Contacts of the helix formed by residues 319 - 332 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D PRO* 3.5 32.8 - - + -
23D LEU* 3.6 11.4 - - + +
37D GLU* 2.5 28.3 + - - +
316D VAL* 5.6 0.2 - - - +
318D GLY* 1.3 77.1 - - - +
320D GLY* 1.3 59.3 + - - +
321D VAL* 3.0 16.8 + - - +
322D ALA* 3.3 2.3 + - - +
323D GLU* 3.0 24.9 + - - +
345D THR* 6.0 1.8 - - - -
350D TYR* 4.0 8.5 - - + -
353D LEU* 3.7 23.6 - - + -
354D CYS* 4.0 9.1 - - - -
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Residues in contact with GLY 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D THR* 1.3 74.0 - - - +
321D VAL* 1.3 56.8 + - - -
323D GLU* 3.7 8.3 - - - -
324D ALA* 2.9 31.5 + - - +
350D TYR 5.4 2.8 + - - -
354D CYS* 3.6 14.5 - - - +
356D HIS 5.2 1.1 - - - -
358D TYR* 5.1 0.6 - - - -
375D GLN* 3.4 19.1 + - - -
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Residues in contact with VAL 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.2 11.0 - - + -
35D LEU* 4.1 17.0 - - + +
36D GLY* 3.8 34.1 - - - +
37D GLU* 3.5 5.6 - - + +
98D ILE* 4.9 3.1 - - + -
319D THR* 3.0 14.0 + - - +
320D GLY* 1.3 73.7 - - - +
322D ALA* 1.3 66.9 + - - +
324D ALA* 3.9 1.2 - - - +
325D ALA* 2.9 25.0 + - - +
354D CYS* 3.7 9.5 - - - -
373D ILE* 3.9 17.6 - - + +
375D GLN* 3.8 18.4 - - + -
376D ASP 5.2 1.1 - - - -
377D ILE* 4.4 11.7 - - + -
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D GLU* 2.9 34.9 + - + +
98D ILE* 6.1 3.1 - - - -
288D ASP* 5.7 4.7 - - - +
289D LEU* 5.0 3.2 - - - +
316D VAL* 4.5 7.8 - - + +
317D ALA 5.5 1.1 - - - +
318D GLY* 4.6 9.2 - - - +
319D THR 3.5 8.7 - - - +
321D VAL* 1.3 76.3 - - - +
323D GLU* 1.3 63.4 + - - +
325D ALA* 3.4 5.1 + - - +
326D SER* 3.0 24.8 + - - -
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D VAL* 3.8 18.2 - - + -
318D GLY 5.8 0.2 - - - +
319D THR 3.0 16.0 + - - +
320D GLY* 3.6 6.5 + - - +
321D VAL 3.3 0.2 - - - -
322D ALA* 1.3 76.7 - - - +
324D ALA* 1.3 62.3 + - - +
326D SER* 2.7 22.3 + - - -
327D LEU* 3.4 10.6 + - + +
339D HIS* 2.9 27.7 + - + +
340D GLU 3.4 7.3 - - - +
341D HIS* 3.0 25.6 + - - -
342D HIS 4.7 0.4 + - - -
345D THR* 3.4 20.8 - - + +
358D TYR* 4.4 5.9 - - + +
365D TYR* 3.3 24.6 + - + +
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Residues in contact with ALA 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D GLY 2.9 20.2 + - - +
321D VAL 3.9 1.3 - - - +
323D GLU* 1.3 75.8 - - - +
325D ALA* 1.3 64.2 + - - +
327D LEU* 3.2 21.5 + - - +
328D HIS* 3.2 20.7 - - - -
358D TYR* 4.2 17.8 - - + -
368D PRO* 4.4 2.1 - - + +
373D ILE* 3.7 18.4 - - + +
375D GLN* 3.8 17.9 - - + -
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D ILE* 4.1 20.0 - - + -
289D LEU* 3.5 12.3 - - + -
295D PHE* 3.2 39.8 - - + -
321D VAL 2.9 18.8 + - - +
322D ALA* 3.7 5.2 - - - +
324D ALA* 1.3 76.6 - - - +
326D SER* 1.3 62.8 + - - +
328D HIS* 3.2 15.0 + - - +
329D ALA 3.2 1.4 + - - -
373D ILE* 4.4 6.7 - - + +
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Residues in contact with SER 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D LEU* 3.6 13.7 - - - +
