Contacts of the helix formed by residues 325 - 342 (chain G) in PDB entry 4ZZ7
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 THR 325 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G PHE* 5.5 10.5 - - + -
176G ARG* 4.1 32.5 + - + +
323G VAL* 3.3 6.1 - - - +
324G ILE* 1.3 88.9 - - + +
326G ARG* 1.3 55.7 + - - +
327G GLN* 4.1 11.5 + - - +
328G HIS* 3.1 21.1 + - - +
329G GLN* 2.8 31.2 + - - +
362G PHE* 3.6 14.6 - - + -
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Residues in contact with ARG 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G GLY* 5.6 2.0 + - - -
325G THR* 1.3 72.4 - - - +
327G GLN* 1.3 55.3 + - - +
329G GLN* 2.9 25.7 + - - +
330G GLU* 2.8 56.3 + - - +
360G ASN* 3.3 29.1 + - - +
361G GLY 3.3 26.1 + - - -
362G PHE* 3.5 37.0 - - + -
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Residues in contact with GLN 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G ARG* 5.3 6.9 + - - -
325G THR* 4.1 10.6 + - - +
326G ARG* 1.3 79.4 - - - +
328G HIS* 1.3 57.8 + - - +
330G GLU* 3.7 12.2 + - - +
331G LYS* 3.1 31.8 + - - +
38J SER* 5.6 2.8 + - - -
39J THR* 5.2 5.5 + - - -
40J LYS* 4.7 24.9 - - + +
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Residues in contact with HIS 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G PHE* 4.9 3.3 - + - -
176G ARG* 6.0 1.6 - - - +
278G GLU* 3.5 24.0 + - - -
323G VAL* 3.6 19.3 - - + -
324G ILE* 4.1 9.9 - - + -
325G THR* 3.1 21.8 + - - +
327G GLN* 1.3 76.6 - - - +
329G GLN* 1.3 60.8 + - - +
331G LYS* 3.3 28.3 + - + +
332G VAL* 2.9 39.8 + - + +
383G ILE 3.7 14.8 - - - -
384G PHE* 2.6 45.1 + + + +
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Residues in contact with GLN 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G VAL* 3.4 13.4 - - + +
325G THR 2.8 16.2 + - - +
326G ARG* 2.9 38.0 + - - +
328G HIS* 1.3 73.4 - - - +
330G GLU* 1.3 60.7 + - - +
332G VAL* 3.2 4.0 + - - +
333G ILE* 2.8 42.7 + - + +
351G ARG 5.5 0.6 + - - -
353G PRO* 5.4 3.6 - - - +
361G GLY 4.0 5.1 + - - -
362G PHE* 4.0 12.7 - - + -
363G PHE 2.9 27.2 + - - +
364G VAL* 3.7 20.4 - - + +
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Residues in contact with GLU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G ARG* 2.8 47.3 + - + +
327G GLN* 3.8 8.4 - - - +
329G GLN* 1.3 76.9 - - - +
331G LYS* 1.3 52.9 + - - +
333G ILE* 3.2 8.9 + - - +
334G GLY* 2.7 33.1 + - - -
40J LYS* 3.9 20.8 + - - -
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Residues in contact with LYS 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G GLN* 3.1 23.8 + - + +
328G HIS* 3.6 30.9 + - + +
329G GLN 3.3 0.2 - - - -
330G GLU* 1.3 75.3 - - - +
332G VAL* 1.3 62.8 + - - +
334G GLY* 3.3 3.3 + - - +
335G TYR* 3.1 58.3 + - + +
382G GLU 5.5 1.9 + - - +
383G ILE 5.0 2.2 + - - +
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Residues in contact with VAL 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G VAL* 4.5 5.2 - - + -
328G HIS* 2.9 45.1 + - + +
329G GLN* 3.6 8.1 - - - +
331G LYS* 1.3 69.3 - - - +
333G ILE* 1.3 70.4 + - - +
335G TYR* 3.3 15.9 + - - +
336G ILE* 3.3 20.6 + - + +
364G VAL* 4.0 26.5 - - + -
383G ILE* 4.1 21.8 - - + +
384G PHE 4.0 9.0 - - - +
385G GLY* 4.2 3.8 - - - -
386G PRO* 4.4 11.2 - - + -
387G VAL* 4.5 2.0 - - + -
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Residues in contact with ILE 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G GLN* 2.8 32.6 + - + +
330G GLU* 3.5 9.4 - - - +
332G VAL* 1.3 73.2 - - - +
334G GLY* 1.3 59.3 + - - +
336G ILE* 2.9 25.8 + - - +
337G ASN* 3.0 27.6 + - - +
351G ARG* 3.2 50.9 - - + +
364G VAL* 4.4 18.6 - - + -
