Contacts of the helix formed by residues 319 - 338 (chain B) in PDB entry 2OT0
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 ASN 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA 2.9 26.1 + - - +
313B TRP* 3.5 19.5 + - - +
316B LYS* 3.1 20.8 + - - +
318B GLU* 1.3 95.0 - - - +
320B LEU* 1.3 64.7 + - - +
321B LYS 3.4 1.3 - - - -
322B ALA* 3.3 11.8 + - + +
323B ALA* 2.8 25.6 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 4.1 25.8 - - + -
60B GLN* 5.7 4.3 - - - +
61B LEU* 3.8 33.4 - - + -
64B THR* 5.9 0.2 - - - +
313B TRP* 5.1 1.6 - - - -
316B LYS 3.9 3.0 + - - -
317B LYS 3.3 16.8 + - - +
318B GLU 3.2 2.2 - - - +
319B ASN* 1.3 76.1 - - - +
321B LYS* 1.3 73.2 + - + +
323B ALA* 3.5 4.3 - - - +
324B GLN* 2.9 48.3 + - - +
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Residues in contact with LYS 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B GLU 4.6 4.5 + - - +
319B ASN 3.4 0.6 - - - -
320B LEU* 1.3 87.4 - - + +
322B ALA* 1.3 62.5 + - - +
324B GLN* 3.5 17.7 + - - +
325B GLU* 3.2 23.9 + - - +
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ALA* 4.6 7.2 - - + +
318B GLU 5.4 0.6 + - - +
319B ASN* 3.3 17.2 + - + +
321B LYS* 1.3 77.7 - - - +
323B ALA* 1.3 64.7 + - - +
325B GLU* 3.3 8.7 + - - +
326B GLU* 3.3 22.5 + - - +
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Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.8 11.9 - - + -
309B ALA* 3.6 27.7 - - - +
312B ALA* 3.8 12.5 - - - +
313B TRP* 3.8 20.0 - - + +
319B ASN 2.8 17.3 + - - +
320B LEU 3.5 3.4 - - - +
322B ALA* 1.3 73.8 - - - +
324B GLN* 1.3 68.1 + - - +
326B GLU* 2.8 21.0 + - - +
327B TYR 3.4 3.3 + - - -
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Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 2.7 45.6 + - + +
64B THR* 3.3 20.8 + - - +
65B ALA* 3.3 26.8 - - + +
66B ASP 5.0 3.3 + - - +
320B LEU* 2.9 38.8 + - - +
321B LYS* 3.8 19.5 - - - +
323B ALA* 1.3 74.6 - - - +
325B GLU* 1.3 59.1 + - - +
327B TYR* 3.1 9.2 + - - +
328B VAL* 2.9 31.3 + - + +
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Residues in contact with GLU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASP* 4.8 2.1 - - - +
68B ARG* 2.7 46.9 + - - -
321B LYS 3.2 11.3 + - - +
322B ALA* 3.5 11.9 - - - +
323B ALA 3.1 0.8 - - - -
324B GLN* 1.3 79.4 - - - +
326B GLU* 1.3 59.7 + - - +
328B VAL* 3.5 14.8 - - - +
329B LYS* 2.9 57.9 + - - +
332B LEU* 5.4 1.0 - - - +
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Residues in contact with GLU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER* 3.7 19.1 + - - +
309B ALA* 3.7 17.5 - - - +
312B ALA* 3.9 20.6 - - + -
322B ALA 3.3 13.8 + - - +
323B ALA 2.8 14.0 + - - +
325B GLU* 1.3 74.4 - - - +
327B TYR* 1.3 63.2 + - - +
329B LYS* 3.3 31.4 + - - +
330B ARG* 3.3 27.1 + - - +
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.7 33.4 - - + +
61B LEU 5.2 0.2 - - - -
62B LEU* 3.3 48.8 + - + -
65B ALA* 3.8 23.6 - - + -
69B VAL* 3.9 15.7 - - + +
73B ILE* 3.3 29.0 - - + +
76B VAL* 5.7 0.5 - - - +
305B LEU* 3.5 38.8 - - + +
309B ALA* 3.9 10.7 - - + +
323B ALA 3.4 1.2 + - - -
324B GLN* 3.1 8.6 + - - +
326B GLU* 1.3 75.2 - - - +
328B VAL* 1.3 67.3 + - - +
330B ARG* 3.1 2.8 + - - +
331B ALA* 2.9 23.3 + - + +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA* 3.9 21.1 - - + -
66B ASP* 4.4 10.8 - - + +
68B ARG* 3.5 35.7 - - + +
69B VAL* 4.4 14.8 - - + +
324B GLN* 2.9 23.5 + - + +
325B GLU* 3.3 19.3 + - - +
327B TYR* 1.3 77.9 - - - +
329B LYS* 1.3 56.8 + - - +
331B ALA* 3.3 7.6 + - - +
332B LEU* 3.0 39.5 + - + +
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B GLU* 2.9 45.0 + - - +
