Contacts of the helix formed by residues 327 - 343 (chain G) in PDB entry 1ZMD
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ASP* 3.7 1.4 + - - +
325G PRO* 2.9 28.5 + - + +
326G MET* 1.3 82.1 - - - +
328G ALA* 1.3 66.4 + - - +
329G HIS* 3.5 14.1 - - + +
330G LYS* 3.3 8.9 + - + +
331G ALA* 3.1 23.0 + - - +
354G VAL* 4.1 4.7 - - + +
355G PRO 3.4 24.7 - - - +
356G SER* 4.3 16.4 - - - +
480G FAD 3.2 18.0 + - - +
481G NAI 3.6 45.5 - - + +
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Residues in contact with ALA 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PRO* 4.0 9.9 - - + -
45G CYS* 3.5 31.9 - - - -
50G CYS* 3.8 1.1 - - - -
327G LEU* 1.3 68.7 - - - +
329G HIS* 1.3 64.4 + - - +
331G ALA* 3.3 3.1 + - - +
332G GLU* 3.0 29.4 + - - +
480G FAD 2.8 35.2 + - + +
452H HIS* 3.5 14.8 - - + -
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Residues in contact with HIS 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G LEU* 3.7 16.9 - - + +
328G ALA* 1.3 76.5 - - - +
330G LYS* 1.3 63.4 + - - +
332G GLU* 4.0 8.0 - - - +
333G ASP* 3.1 31.4 + - - +
354G VAL* 3.8 6.9 - - + +
355G PRO* 2.9 31.4 + - + -
356G SER* 5.4 1.3 - - - -
357G VAL* 5.7 2.0 - - + -
480G FAD 3.3 18.3 + + - -
481G NAI 5.5 1.3 - - - -
449H CYS* 3.4 26.0 - - - -
450H HIS 3.1 25.4 - - - +
451H ALA* 3.9 10.2 - - + -
452H HIS* 3.0 29.8 + - + +
457H GLU* 5.2 2.0 - - - +
460H ARG* 5.2 2.0 - - - +
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Residues in contact with LYS 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319G GLY* 2.9 22.6 + - - +
320G ASP* 5.1 0.8 - - - +
322G VAL* 3.6 3.4 + - - +
323G ALA 2.9 25.6 + - - -
324G GLY* 3.8 9.6 - - - -
325G PRO* 3.2 32.4 + - + +
326G MET* 5.7 0.4 - - - +
327G LEU* 3.3 16.1 + - + +
328G ALA 3.1 0.8 - - - -
329G HIS* 1.3 84.2 - - - +
331G ALA* 1.3 65.2 + - - +
333G ASP* 3.3 3.6 + - - +
334G GLU* 2.9 61.2 + - - +
349G ILE* 4.5 2.6 - - + +
351G TYR* 3.9 17.5 - - + -
354G VAL* 4.4 13.0 - - + -
449H CYS* 4.6 6.7 - - - -
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Residues in contact with ALA 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLY* 3.5 18.8 - - - +
318G ILE* 3.9 1.7 - - - +
319G GLY* 3.6 30.1 - - - -
327G LEU 3.1 13.4 + - - +
328G ALA 3.3 8.3 + - - +
330G LYS* 1.3 78.6 - - - +
332G GLU* 1.3 56.9 + - - +
334G GLU* 3.3 2.9 + - - +
335G GLY 2.9 23.9 + - - -
480G FAD 3.8 23.6 - - - +
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Residues in contact with GLU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PRO* 3.3 38.6 - - + +
17G GLY* 4.3 0.4 - - - -
19G TYR* 4.5 7.9 + - - -
20G VAL* 3.7 24.9 - - + +
328G ALA 3.0 21.9 + - - +
329G HIS* 4.0 7.2 - - - +
331G ALA* 1.3 75.7 - - - +
333G ASP* 1.3 66.2 + - - +
335G GLY* 3.4 1.0 + - - -
336G ILE* 3.1 30.5 + - + +
452H HIS* 4.0 24.8 + - - -
457H GLU* 4.4 10.2 - - - +
460H ARG* 5.7 2.4 + - - -
473H ASN* 5.3 5.6 + - - -
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Residues in contact with ASP 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G HIS* 3.1 22.4 + - - +
330G LYS 3.8 3.4 - - - +
332G GLU* 1.3 78.5 - - - +
334G GLU* 1.3 58.3 + - - +
336G ILE* 3.4 9.3 + - - +
337G ILE* 3.0 38.9 + - + +
349G ILE* 4.1 16.5 - - + +
447H ARG 4.2 4.2 - - - +
449H CYS* 3.5 22.7 + - - +
460H ARG* 2.9 45.2 + - - -
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Residues in contact with GLU 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 3.4 27.3 - - + -
318G ILE* 3.8 11.6 - - + +
319G GLY* 2.8 31.2 + - - -
322G VAL* 3.6 1.9 - - - +
323G ALA 3.9 1.9 - - - +
330G LYS* 2.9 52.5 + - - +
331G ALA 3.7 3.6 - - - +
333G ASP* 1.3 72.8 - - - +
335G GLY* 1.3 68.0 + - - +
337G ILE* 3.6 8.4 - - - +
338G CYS* 2.9 28.1 + - - +
349G ILE* 4.1 10.3 - - + -
351G TYR* 2.5 25.8 + - - +
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Residues in contact with GLY 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLY 4.1 1.8 - - - -