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Residues in contact with GLY 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330G GLU 2.7 18.1 + - - -
331G LYS* 3.5 5.4 - - - -
332G VAL 3.2 0.2 - - - -
333G ILE* 1.3 73.0 - - - +
335G TYR* 1.3 56.9 + - - +
337G ASN* 3.3 12.8 + - - +
338G SER* 2.9 29.0 + - - -
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Residues in contact with TYR 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LYS* 3.1 57.4 + - + +
332G VAL* 3.8 5.6 - - - +
333G ILE 3.2 0.6 + - - -
334G GLY* 1.3 72.9 - - - +
336G ILE* 1.3 62.0 + - + +
338G SER* 3.9 6.2 - - - -
339G ALA* 3.1 26.2 + - - +
369G ILE* 4.9 1.0 - - - +
377G THR* 4.4 7.9 - - + -
378G SER* 3.5 27.2 - - - -
381G GLU* 2.6 41.9 + - + +
382G GLU 4.0 17.7 + - - -
383G ILE* 4.0 37.0 - - + -
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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
----------------------------------------------------------
332G VAL* 3.4 27.8 - - + +
333G ILE* 2.9 6.7 + - - +
335G TYR* 1.3 75.5 - - + +
337G ASN* 1.3 65.1 + - - +
339G ALA* 3.5 0.5 + - - +
340G GLU* 3.2 19.6 + - - +
346G ILE* 3.6 28.0 - - + +
349G ASP* 4.6 1.3 - - - +
351G ARG* 3.6 37.4 + - + +
364G VAL* 4.5 7.0 - - + -
367G THR* 3.7 32.1 - - + +
369G ILE* 4.3 12.8 - - + -
383G ILE* 6.3 0.2 - - + -
387G VAL* 4.3 15.3 - - + -
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Residues in contact with ASN 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G ILE* 3.0 31.5 + - - +
334G GLY* 3.5 10.9 - - - +
335G TYR 3.3 0.2 - - - -
336G ILE* 1.3 75.6 - - - +
338G SER* 1.3 58.5 + - - +
340G GLU* 3.4 2.4 + - - +
341G GLN* 2.8 32.4 + - - +
351G ARG* 2.7 43.7 + - - +
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Residues in contact with SER 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G GLY 2.9 17.2 + - - -
335G TYR* 3.9 10.8 - - - -
337G ASN* 1.3 74.9 - - - +
339G ALA* 1.3 59.0 + - - +
341G GLN* 4.0 11.4 + - - -
342G GLN* 3.0 50.1 + - - +
377G THR* 4.2 11.8 + - - -
378G SER* 4.8 4.3 - - - -
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Residues in contact with ALA 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G TYR 3.1 17.5 + - - +
336G ILE 3.7 2.2 - - - +
337G ASN 3.2 0.2 - - - -
338G SER* 1.3 75.4 - - - +
340G GLU* 1.3 63.0 + - - +
342G GLN* 3.3 6.1 + - - +
343G GLY 3.3 5.7 + - - -
344G ALA* 2.9 38.1 + - + +
369G ILE* 3.6 28.9 - - + -
376G MET* 4.7 3.3 - - - +
378G SER* 3.6 18.1 + - - +
389G GLN* 4.9 0.7 - - - +
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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
----------------------------------------------------------
336G ILE 3.2 14.2 + - - +
337G ASN* 3.7 4.4 - - - +
339G ALA* 1.3 77.8 - - - +
341G GLN* 1.3 61.8 + - - +
343G GLY* 3.3 12.8 + - - -
344G ALA 3.7 13.9 + - - +
346G ILE* 3.6 21.2 - - + +
351G ARG* 2.8 41.1 + - - +
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Residues in contact with GLN 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G ASN 2.8 18.5 + - - +
338G SER* 4.0 11.4 + - - +
340G GLU* 1.3 77.1 - - - +
342G GLN* 1.3 61.1 + - + +
343G GLY* 3.3 2.7 + - - -
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Residues in contact with GLN 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G SER* 3.0 31.9 + - - +
339G ALA 3.6 5.4 - - - +
340G GLU 3.3 0.4 - - - -
341G GLN* 1.3 79.3 - - + +
343G GLY* 1.3 55.3 + - - +
344G ALA 3.6 0.2 - - - -
375G GLU 4.7 3.8 + - - -
376G MET* 3.3 37.2 - - + +
377G THR* 3.1 41.4 + - - +
378G SER 4.4 0.9 + - - -
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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