Contacts of the helix formed by residues 336 - 354 (chain B) in PDB entry 4OSI
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 GLY 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP 3.6 11.3 + - - -
334B HIS 3.4 0.4 + - - -
335B ASP* 1.3 74.3 - - - +
337B GLY* 1.3 64.5 + - - +
338B LYS 3.4 2.9 - - - -
339B GLN* 3.1 8.7 + - - +
340B ALA* 3.1 21.4 + - - +
4G C 3.6 40.6 + - - +
5G C 4.0 4.4 + - - -
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY 5.6 1.6 + - - -
306B ALA* 4.1 12.4 - - - +
331B ILE 4.5 5.2 - - - -
332B ALA* 4.0 20.2 - - - -
334B HIS* 3.3 14.2 + - - -
335B ASP 4.5 0.2 - - - -
336B GLY* 1.3 72.8 - - - +
338B LYS* 1.3 66.6 + - - +
340B ALA* 3.1 3.3 + - - +
341B LEU* 2.9 32.2 + - - +
4G C 4.6 1.0 + - - -
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLN* 3.9 34.8 - - + +
306B ALA* 4.0 8.5 - - - +
308B GLU* 6.2 2.7 - - - -
309B THR* 2.8 33.7 - - - +
312B ARG* 4.4 7.4 - - - +
337B GLY* 1.3 73.9 - - - +
339B GLN* 1.3 65.5 - - - +
341B LEU* 3.4 1.9 + - - +
342B GLU* 2.6 59.7 + - - +
4G C 3.7 20.8 + - - +
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Residues in contact with GLN 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLY 3.1 12.2 + - - +
338B LYS* 1.3 82.5 - - - +
340B ALA* 1.3 64.4 + - - +
341B LEU 3.2 0.2 + - - -
342B GLU* 3.3 15.1 + - - +
343B THR* 2.9 29.1 + - - -
372B LYS* 3.5 24.5 - - + +
4G C 2.6 42.4 + - - +
5G C 3.3 35.0 - - - +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.9 23.3 - - + +
334B HIS* 6.5 0.4 - - + -
335B ASP 5.8 0.7 - - - +
336B GLY 3.1 9.3 + - - +
337B GLY* 3.9 5.6 - - - +
339B GLN* 1.3 78.8 - - - +
341B LEU* 1.3 57.5 + - - +
343B THR* 3.5 3.0 + - - -
344B VAL* 2.9 34.0 + - - +
366B ALA* 4.1 17.5 - - + +
368B HIS 5.3 1.3 - - - +
371B GLY* 4.5 4.7 - - - +
372B LYS* 4.3 20.6 - - - +
375B LEU* 4.1 0.7 - - - +
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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
----------------------------------------------------------
306B ALA 4.8 0.7 - - - +
309B THR* 3.8 19.7 - - + +
310B VAL* 3.6 35.0 - - + +
313B LEU* 3.9 16.7 - - + +
317B LEU* 4.1 18.3 - - + +
328B VAL* 4.1 11.7 - - + +
331B ILE* 3.3 36.3 - - + -
332B ALA* 4.5 4.7 - - + -
337B GLY 2.9 19.9 + - - +
338B LYS 3.7 2.7 - - - +
340B ALA* 1.3 71.6 - - - +
342B GLU* 1.3 69.8 + - - +
343B THR 2.9 2.6 + - - -
344B VAL* 3.0 5.6 + - + +
345B GLN* 2.9 22.5 + - - +
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 4.6 1.3 - - + -
312B ARG* 3.0 27.9 + - - +
313B LEU* 3.9 12.1 - - + -
338B LYS* 2.6 58.4 + - - +
339B GLN* 4.1 18.8 + - - +
341B LEU* 1.3 73.1 - - - +
343B THR* 1.3 57.6 + - - +
345B GLN* 2.9 27.6 - - - +
346B ARG* 2.9 18.5 + - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN 2.9 13.1 + - - -
340B ALA 3.6 4.9 - - - -
341B LEU 2.9 1.8 + - - -
342B GLU* 1.3 74.5 - - - +
344B VAL* 1.3 64.3 + - - -
346B ARG* 3.0 19.7 + - - +
347B LEU* 2.9 32.0 + - + +
372B LYS* 2.8 40.8 - - + +
375B LEU* 3.2 33.0 - - + -
376B GLU* 4.6 3.9 + - + -
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 4.5 14.1 - - + -
323B LEU* 4.8 11.7 - - + -
331B ILE* 4.6 15.5 - - + -
340B ALA 2.9 25.4 + - - +
341B LEU* 3.0 6.7 + - + +
343B THR* 1.3 72.7 - - - +
345B GLN* 1.3 57.4 + - - +
347B LEU* 4.5 0.9 - - - +
348B LEU* 2.9 53.2 + - + +
362B VAL* 4.5 9.9 - - + +
363B VAL* 6.1 0.9 - - + -
366B ALA* 3.6 20.0 - - + -
