Contacts of the helix formed by residues 333 - 346 (chain B) in PDB entry 5OO2
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 PRO 333 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B VAL* 4.7 6.3 - - + -
331B GLY 4.0 4.3 - - - +
332B LEU* 1.3 95.8 - - + +
334B HIS* 1.3 66.7 - - - +
335B ASP* 3.3 2.9 - - + +
336B ARG* 3.0 36.4 + - + +
337B GLU* 3.0 20.1 + - - +
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Residues in contact with HIS 334 (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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268A GLU* 5.3 4.5 - - + -
271A GLU* 2.9 37.1 + - - -
284A TYR* 3.3 22.3 + + - -
332B LEU 3.5 2.7 + - - -
333B PRO* 1.3 72.1 - - - +
335B ASP* 1.3 85.3 + - - +
337B GLU* 3.2 5.9 + - - +
338B ARG* 3.0 38.9 + - + +
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Residues in contact with ASP 335 (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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271A GLU* 4.5 4.7 - - - +
333B PRO* 3.3 2.5 - - + +
334B HIS* 1.3 94.1 - - - +
336B ARG* 1.3 62.6 + - - +
338B ARG* 3.4 9.0 + - - +
339B ALA* 3.1 21.8 + - - +
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Residues in contact with ARG 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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295B VAL* 4.2 10.3 + - - +
298B THR* 2.9 28.2 + - - -
299B ASP 3.5 13.5 - - - -
300B GLN* 3.8 35.0 + - - +
301B ARG 4.8 1.1 - - - +
302B THR 3.9 1.5 - - - +
303B GLY* 3.5 18.7 - - - +
332B LEU* 3.6 23.0 - - + +
333B PRO* 3.0 35.6 + - + +
335B ASP* 1.3 79.1 - - - +
337B GLU* 1.3 57.7 + - - +
339B ALA* 3.3 7.1 + - - +
340B LEU* 3.0 25.5 + - - +
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Residues in contact with GLU 337 (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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326B PRO 4.2 3.6 - - - +
327B LEU* 3.7 19.3 - - + +
330B GLY* 4.8 1.6 - - - -
332B LEU* 4.0 28.5 + - + +
333B PRO 3.0 13.0 + - - +
334B HIS* 3.6 8.9 - - - +
336B ARG* 1.3 76.7 - - - +
338B ARG* 1.3 65.4 + - + +
340B LEU* 3.0 3.1 + - - +
341B LEU* 2.9 27.2 + - + +
395B ARG* 2.9 42.6 + - - -
397B TRP* 3.7 18.7 - - + -
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Residues in contact with ARG 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 4.5 7.1 + - - +
271A GLU* 3.5 43.4 + - - +
272A ASP* 2.9 31.9 + - - +
334B HIS* 3.0 48.9 + - + +
335B ASP* 3.4 9.8 + - - +
337B GLU* 1.3 75.7 - - + +
339B ALA* 1.3 63.5 + - - +
341B LEU* 3.4 13.1 + - + +
342B LYS* 3.0 23.7 + - - +
400B ARG* 6.0 1.6 - - - +
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Residues in contact with ALA 339 (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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301B ARG 3.3 26.0 - - - +
302B THR* 3.5 9.5 - - - +
335B ASP 3.1 14.3 + - - +
336B ARG* 3.4 10.5 - - - +
337B GLU 3.1 0.2 - - - -
338B ARG* 1.3 77.0 - - - +
340B LEU* 1.3 61.7 + - - +
342B LYS* 3.3 11.3 + - - +
343B LEU* 3.1 20.4 + - - +
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Residues in contact with LEU 340 (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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302B THR 3.2 17.9 + - - +
303B GLY* 3.6 15.5 - - - +
304B ALA* 3.7 19.3 - - - +
323B GLN 4.0 3.6 - - - +
324B PHE* 3.6 25.6 - - + -
326B PRO* 3.9 22.4 - - + -
327B LEU* 3.6 28.7 - - + -
332B LEU* 3.9 6.5 - - + -
336B ARG 3.0 10.2 + - - +
337B GLU* 3.0 9.6 + - - +
339B ALA* 1.3 73.4 - - - +
341B LEU* 1.3 61.6 + - - +
343B LEU* 3.3 11.9 + - + +
344B LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 341 (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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327B LEU* 3.9 19.7 - - + -
337B GLU* 2.9 23.1 + - + +
338B ARG* 3.7 11.7 - - + +
340B LEU* 1.3 76.5 - - - +
342B LYS* 1.3 61.8 + - - +
344B LEU* 3.2 11.1 + - + +
345B GLU* 3.0 33.4 + - - +
392B PHE* 5.0 0.2 - - + -
397B TRP* 3.9 39.0 - - + +
400B ARG* 3.7 47.1 - - - +
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Residues in contact with LYS 342 (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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274A LYS* 5.8 5.7 - - - +
338B ARG 3.0 13.6 + - - +
339B ALA* 3.4 14.1 - - - +
340B LEU 3.2 0.2 - - - -
341B LEU* 1.3 77.8 - - - +
343B LEU* 1.3 56.5 + - - +
345B GLU* 3.3 5.0 + - - +
346B GLY* 2.9 28.9 + - - -
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Residues in contact with LEU 343 (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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302B THR* 4.7 13.9 - - + +
304B ALA* 4.4 11.7 - - + -
323B GLN* 4.1 20.0 - - - +
324B PHE* 3.9 19.3 - - + -
339B ALA 3.1 12.8 + - - +
340B LEU* 3.5 20.0 - - + +
342B LYS* 1.3 75.9 - - - +
344B LEU* 1.3 62.4 + - - +
345B GLU 3.3 0.5 + - - -
346B GLY* 3.4 11.3 + - - +
348B ARG* 3.9 33.7 - - + +
349B PHE* 3.9 16.0 + - + +
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Residues in contact with LEU 344 (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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324B PHE* 3.4 44.8 - - + -
327B LEU* 3.9 8.5 - - + -
340B LEU 3.0 10.0 + - - +
341B LEU* 3.2 15.9 + - + +
343B LEU* 1.3 75.6 - - - +
345B GLU* 1.3 67.6 + - + +
349B PHE* 3.4 1.5 - - + +
350B CYS* 3.0 35.0 + - - +
360B ILE* 3.9 31.4 - - + -
392B PHE* 3.7 35.4 - - + -
400B ARG* 5.8 0.4 - - - -
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Residues in contact with GLU 345 (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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502A GOL 5.0 6.9 + - - -
341B LEU* 3.0 22.2 + - - +
342B LYS* 3.7 3.8 - - - +
344B LEU* 1.3 86.9 - - + +
346B GLY* 1.3 60.6 + - - +
350B CYS* 4.1 7.6 - - + -
351B GLY* 3.2 19.3 + - - -
400B ARG* 2.8 45.9 + - - +
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Residues in contact with GLY 346 (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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342B LYS 2.9 16.2 + - - -
343B LEU* 3.4 5.1 + - - -
345B GLU* 1.3 78.6 - - - +
347B PRO* 1.3 69.7 - - - +
348B ARG 3.0 10.5 + - - -
349B PHE 3.0 8.2 + - - -
351B GLY* 2.8 20.3 + - - -
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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