Contacts of the helix formed by residues 312 - 328 (chain H) in PDB entry 1NZX
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 GLU 312 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H VAL 3.4 1.4 + - - -
311H GLN* 1.3 82.2 + - - +
313H ASP* 1.3 75.6 + - - +
314H ILE 3.1 1.2 + - - -
315H TYR* 3.2 14.5 + - - +
316H ASP* 4.6 3.3 + - - -
409H LYS* 3.8 27.6 - - + +
410H PHE 2.9 13.8 + - - +
411H LYS* 3.5 44.0 + - - +
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Residues in contact with ASP 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H SER* 4.6 9.8 + - - -
311H GLN* 3.0 20.9 + - - +
312H GLU* 1.3 90.8 - - - +
314H ILE* 1.3 61.4 + - + +
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Residues in contact with ILE 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE* 4.0 15.5 - - + +
278H MET 3.5 26.0 - - - +
279H SER* 3.7 29.8 - - - +
281H ALA* 5.3 2.2 - - + +
283H MET* 3.7 26.4 - - + +
310H VAL* 3.7 15.9 - - + -
311H GLN 3.2 13.0 - - - +
313H ASP* 1.3 82.9 - - + +
315H TYR* 1.3 65.5 + - - +
316H ASP 3.4 2.7 - - - -
317H GLU* 3.4 8.8 + - - +
318H PHE* 3.0 23.2 + - + +
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Residues in contact with TYR 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H VAL* 3.8 18.6 - - + -
311H GLN 3.1 8.5 + - - +
312H GLU* 3.2 16.2 + - - +
314H ILE* 1.3 77.7 - - - +
316H ASP* 1.3 80.4 + - - +
318H PHE* 3.2 1.0 + - - +
319H VAL* 2.9 48.9 + - + +
387H GLY* 3.7 7.4 - - - -
388H ASP* 2.8 39.6 + - - -
407H ILE* 3.6 19.1 + - + +
408H LEU 4.0 6.5 - - - -
409H LYS* 3.3 58.1 - - + +
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Residues in contact with ASP 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H GLU 4.6 2.4 + - - -
313H ASP 5.6 0.2 - - - -
314H ILE 3.4 0.8 - - - -
315H TYR* 1.3 95.2 - - - +
317H GLU* 1.3 63.1 + - - +
319H VAL* 3.3 4.2 + - - +
320H GLU* 3.0 23.7 + - - +
409H LYS* 4.8 4.7 + - - -
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Residues in contact with GLU 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET* 3.5 22.5 - - + +
314H ILE* 3.4 12.0 + - - +
315H TYR 3.3 0.4 - - - -
316H ASP* 1.3 78.0 - - - +
318H PHE* 1.3 63.1 + - - +
320H GLU* 3.3 15.2 + - - +
321H ARG* 3.1 66.2 + - - +
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Residues in contact with PHE 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ILE* 4.2 23.6 - - + -
283H MET* 4.0 19.0 - - + +
286H ALA* 4.0 5.2 - - + -
287H VAL* 3.7 34.1 - - + -
290H ALA* 3.5 26.5 - - + -
308H THR* 4.0 14.8 - - + -
310H VAL* 3.6 31.4 - - + -
314H ILE 3.0 19.5 + - - +
315H TYR 3.6 3.1 - - - +
317H GLU* 1.3 76.1 - - - +
319H VAL* 1.3 62.5 + - + +
321H ARG* 3.4 2.6 + - - +
322H SER* 2.8 49.7 + - - -
405H MET* 5.5 1.3 - - - -
407H ILE* 4.2 13.0 - - + -
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Residues in contact with VAL 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H TYR* 2.9 60.1 + - + +
316H ASP* 3.5 5.4 - - - +
318H PHE* 1.3 77.5 - - + +
320H GLU* 1.3 64.4 + - - +
322H SER* 3.1 7.6 + - - -
323H VAL* 2.9 26.3 + - + +
368H LEU* 3.5 34.1 - - + -
407H ILE* 4.0 16.6 - - + -
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Residues in contact with GLU 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLU 6.1 0.4 - - - +
323A VAL* 5.1 7.4 - - + +
324A ALA* 5.9 8.1 - - + -
327A LYS* 2.8 35.3 + - - +
316H ASP 3.0 13.4 + - - +
317H GLU* 3.5 21.0 - - - +
318H PHE 3.3 0.2 - - - -