314D ALA* 4.2 11.0 - - - -
315D HIS 5.6 0.2 - - - -
316D VAL* 3.5 22.8 - - - +
322D ALA 3.0 13.8 + - - -
323D GLU* 2.7 20.4 + - - -
325D ALA* 1.3 77.3 - - - +
327D LEU* 1.3 60.8 + - - +
329D ALA* 3.2 2.9 + - - +
330D GLU* 3.0 30.1 + - - +
339D HIS* 3.1 21.0 - - - -
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Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D LEU* 3.8 16.9 - - + +
323D GLU* 3.4 15.5 - - + +
324D ALA* 3.2 11.4 + - - +
325D ALA 3.2 0.8 - - - -
326D SER* 1.3 78.0 + - - +
328D HIS* 1.3 60.4 + - - +
330D GLU* 4.0 0.5 - - - +
331D ILE* 3.1 28.2 + - - +
339D HIS* 3.6 28.7 - - + +
358D TYR* 4.6 7.9 - - + -
365D TYR* 3.7 40.2 - - + -
366D LYS 3.9 11.2 - - - +
367D VAL* 3.7 9.0 - - + +
368D PRO* 3.8 29.4 - - + -
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Residues in contact with HIS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PRO* 3.7 4.7 - - + -
112D VAL* 3.5 12.5 + - + -
113D TYR* 3.1 30.1 + - - +
116D LEU* 3.8 2.5 - - - +
295D PHE* 4.1 9.4 - - + -
324D ALA 3.2 25.4 - - - -
325D ALA* 3.2 7.9 + - - +
327D LEU* 1.3 74.0 - - - +
329D ALA* 1.3 65.5 + - - +
331D ILE* 3.6 2.9 - - - +
332D ALA* 3.4 24.6 + - - +
367D VAL* 3.5 13.8 - - + +
368D PRO* 3.5 31.4 - - + +
372D GLY 3.5 17.7 - - - -
373D ILE* 3.0 34.5 + - + -
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Residues in contact with ALA 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.1 10.9 - - - +
289D LEU* 4.0 21.5 - - + -
295D PHE* 4.0 5.7 - - + -
298D PHE* 3.7 31.7 - - + -
325D ALA 3.2 9.5 + - - +
326D SER* 3.6 7.6 - - - +
328D HIS* 1.3 81.3 - - - +
330D GLU* 1.3 61.1 + - - +
332D ALA* 3.5 8.3 + - - +
333D ILE* 3.6 20.4 + - - +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG* 3.0 18.9 + - - -
124D LEU* 3.6 15.4 - - + +
298D PHE* 4.5 6.5 - - + -
312D VAL* 5.5 0.4 - - + +
314D ALA* 3.0 42.8 + - + +
326D SER 3.0 18.6 + - - +
329D ALA* 1.3 73.9 - - - +
331D ILE* 1.3 62.7 + - - +
332D ALA 3.1 2.1 + - - -
333D ILE* 3.4 18.2 - - + +
336D PHE* 3.5 33.3 - - + +
338D ILE 3.8 4.3 - - - +
339D HIS* 2.5 37.6 + - - -
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Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 3.6 37.7 - - + -
118D GLY 4.1 0.2 - - - -
119D LYS* 3.6 12.1 - - + -
120D ASN* 2.8 35.2 + - - +
121D ARG* 3.4 38.4 + - + +
122D GLU 4.4 11.7 - - - +
123D ASP* 4.6 1.3 - - - +
124D LEU* 4.1 18.3 - - + +
327D LEU 3.1 19.8 + - - +
328D HIS 3.6 0.2 - - - +
330D GLU* 1.3 75.9 - - - +
332D ALA* 1.3 59.2 + - - +
333D ILE 3.3 0.2 - - - -
367D VAL* 3.8 31.6 - - + +
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 4.2 5.2 - - + +
116D LEU* 3.7 33.0 - - + +
118D GLY 3.1 18.8 - - - +
120D ASN* 3.1 13.7 + - - -
299D LYS* 5.2 1.7 + - + +
328D HIS 3.4 16.0 + - - +
329D ALA 3.5 4.5 + - - +
330D GLU 3.1 0.8 - - - -
331D ILE* 1.3 77.1 - - - +
333D ILE* 1.3 60.1 + - + +
69G GLU* 3.6 20.8 - - - +
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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