Contacts of the helix formed by residues 319 - 332 (chain H) in PDB entry 2OX4
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 319 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H PRO* 3.5 31.9 - - + -
23H LEU* 3.6 12.5 - - + +
37H GLU* 2.5 32.6 + - - +
316H VAL* 5.6 0.2 - - - +
318H GLY* 1.3 76.6 - - - +
320H GLY* 1.3 60.7 + - - +
321H VAL* 3.0 14.7 + - - +
322H ALA 3.2 3.3 + - - -
323H GLU* 3.0 25.5 + - - +
345H THR* 6.1 1.3 - - - -
350H TYR* 4.1 8.5 - - + -
353H LEU* 3.7 22.9 - - + -
354H CYS* 3.9 8.9 - - - -
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Residues in contact with GLY 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H THR* 1.3 73.6 - - - +
321H VAL* 1.3 58.3 - - - +
323H GLU* 3.8 8.3 - - - -
324H ALA* 2.9 31.7 + - - +
350H TYR 5.5 2.2 + - - -
354H CYS* 3.7 10.2 - - - -
356H HIS 5.1 1.6 - - - -
358H TYR* 5.3 0.3 - - - -
375H GLN* 3.3 22.4 + - - -
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Residues in contact with VAL 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU* 3.9 11.2 - - + -
35H LEU* 4.1 14.4 - - + +
36H GLY* 3.9 32.5 - - - +
37H GLU* 3.5 5.8 - - + +
98H ILE* 5.0 2.5 - - + -
319H THR* 3.0 14.2 + - - +
320H GLY* 1.3 73.6 - - - +
322H ALA* 1.3 65.3 + - - +
324H ALA* 4.0 1.2 - - - +
325H ALA* 3.0 26.0 + - - +
354H CYS* 3.7 14.3 - - - -
373H ILE* 3.9 17.9 - - + +
375H GLN* 3.9 15.0 - - + -
376H ASP 5.0 0.9 - - - -
377H ILE* 4.3 13.5 - - + -
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Residues in contact with ALA 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU* 3.0 36.7 + - + +
98H ILE* 6.0 3.1 - - - -
288H ASP* 5.7 4.9 - - - +
289H LEU* 4.9 3.3 - - - +
316H VAL* 4.6 6.7 - - + -
317H ALA 5.5 1.3 - - - +
318H GLY* 4.6 9.0 - - - +
319H THR 3.2 9.2 + - - +
321H VAL* 1.3 75.2 - - - +
323H GLU* 1.3 62.7 + - - +
325H ALA* 3.6 5.7 - - - +
326H SER* 3.0 24.1 + - - -
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Residues in contact with GLU 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H VAL* 3.8 20.6 - - + +
318H GLY 5.8 0.4 - - - +
319H THR 3.0 14.8 + - - +
320H GLY* 3.6 7.4 + - - +
321H VAL 3.3 0.2 - - - -
322H ALA* 1.3 72.7 - - - +
324H ALA* 1.3 67.3 + - - +
326H SER* 2.6 22.9 + - - -
327H LEU* 3.3 9.9 + - + +
339H HIS* 2.9 27.5 + - + +
340H GLU 3.4 7.1 - - - +
341H HIS* 2.9 29.4 + - - -
342H HIS 5.5 0.2 - - - -
345H THR* 3.3 21.2 - - + +
358H TYR* 4.6 5.2 - - + +
365H TYR* 3.4 20.8 + - + +
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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
----------------------------------------------------------
320H GLY 2.9 20.2 + - - +
321H VAL 4.0 1.3 - - - +
323H GLU* 1.3 74.5 - - - +
325H ALA* 1.3 64.7 + - - +
327H LEU* 3.1 23.0 + - - +
328H HIS* 3.2 18.2 - - - -
358H TYR* 4.2 18.5 - - + +
368H PRO* 4.4 2.1 - - + +
373H ILE* 3.7 18.6 - - + +
375H GLN* 3.8 18.2 - - + -
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Residues in contact with ALA 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H ILE* 4.1 17.9 - - + -
289H LEU* 3.5 17.0 - - + -
295H PHE* 3.3 27.5 - - + -
321H VAL 3.0 18.8 + - - +
322H ALA* 3.6 6.5 - - - +
324H ALA* 1.3 74.3 - - - +
326H SER* 1.3 63.2 + - - +
328H HIS* 3.2 15.6 + - - +
329H ALA 3.3 9.0 + - - -
373H ILE* 4.4 7.3 - - + +
