Contacts of the helix formed by residues 319 - 332 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E PRO* 3.5 30.7 - - + -
23E LEU* 3.7 11.3 - - + +
37E GLU* 2.6 33.7 + - - +
316E VAL* 5.6 0.2 - - - +
318E GLY* 1.3 75.8 - - - +
320E GLY* 1.3 60.3 + - - +
321E VAL* 3.0 15.5 + - - +
322E ALA* 3.2 3.1 + - - +
323E GLU* 3.0 24.4 + - - +
345E THR* 6.0 1.6 - - - -
350E TYR* 3.9 9.9 - - + -
353E LEU* 3.7 18.4 - - + -
354E CYS* 3.8 10.1 - - - -
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Residues in contact with GLY 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E THR* 1.3 71.6 - - - +
321E VAL* 1.3 59.4 + - - +
323E GLU* 3.8 8.3 - - - -
324E ALA* 2.9 32.2 + - - +
350E TYR 5.4 3.2 + - - -
354E CYS* 3.6 10.0 - - - -
356E HIS 5.2 0.7 - - - -
375E GLN* 3.4 22.1 + - - -
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Residues in contact with VAL 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E LEU* 3.9 12.8 - - + -
35E LEU* 4.1 17.0 - - + +
36E GLY* 3.9 33.0 - - - +
37E GLU* 3.5 7.0 - - + +
98E ILE* 4.9 3.4 - - + -
319E THR* 3.0 13.5 + - - +
320E GLY* 1.3 75.9 - - - +
322E ALA* 1.3 64.7 + - - +
324E ALA* 4.0 1.0 - - - +
325E ALA* 3.0 25.5 + - - +
354E CYS* 3.6 9.5 - - - -
373E ILE* 4.0 16.4 - - + +
375E GLN* 3.9 19.3 - - + -
376E ASP 5.0 1.8 - - - -
377E ILE* 4.4 9.9 - - + -
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E GLU* 2.9 36.5 + - + +
98E ILE* 6.0 2.7 - - - -
288E ASP* 5.7 4.7 - - - +
289E LEU* 4.9 3.0 - - - +
316E VAL* 4.6 7.1 - - + +
317E ALA 5.4 1.1 - - - +
318E GLY 4.6 9.6 - - - +
319E THR 3.2 8.7 + - - +
321E VAL* 1.3 74.5 - - - +
323E GLU* 1.3 57.7 + - - +
325E ALA* 3.5 5.7 + - - +
326E SER* 3.0 29.8 + - - -
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Residues in contact with GLU 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E VAL* 3.9 16.2 - - + +
318E GLY 5.7 0.2 - - - +
319E THR 3.0 15.0 + - - +
320E GLY* 3.6 7.2 + - - +
321E VAL 3.3 0.2 - - - -
322E ALA* 1.3 73.1 - - - +
324E ALA* 1.3 66.6 + - - +
326E SER* 2.7 22.4 + - - -
327E LEU* 3.3 10.5 + - + +
339E HIS* 2.8 30.2 + - + +
340E GLU 3.4 6.6 - - - +
341E HIS* 2.9 33.4 + - - -
342E HIS 4.8 0.4 + - - -
345E THR* 3.4 17.1 - - + +
358E TYR* 4.5 6.2 - - + +
359E GLN* 5.3 0.2 + - - -
365E TYR* 3.3 20.0 + - + +
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Residues in contact with ALA 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320E GLY 2.9 19.7 + - - +
321E VAL 4.0 1.1 - - - +
323E GLU* 1.3 75.1 - - - +
325E ALA* 1.3 64.2 + - - +
327E LEU* 3.2 21.9 + - - +
328E HIS* 3.2 19.5 - - - -
358E TYR* 4.2 19.1 - - + +
368E PRO* 4.3 2.0 - - + +
373E ILE* 3.7 18.8 - - + +
375E GLN* 3.8 17.0 - - + -
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Residues in contact with ALA 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E ILE* 4.0 19.7 - - + -
289E LEU* 3.5 18.2 - - + -
295E PHE* 3.3 33.3 - - + -
321E VAL 3.0 19.3 + - - +
322E ALA* 3.7 5.6 - - - +
324E ALA* 1.3 76.0 - - - +
326E SER* 1.3 61.9 + - - +
328E HIS* 3.1 15.4 + - - +
329E ALA 3.3 0.7 + - - -
373E ILE* 4.5 8.0 - - + +
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Residues in contact with SER 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289E LEU* 3.6 14.3 - - - +