375B LEU* 3.5 19.5 - - + +
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Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 5.7 0.4 - - - +
313B LEU* 4.0 29.3 - - + +
316B VAL* 5.9 6.3 - - + -
317B LEU* 3.9 24.9 - - + +
321B HIS* 4.7 6.2 + - - -
341B LEU 2.9 12.2 + - - +
342B GLU* 2.9 33.1 - - - +
344B VAL* 1.3 78.8 - - - +
346B ARG* 1.3 70.8 + - - +
347B LEU 3.5 0.2 + - - -
349B PRO* 4.4 8.7 - - - +
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Residues in contact with ARG 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B GLU* 2.9 14.8 + - - +
343B THR* 3.0 23.8 + - - +
345B GLN* 1.3 84.1 + - - +
347B LEU* 1.3 82.5 + - + +
348B LEU 3.8 0.2 - - - -
349B PRO* 4.1 7.8 - - - +
350B VAL* 4.3 5.9 - - - +
372B LYS* 5.9 1.9 - - - +
376B GLU* 3.1 32.7 + - - +
379B GLN* 5.7 2.4 + - - -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 2.9 18.4 + - + +
344B VAL* 4.7 1.3 - - - -
346B ARG* 1.3 118.0 - - + +
348B LEU* 1.3 68.3 + - - +
349B PRO* 3.2 2.9 - - - -
350B VAL* 4.0 15.5 - - + -
351B LEU* 3.2 38.2 + - + +
362B VAL* 6.0 0.2 - - - -
375B LEU* 4.1 24.2 - - + +
376B GLU* 4.3 7.0 - - - +
379B GLN* 4.0 32.3 - - + +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B HIS* 3.7 38.6 - - + +
323B LEU* 5.0 8.3 - - + -
344B VAL* 2.9 28.3 + - + +
347B LEU* 1.3 76.6 - - - +
349B PRO* 1.3 68.8 - - + +
351B LEU* 3.8 1.5 - - - -
352B CYS* 2.6 64.6 + - + +
359B PRO* 4.7 16.4 - - + +
362B VAL* 3.5 38.1 - - + -
363B VAL* 5.6 1.3 - - + +
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B HIS* 4.1 19.7 - - + +
345B GLN 4.4 5.4 - - - +
346B ARG 4.1 7.9 - - - +
347B LEU* 3.4 7.0 - - - +
348B LEU* 1.3 93.7 - - + +
350B VAL* 1.3 53.4 + - + +
352B CYS* 2.5 28.8 + - + -
353B GLN* 2.6 43.9 + - + +
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG 4.3 6.5 - - - +
347B LEU* 3.9 27.8 - - + +
349B PRO* 1.3 75.3 - - + +
351B LEU* 1.3 74.8 + - + +
353B GLN* 4.2 2.7 - - - -
354B ALA* 2.2 56.6 + - + +
355B HIS* 3.2 2.4 + - + +
379B GLN* 3.9 19.1 - - + +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.2 29.6 + - + +
348B LEU 3.8 2.2 - - - +
349B PRO 3.1 0.8 - - - -
350B VAL* 1.3 92.6 - - + +
352B CYS* 1.3 52.1 + - - +
355B HIS* 4.2 13.7 - - + +
356B GLY 4.0 2.3 + - - -
357B LEU* 2.5 41.9 + - + +
362B VAL* 4.3 17.5 - - + -
365B ILE* 6.3 1.3 - - + -
375B LEU* 3.9 35.0 - - + +
378B VAL* 4.0 18.8 - - + -
379B GLN* 3.3 32.3 - - + -
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Residues in contact with CYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 2.6 57.3 + - + +
349B PRO* 2.5 13.7 + - + +
351B LEU* 1.3 76.3 - - - +
353B GLN* 1.3 59.5 + - + +
356B GLY* 3.2 6.4 - - - -
357B LEU 3.1 36.9 + - - +
358B THR 4.3 5.4 - - - -
359B PRO* 4.6 2.5 - - - -
362B VAL* 4.1 8.5 - - - -
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B PRO* 2.6 49.1 + - - +
350B VAL* 3.9 2.2 - - - +
352B CYS* 1.3 78.3 - - - +
354B ALA* 1.3 63.2 + - + +
355B HIS 3.3 1.3 - - - -
356B GLY* 3.7 6.4 + - - +
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Residues in contact with ALA 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B VAL* 2.2 51.0 + - + +
353B GLN* 1.3 76.8 - - - +
355B HIS* 1.3 73.4 + - + +
----------------------------------------------------------
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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