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Residues in contact with SER 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H LEU* 3.6 13.9 - - - +
314H ALA* 4.2 10.5 - - - -
315H HIS 5.6 0.2 - - - -
316H VAL* 3.4 22.9 - - - +
322H ALA 3.0 14.7 + - - -
323H GLU 2.6 19.9 + - - -
325H ALA* 1.3 75.7 - - - +
327H LEU* 1.3 56.6 + - - +
329H ALA* 3.3 3.0 + - - +
330H GLU* 3.0 35.3 + - - +
339H HIS* 3.2 20.2 - - - -
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Residues in contact with LEU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 3.6 21.5 - - + +
323H GLU* 3.5 16.6 - - + +
324H ALA* 3.1 11.9 + - - +
326H SER* 1.3 78.7 + - - +
328H HIS* 1.3 57.1 + - - +
330H GLU* 4.0 2.3 - - - +
331H ILE* 3.0 33.1 + - - +
339H HIS* 3.6 25.6 - - + +
358H TYR* 4.9 7.0 - - + -
365H TYR* 3.7 36.1 - - + -
366H LYS 3.8 20.2 - - - +
367H VAL* 3.7 7.4 - - + +
368H PRO* 3.9 21.3 - - + -
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Residues in contact with HIS 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H PRO* 3.8 5.2 - - + -
112H VAL* 3.5 13.0 + - + -
113H TYR* 3.1 29.7 + - - +
116H LEU* 3.8 2.6 - - - +
295H PHE* 4.0 10.8 - - + -
324H ALA 3.2 25.6 - - - -
325H ALA* 3.2 7.1 + - - +
327H LEU* 1.3 74.4 - - - +
329H ALA* 1.3 65.9 + - - +
331H ILE* 3.6 3.1 + - - +
332H ALA* 3.3 25.1 + - - +
367H VAL* 3.5 12.9 - - + +
368H PRO* 3.5 29.9 - - + +
370H LEU 5.0 0.2 - - - -
372H GLY 3.5 16.8 - - - -
373H ILE* 2.8 34.9 + - + -
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Residues in contact with ALA 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H LEU* 4.0 10.3 - - - -
289H LEU* 4.0 22.0 - - + -
295H PHE* 4.0 6.5 - - + -
298H PHE* 3.8 30.6 - - + -
325H ALA 3.3 8.6 + - - +
326H SER* 3.3 7.6 + - - +
328H HIS* 1.3 80.8 - - - +
330H GLU* 1.3 62.0 + - - +
332H ALA* 3.5 8.0 + - - +
333H ILE* 3.6 21.3 + - - +
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Residues in contact with GLU 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H ARG* 2.9 20.0 + - - -
124H LEU* 3.6 14.7 - - + +
298H PHE* 4.5 6.5 - - + -
312H VAL* 5.5 0.4 - - + +
314H ALA* 2.9 43.1 + - + +
326H SER 3.0 19.9 + - - +
329H ALA* 1.3 74.1 - - - +
331H ILE* 1.3 62.6 + - - +
332H ALA 3.1 3.2 + - - -
333H ILE* 3.4 17.9 - - + +
336H PHE* 3.5 31.7 - - + +
338H ILE 3.8 3.8 - - - +
339H HIS* 2.5 37.2 + - - -
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Residues in contact with ILE 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H TYR* 3.6 37.5 - - + -
118H GLY 3.6 0.4 - - - +
119H LYS* 4.0 12.1 - - + -
120H ASN* 2.9 35.0 + - - +
121H ARG* 3.5 36.5 + - + +
122H GLU 4.3 12.3 - - - +
123H ASP* 4.6 1.1 - - - +
124H LEU* 4.2 17.6 - - + +
327H LEU 3.0 19.6 + - - +
328H HIS 3.6 0.7 - - - +
330H GLU* 1.3 79.7 - - - +
332H ALA* 1.3 59.2 + - - +
367H VAL* 3.8 31.9 - - + +
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLU* 3.4 21.3 - - - +
113H TYR* 4.2 4.3 - - + +
116H LEU* 3.7 33.8 - - + +
118H GLY 3.1 16.8 - - - +
120H ASN* 3.1 14.8 + - - -
299H LYS* 4.9 1.2 + - - -
328H HIS 3.3 17.4 + - - +
329H ALA 3.9 4.9 - - - +
330H GLU 3.1 1.2 - - - -
331H ILE* 1.3 75.8 - - - +
333H ILE* 1.3 59.1 + - + +
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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