314E ALA* 4.2 11.7 - - - -
315E HIS 5.5 0.2 - - - -
316E VAL* 3.5 23.0 - - - +
322E ALA 3.0 14.3 + - - -
323E GLU 2.7 19.1 + - - -
325E ALA* 1.3 76.7 - - - +
327E LEU* 1.3 57.0 + - - +
329E ALA* 3.3 3.4 + - - +
330E GLU* 3.0 34.7 + - - +
339E HIS* 3.2 20.0 - - - -
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Residues in contact with LEU 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E LEU* 3.6 22.4 - - + +
323E GLU* 3.4 15.9 - - + +
324E ALA* 3.2 9.4 + - - +
325E ALA 3.2 1.0 + - - -
326E SER* 1.3 75.8 + - - +
328E HIS* 1.3 61.9 + - - +
330E GLU* 4.1 3.0 - - - +
331E ILE* 3.0 27.4 + - - +
339E HIS* 3.6 24.9 - - + +
358E TYR* 4.9 7.0 - - + -
365E TYR* 3.7 35.4 - - + -
366E LYS 3.8 11.4 - - - +
367E VAL* 3.7 8.7 - - + +
368E PRO* 3.8 29.4 - - + -
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Residues in contact with HIS 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PRO* 3.8 5.4 - - + -
112E VAL* 3.6 13.2 + - + -
113E TYR* 3.1 28.4 + - - +
116E LEU* 3.8 2.4 - - - +
295E PHE* 4.1 9.6 - - + -
324E ALA 3.2 25.4 - - - -
325E ALA* 3.1 6.7 + - - +
327E LEU* 1.3 79.2 - - - +
329E ALA* 1.3 63.1 + - - +
331E ILE* 3.6 2.9 + - - +
332E ALA* 3.4 25.1 + - - +
367E VAL* 3.5 14.4 - - + +
368E PRO* 3.4 30.7 - - + +
370E LEU 5.0 0.2 - - - -
372E GLY 3.6 16.8 - - - -
373E ILE* 2.9 34.2 + - + -
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Residues in contact with ALA 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E LEU* 4.0 10.1 - - - -
289E LEU* 4.1 11.4 - - + -
295E PHE* 4.0 22.1 - - + -
298E PHE* 3.8 30.4 - - + -
325E ALA 3.3 2.9 + - - +
326E SER* 3.3 8.4 + - - +
328E HIS* 1.3 80.5 - - - +
330E GLU* 1.3 62.5 + - - +
332E ALA* 3.5 8.0 + - - +
333E ILE* 3.6 20.6 + - - +
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Residues in contact with GLU 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ARG* 2.9 19.2 + - - -
124E LEU* 3.7 12.3 - - + +
298E PHE* 4.5 6.1 - - + -
312E VAL* 5.5 0.7 - - + +
314E ALA* 2.9 42.6 + - + +
326E SER 3.0 18.9 + - - +
327E LEU 4.1 2.0 - - - +
329E ALA* 1.3 74.7 - - - +
331E ILE* 1.3 62.3 + - - +
332E ALA 3.1 2.6 + - - -
333E ILE* 3.4 17.9 - - + +
336E PHE* 3.5 32.8 - - + +
338E ILE 3.8 4.5 - - - +
339E HIS* 2.6 35.2 + - - -
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Residues in contact with ILE 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 3.6 36.8 - - + -
118E GLY 4.0 0.4 - - - +
119E LYS* 3.6 13.9 - - + -
120E ASN* 2.8 37.8 + - - +
121E ARG* 3.3 38.7 + - + +
122E GLU 4.4 11.0 - - - +
123E ASP* 4.6 0.9 - - - +
124E LEU* 4.1 16.3 - - + +
327E LEU 3.0 16.3 + - - +
328E HIS 3.6 4.0 - - - +
330E GLU* 1.3 78.6 - - - +
332E ALA* 1.3 57.3 + - - +
367E VAL* 3.8 31.9 - - + +
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Residues in contact with ALA 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 4.3 4.5 - - + +
116E LEU* 3.7 34.0 - - + +
118E GLY 3.1 18.6 - - - +
120E ASN* 3.0 14.1 + - - -
299E LYS* 5.3 0.7 + - - -
328E HIS 3.4 15.2 + - - +
329E ALA 3.9 4.5 - - - +
330E GLU 3.1 1.4 - - - -
331E ILE* 1.3 76.9 - - - +
333E ILE* 1.3 59.3 + - + +
69F GLU* 3.5 21.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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