21G ALA* 3.8 16.8 - - - +
145G LEU* 5.0 0.2 - - - -
318G ILE* 3.4 23.7 - - - +
331G ALA 2.9 13.5 + - - -
332G GLU 3.4 2.4 + - - -
333G ASP 3.3 0.2 - - - -
334G GLU* 1.3 77.1 - - - +
336G ILE* 1.3 60.9 + - - +
338G CYS* 3.7 2.8 - - - +
339G VAL* 3.2 29.5 + - - +
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Residues in contact with ILE 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G VAL* 3.4 30.7 - - + -
24G LYS* 4.2 21.1 - - + +
332G GLU* 3.1 11.6 + - + +
333G ASP* 3.7 12.8 - - - +
335G GLY* 1.3 72.2 - - - +
337G ILE* 1.3 64.6 + - + +
339G VAL* 3.1 11.9 - - - +
340G GLU* 2.9 48.5 + - - +
447H ARG* 5.1 2.7 - - - +
460H ARG* 5.7 5.6 - - - +
464H LEU* 5.4 6.1 - - + -
472H ILE* 4.2 16.6 - - + -
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Residues in contact with ILE 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G PHE* 3.7 18.6 - - + -
333G ASP* 3.0 24.3 + - + +
334G GLU* 3.6 9.9 - - - +
336G ILE* 1.3 79.4 - - + +
338G CYS* 1.3 59.8 + - - +
340G GLU* 3.7 18.1 - - - +
341G GLY 2.9 23.6 + - - -
346G ALA 5.2 0.4 - - - +
347G VAL* 3.5 32.9 - - + +
348G HIS 3.7 16.6 - - - +
349G ILE* 3.7 30.7 - - + -
447H ARG* 4.5 9.9 - - - +
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Residues in contact with CYS 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G LEU* 4.2 5.2 - - + -
307G ARG 3.9 12.1 - - - +
308G PHE* 4.0 11.9 - - + -
316G TYR* 3.4 38.2 - - - -
318G ILE* 3.8 15.3 - - + -
334G GLU 2.9 21.2 + - - +
335G GLY* 3.7 4.7 - - - +
337G ILE* 1.3 79.9 - - - +
339G VAL* 1.3 56.3 + - - +
341G GLY* 3.3 2.8 + - - -
342G MET* 3.0 38.7 + - - +
347G VAL* 5.1 0.7 - - - -
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Residues in contact with VAL 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 5.1 1.8 - - + -
21G ALA* 3.7 14.6 - - + +
24G LYS* 3.4 32.8 - - + -
25G ALA* 4.0 22.0 - - + +
28G LEU* 3.7 9.6 - - + +
30G PHE* 3.9 2.9 - - + -
145G LEU* 4.1 20.6 - - + -
335G GLY 3.2 13.9 + - - +
336G ILE 3.1 17.3 - - - +
338G CYS* 1.3 73.8 - - - +
340G GLU* 1.3 65.4 + - - +
342G MET* 3.1 22.0 + - + +
343G ALA* 3.1 16.8 + - - +
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Residues in contact with GLU 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G LYS* 3.8 21.4 + - - -
28G LEU* 3.8 21.3 - - + -
336G ILE* 2.9 28.4 + - - +
337G ILE* 3.7 17.0 - - - +
339G VAL* 1.3 75.6 - - - +
341G GLY* 1.3 59.6 + - - +
343G ALA* 3.1 12.2 + - - +
344G GLY 3.3 0.2 + - - -
345G GLY* 3.0 24.2 + - - -
346G ALA 4.8 9.6 - - - +
447H ARG* 2.8 43.4 + - - -
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Residues in contact with GLY 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G ARG* 5.1 9.2 - - - +
316G TYR* 5.6 1.8 - - - -
337G ILE 2.9 10.7 + - - -
338G CYS 3.3 3.6 + - - -
340G GLU* 1.3 74.2 - - - +
342G MET* 1.3 56.3 + - - +
343G ALA 3.0 2.0 - - - -
344G GLY* 2.7 24.9 + - - -
345G GLY 3.4 17.2 - - - +
347G VAL* 3.5 17.0 - - - +
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Residues in contact with MET 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 3.9 29.6 - - + -
30G PHE* 3.7 17.3 - - + -
143G ASN* 4.3 16.8 - - + +
144G ILE 5.0 0.2 - - - +
145G LEU* 4.3 19.3 - - + -
316G TYR* 3.6 50.4 + - + +
338G CYS* 3.0 33.9 + - - +
339G VAL* 3.1 24.2 + - + +
341G GLY* 1.3 76.0 - - - +
343G ALA* 1.3 57.4 + - - +
344G GLY 3.4 2.3 + - - -
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Residues in contact with ALA 343 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 4.3 20.0 - - + +
30G PHE* 4.0 17.7 - - + -
339G VAL 3.1 9.5 + - - +
340G GLU* 3.1 11.7 + - - +
341G GLY 3.0 1.2 - - - -
342G MET* 1.3 75.6 - - - +
344G GLY* 1.3 58.0 + - - +
345G GLY 3.4 1.3 + - - -
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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
------------------------------------------------------------
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