319H VAL* 1.3 78.9 - - - +
321H ARG* 1.3 76.6 + - - +
323H VAL* 3.3 6.4 + - - +
324H ALA* 3.1 22.2 + - + +
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Residues in contact with ARG 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS* 4.8 8.5 - - - +
283H MET* 3.7 17.7 - - - +
284H ASP* 2.8 39.1 + - - +
287H VAL* 3.7 27.3 - - + +
317H GLU* 3.1 44.0 + - - +
318H PHE 3.8 0.2 - - - +
320H GLU* 1.3 91.2 + - - +
322H SER* 1.3 56.3 + - - +
324H ALA* 3.5 6.1 + - - +
325H ARG* 3.0 28.6 + - - +
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Residues in contact with SER 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 4.5 10.3 + - - +
290H ALA* 5.4 0.2 - - - +
291H HIS* 4.6 4.4 - - - -
318H PHE* 2.8 47.2 + - - -
319H VAL 3.5 4.3 - - - -
321H ARG* 1.3 73.7 - - - +
323H VAL* 1.3 59.6 + - - +
325H ARG* 3.3 7.0 + - - +
326H ALA* 2.9 30.2 + - - +
385H VAL* 4.7 3.7 - - - +
405H MET* 4.6 12.6 - - - +
407H ILE* 4.1 19.1 - - - -
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Residues in contact with VAL 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 6.2 4.9 - - + -
319H VAL* 2.9 20.4 + - + +
320H GLU* 3.7 6.5 - - - +
322H SER* 1.3 75.5 - - - +
324H ALA* 1.3 60.1 + - - +
326H ALA* 3.2 6.7 + - - +
327H LYS* 2.9 39.6 + - + +
368H LEU* 3.4 54.1 - - + +
369H CYS* 4.3 7.8 - - + -
385H VAL* 4.5 9.2 - - + -
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Residues in contact with ALA 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 5.6 3.8 - - - +
327A LYS* 4.1 38.4 - - + +
328A SER* 5.4 4.1 - - - -
320H GLU* 3.1 13.3 + - + +
321H ARG* 3.6 11.0 - - - +
323H VAL* 1.3 79.9 - - - +
325H ARG* 1.3 56.5 + - - +
327H LYS* 3.3 7.5 + - - +
328H SER* 3.0 30.8 + - - -
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Residues in contact with ARG 325 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H VAL* 4.8 10.3 - - + -
288H GLU* 3.0 39.6 + - - +
291H HIS* 3.4 40.3 + - + -
321H ARG 3.0 18.3 + - - +
322H SER* 3.6 7.0 - - - +
324H ALA* 1.3 75.6 - - - +
326H ALA* 1.3 61.5 + - - +
328H SER* 3.1 27.3 + - - -
329H ARG* 3.2 7.3 + - - +
340H GLU* 3.2 32.1 + - - -
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Residues in contact with ALA 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H HIS* 3.7 17.2 + - + +
295H PHE* 4.4 2.0 - - + -
322H SER 2.9 17.7 + - - +
323H VAL 3.6 4.0 - - - +
325H ARG* 1.3 76.7 - - - +
327H LYS* 1.3 62.7 + - - +
329H ARG* 3.2 18.6 + - - +
369H CYS* 3.7 8.7 - - - -
383H PRO* 3.5 23.3 - - + +
385H VAL* 3.6 26.5 - - + -
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Residues in contact with LYS 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 6.2 1.4 - - - +
328A SER* 3.9 36.3 + - - +
330A VAL* 5.7 3.8 - - - +
323H VAL* 2.9 26.6 + - + +
324H ALA* 3.3 5.6 + - - +
326H ALA* 1.3 76.7 - - - +
328H SER* 1.3 59.9 + - - +
329H ARG 3.5 3.6 + - - +
368H LEU 4.9 3.6 - - - -
369H CYS* 3.9 28.7 - - + +
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Residues in contact with SER 328 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LYS 4.9 11.4 - - - -
328A SER* 5.6 4.3 - - - -
330A VAL* 6.2 2.7 - - - -
324H ALA 3.0 14.4 + - - -
325H ARG* 3.1 25.3 + - - -
326H ALA 3.2 0.2 - - - -
327H LYS* 1.3 76.5 - - - +
329H ARG* 1.3 62.4 + - - +
330H VAL* 3.2 11.1 + - - +
340H GLU* 3.6 6.6 - - - +
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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