326B GLU* 3.6 29.2 + - - +
327B TYR 3.1 0.2 - - - -
328B VAL* 1.3 75.0 - - - +
330B ARG* 1.3 67.8 + - - +
332B LEU* 3.3 13.4 + - + +
333B ALA* 3.0 26.9 + - - +
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU* 3.5 52.4 + - - +
277B GLU* 2.9 31.2 + - - +
280B SER* 3.1 27.7 + - - -
304B ALA 3.9 8.9 + - - +
305B LEU* 3.8 21.3 - - + +
308B SER* 5.2 3.1 - - - +
326B GLU* 3.3 14.3 + - - +
327B TYR 3.1 7.6 + - - +
329B LYS* 1.3 82.5 + - - +
331B ALA* 1.3 57.5 + - - +
333B ALA* 3.4 9.2 + - - +
334B ASN* 2.9 36.4 + - - +
342B TYR* 3.8 7.1 + - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 3.4 30.3 - - + -
72B CYS* 3.5 13.9 - - + +
73B ILE* 4.6 3.8 - - + -
299B PHE* 4.6 2.9 - - - -
305B LEU* 3.7 14.1 - - + +
327B TYR* 2.9 17.3 + - + +
328B VAL 3.4 9.0 - - - +
330B ARG* 1.3 76.9 - - - +
332B LEU* 1.3 56.8 + - - +
334B ASN* 3.4 3.3 + - - +
335B SER* 2.9 29.5 + - - -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 3.7 23.8 - - + +
71B PRO* 6.4 0.2 - - + -
72B CYS* 3.5 23.3 - - - -
325B GLU* 5.4 0.7 - - - +
328B VAL* 3.0 37.4 + - + +
329B LYS* 3.7 11.9 - - + +
331B ALA* 1.3 74.6 - - - +
333B ALA* 1.3 62.7 + - - +
335B SER* 3.3 3.8 + - - -
336B LEU* 3.2 28.2 + - + +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B SER* 4.1 2.7 - - - +
329B LYS 3.0 17.4 + - - +
330B ARG* 3.6 24.2 - - - +
331B ALA 3.3 0.2 - - - -
332B LEU* 1.3 77.8 - - - +
334B ASN* 1.3 58.6 + - - +
336B LEU* 3.2 7.8 + - - +
337B ALA* 2.9 26.1 + - - +
342B TYR* 3.5 37.8 - - + +
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Residues in contact with ASN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B GLU 5.3 0.4 + - - -
280B SER* 2.6 31.9 + - - -
283B LEU* 4.3 3.5 - - + +
299B PHE* 3.5 28.6 - - + -
301B TYR* 3.4 35.6 - - - -
304B ALA 4.4 6.9 + - - -
305B LEU* 3.7 12.7 - - - +
330B ARG* 2.9 25.9 + - - +
331B ALA 4.0 0.4 - - - +
333B ALA* 1.3 73.2 - - - +
335B SER* 1.3 60.8 + - - +
337B ALA* 3.7 4.6 - - - +
338B CYS* 2.9 32.2 + - - +
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 2.8 29.3 + - - -
71B PRO* 4.4 4.0 + - - +
72B CYS* 3.7 20.0 - - - -
299B PHE* 4.1 2.4 - - - -
331B ALA 2.9 17.5 + - - -
332B LEU* 3.4 7.9 - - - -
334B ASN* 1.3 76.4 - - - +
336B LEU* 1.3 63.0 + - - +
338B CYS* 3.2 16.0 - - - -
339B GLN* 2.9 24.0 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B LEU* 3.2 15.3 + - + +
333B ALA* 3.5 7.2 - - - +
334B ASN 3.2 0.2 - - - -
335B SER* 1.3 79.8 - - - +
337B ALA* 1.3 58.5 + - - +
339B GLN* 2.9 25.7 + - - +
341B LYS* 2.9 55.6 + - + +
342B TYR* 3.8 20.4 - - + -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.3 29.8 - - - +
283B LEU* 4.0 10.1 - - + -
284B ASN* 3.4 18.1 - - - +
287B ASN* 3.2 9.9 + - - -
333B ALA 2.9 16.6 + - - +
334B ASN* 3.3 10.7 + - - +
336B LEU* 1.3 72.4 - - - +
338B CYS* 1.3 56.7 + - - +
339B GLN 2.9 5.2 - - - -
340B GLY 2.9 15.2 + - - -
342B TYR* 3.5 13.2 - - + +
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Residues in contact with CYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 3.4 33.9 + - - -
27B LYS 3.8 1.8 - - - -
283B LEU* 3.9 5.1 - - + +
287B ASN* 3.3 24.7 + - - +
297B LEU 3.6 5.5 + - - +
298B THR* 3.3 36.3 - - - +
299B PHE* 4.3 1.3 - - - -
334B ASN 2.9 16.7 + - - +
335B SER* 3.2 22.7 - - - -
336B LEU 3.3 0.2 - - - -
337B ALA* 1.3 74.6 - - - +
339B GLN* 1.3 56.9 + - - +
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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) + - + + + + + -
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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