chain H) in PDB entry 1ZMC
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 327 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ASP* 4.3 1.0 - - - +
325H PRO* 3.0 27.5 + - + +
326H MET* 1.3 83.5 - - - +
328H ALA* 1.3 64.5 + - - +
329H HIS* 3.7 13.0 - - + +
330H LYS* 3.4 10.7 + - + +
331H ALA* 3.2 21.0 + - - +
354H VAL* 4.3 3.1 - - + -
355H PRO 3.3 26.7 - - - +
356H SER* 4.0 18.2 - - - +
357H VAL 6.2 0.7 - - - +
480H FAD 3.2 29.9 + - + +
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Residues in contact with ALA 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G HIS* 3.8 25.6 - - + -
16H PRO* 3.7 14.5 - - + +
45H CYS* 3.8 17.5 - - - -
50H CYS* 3.9 2.9 - - - -
327H LEU* 1.3 66.8 - - - +
329H HIS* 1.3 59.7 + - - +
330H LYS 3.0 1.6 - - - -
331H ALA* 3.1 4.6 + - - +
332H GLU* 2.9 33.1 + - - +
480H FAD 2.8 32.0 + - - +
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Residues in contact with HIS 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G CYS* 3.7 24.2 - - - -
450G HIS 3.0 19.5 - - - +
451G ALA* 3.6 17.4 - - + -
452G HIS* 2.8 35.2 + - + +
457G GLU* 5.2 0.2 - - - +
460G ARG* 5.0 1.3 - - - +
327H LEU* 3.7 12.3 - - + +
328H ALA* 1.3 73.9 - - - +
330H LYS* 1.3 61.4 + - - +
332H GLU* 3.6 9.3 - - - +
333H ASP* 3.0 37.5 + - - +
354H VAL* 3.9 8.7 - - + +
355H PRO* 2.8 30.0 + - + -
356H SER* 5.3 2.0 - - - -
357H VAL* 5.8 1.3 - - + -
480H FAD 3.4 20.3 + + - -
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Residues in contact with LYS 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449G CYS* 4.9 2.2 - - - -
319H GLY* 3.1 21.6 + - - +
322H VAL* 3.7 1.0 + - - +
323H ALA 2.8 28.0 + - - -
324H GLY* 3.9 4.4 + - - -
325H PRO* 3.2 34.0 + - + +
326H MET* 5.5 0.2 - - - -
327H LEU* 3.4 14.3 + - + +
328H ALA 3.0 0.8 - - - -
329H HIS* 1.3 85.6 - - - +
331H ALA* 1.3 65.3 + - + +
333H ASP* 3.4 4.5 + - - +
334H GLU* 2.9 53.9 + - - +
349H ILE* 4.6 1.9 - - + +
351H TYR* 3.6 17.9 - - + -
354H VAL* 4.1 20.9 - - + -
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Residues in contact with ALA 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PRO* 4.4 0.2 - - + -
17H GLY* 3.4 27.0 - - - +
318H ILE* 4.0 1.7 - - - +
319H GLY* 3.7 31.0 - - - -
327H LEU 3.2 9.6 + - - +
328H ALA 3.1 7.8 + - - +
330H LYS* 1.3 77.8 - - - +
332H GLU* 1.3 66.8 + - - +
334H GLU* 3.4 4.4 + - - +
335H GLY 3.0 17.3 + - - -
480H FAD 3.8 14.8 - - - +
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Residues in contact with GLU 332 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452G HIS* 3.8 23.7 + - - -
457G GLU* 4.0 13.2 - - - +
460G ARG* 5.3 5.4 + - - +
473G ASN* 5.5 4.0 + - - -
16H PRO* 3.5 34.9 - - + +
17H GLY* 4.3 0.4 - - - -
19H TYR* 4.2 8.2 + - - -
20H VAL* 3.9 26.5 - - + +
328H ALA 2.9 21.3 + - - +
329H HIS* 3.6 10.8 - - - +
331H ALA* 1.3 76.7 - - - +
333H ASP* 1.3 65.8 + - - +
335H GLY* 2.9 12.1 + - - -
336H ILE* 3.1 18.5 + - + +
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Residues in contact with ASP 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G ARG 4.2 5.5 - - - +
449G CYS* 3.5 25.3 + - - +
460G ARG* 2.7 43.1 + - - -
329H HIS 3.0 22.1 + - - +
330H LYS* 3.9 3.6 - - - +
332H GLU* 1.3 77.8 - - - +
334H GLU* 1.3 63.6 + - - +
336H ILE* 3.3 8.3 + - - +
337H ILE* 3.0 33.9 + - + +
349H ILE* 4.5 16.0 - - + +
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Residues in contact with GLU 334 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H PHE* 3.3 27.8 - - + -
318H ILE* 3.8 10.4 - - + +
319H GLY* 3.1 18.0 + - - -
322H VAL* 3.9 2.4 - - - +
323H ALA 4.1 1.0 - - - +
330H LYS* 2.9 53.2 + - - +
331H ALA 3.7 4.0 - - - +
332H GLU 3.2 0.2 - - - -
333H ASP* 1.3 78.0 - - - +
335H GLY* 1.3 56.2 + - - +
337H ILE* 3.4 7.5 - - - +
338H CYS* 2.9 32.6 + - - +
349H ILE* 3.9 11.9 - - + -
351H TYR* 2.5 27.9 + - - -
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Residues in contact with GLY 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLY 4.2 1.8 - - - -
21H ALA* 3.9 16.6 - - - -
318H ILE* 3.5 23.9 - - - +
331H ALA 3.0 8.0 + - - -
332H GLU 2.9 8.1 + - - -
334H GLU* 1.3 76.0 - - - +
336H ILE* 1.3 61.2 + - - +
338H CYS* 3.2 4.7 + - - +
339H VAL* 3.1 28.2 + - - +
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Residues in contact with ILE 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G ARG* 5.1 3.4 - - - +
460G ARG* 5.7 7.2 - - - +
464G LEU* 5.6 3.8 - - + -
472G ILE* 4.1 17.9 - - + -
20H VAL* 3.5 31.2 - - + +
21H ALA* 4.6 0.4 - - - +
24H LYS* 4.1 26.5 - - + +
332H GLU* 3.1 9.9 + - + +
333H ASP* 3.7 9.9 - - - +
335H GLY* 1.3 74.2 - - - +
337H ILE* 1.3 66.8 + - + +
339H VAL* 3.1 10.4 - - - +
340H GLU* 3.0 46.6 + - - +
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Residues in contact with ILE 337 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G ARG* 4.6 9.6 - - - +
308H PHE* 3.7 24.9 - - + -
333H ASP* 3.0 22.7 + - + +
334H GLU* 3.4 11.0 - - - +
336H ILE* 1.3 77.8 - - + +
338H CYS* 1.3 65.2 + - - +
340H GLU* 3.7 19.9 - - - +
341H GLY* 3.0 20.3 + - - -
346H ALA 4.7 2.1 - - - +
347H VAL* 3.8 17.8 - - + +
348H HIS 4.3 17.9 - - - +
349H ILE* 3.8 26.9 - - + -
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Residues in contact with CYS 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H LEU* 4.0 11.4 - - + -
307H ARG 4.1 5.3 - - - +
308H PHE* 4.0 17.0 - - + -
316H TYR* 3.5 38.3 - - - -
318H ILE* 3.9 8.5 - - + -
334H GLU 2.9 21.9 + - - +
335H GLY* 3.5 4.7 - - - +
337H ILE* 1.3 79.4 - - - +
339H VAL* 1.3 62.7 + - + +
341H GLY* 3.3 3.2 + - - -
342H MET* 3.1 34.3 + - - +
347H VAL* 5.0 0.9 - - - -
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Residues in contact with VAL 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 4.9 1.6 - - + -
21H ALA 3.7 15.5 - - - +
24H LYS* 3.8 30.3 - - + -
25H ALA* 4.0 16.8 - - + +
28H LEU* 3.7 12.7 - - + +
30H PHE* 3.8 3.6 - - + -
145H LEU* 4.1 21.1 - - + -
335H GLY 3.1 12.5 + - - +
336H ILE 3.1 14.8 - - - +
338H CYS* 1.3 72.9 - - - +
340H GLU* 1.3 66.1 + - - +
341H GLY 3.1 1.3 - - - -
342H MET* 3.0 30.3 + - - +
343H ALA 3.0 9.7 + - - -
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Residues in contact with GLU 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447G ARG* 3.0 44.4 + - - -
24H LYS* 3.9 15.0 + - - -
28H LEU* 3.8 20.8 - - + +
336H ILE* 3.0 40.8 + - + +
337H ILE* 3.7 15.4 - - - +
339H VAL* 1.3 77.7 - - - +
341H GLY* 1.3 54.4 + - - +
343H ALA* 3.2 12.1 + - - +
344H GLY 3.2 0.5 + - - -
345H GLY* 2.8 30.0 + - - -
346H ALA 4.9 9.1 - - - +
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Residues in contact with GLY 341 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ARG* 3.0 22.4 + - - -
316H TYR* 5.4 2.9 + - - -
337H ILE 3.0 10.1 + - - -
338H CYS 3.6 4.3 - - - -
340H GLU* 1.3 76.0 - - - +
342H MET* 1.3 64.1 + - - +
344H GLY* 3.0 9.0 + - - -
345H GLY* 3.7 5.4 - - - -
347H VAL* 3.5 29.1 - - - +
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Residues in contact with MET 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H VAL* 3.9 26.9 - - + -
30H PHE* 3.8 16.1 - - + -
143H ASN* 4.3 18.2 - - + +
145H LEU* 4.4 14.1 - - + -
316H TYR* 3.5 48.9 - - + +
338H CYS* 3.1 29.3 + - - +
339H VAL* 3.0 26.1 + - + +
341H GLY* 1.3 78.1 - - - +
343H ALA* 1.3 58.0 + - - +
344H GLY* 3.1 4.5 + - - -
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Residues in contact with ALA 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 4.4 20.9 - - + +
30H PHE* 3.7 17.2 - - + -
339H VAL 3.0 10.9 + - - +
340H GLU* 3.2 10.5 + - - +
342H MET* 1.3 74.6 - - - +
344H GLY* 1.3 57.8 + - - +
345H GLY 3.6 0.2 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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