Contacts of the helix formed by residues 370 - 387 (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 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ASP 4.5 4.8 + - - -
369B ASP* 1.3 72.5 - - - +
371B GLY* 1.3 54.0 + - - +
372B LYS 3.0 2.7 - - - -
373B GLN* 2.5 39.1 + - - +
374B ALA* 3.2 3.2 + - - -
5G C 3.6 46.9 + - - +
6G C 3.8 5.2 - - - -
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Residues in contact with GLY 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 4.5 6.5 - - - +
365B ILE 4.4 5.3 - - - +
366B ALA* 4.0 18.4 - - - -
368B HIS* 3.1 13.5 + - - -
369B ASP 3.0 7.5 + - - -
370B GLY* 1.3 73.6 - - - +
372B LYS* 1.3 62.8 + - - +
374B ALA* 3.0 7.6 + - - +
375B LEU* 2.9 32.0 + - - +
5G C 5.1 0.2 + - - -
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Residues in contact with LYS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLN* 3.5 37.4 - - + +
340B ALA* 4.3 7.4 - - - +
343B THR* 2.8 36.3 - - - +
346B ARG* 5.9 2.4 - - - +
370B GLY 2.7 4.2 + - - -
371B GLY* 1.3 70.5 - - - +
373B GLN* 1.3 77.4 + - - +
375B LEU* 3.1 3.3 + - - +
376B GLU* 2.9 53.6 + - - +
5G C 3.5 21.9 + - - +
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Residues in contact with GLN 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B GLY 2.5 17.6 + - - +
372B LYS* 1.3 81.2 - - - +
374B ALA* 1.3 61.0 + - - +
376B GLU* 3.4 22.7 + - - +
377B THR* 2.7 31.6 + - - -
406B LYS* 3.6 31.9 - - + +
5G C 2.8 38.6 + - - +
6G C 3.7 22.7 - - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ILE* 3.9 23.8 - - + +
370B GLY 3.2 2.9 + - - +
371B GLY* 3.0 12.3 + - - +
373B GLN* 1.3 77.3 - - - +
375B LEU* 1.3 57.9 + - - +
377B THR* 3.4 2.5 + - - -
378B VAL* 2.9 32.2 + - - +
400B ALA* 4.2 17.3 - - + +
402B ASN 5.0 2.0 - - - +
405B GLY* 4.5 4.9 - - - +
406B LYS 4.1 18.9 - - - +
409B LEU* 4.0 1.5 - - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA 4.1 2.2 - - - +
343B THR* 3.2 32.1 - - + +
344B VAL* 3.5 32.1 - - + +
347B LEU* 4.2 9.6 - - + -
351B LEU* 3.9 12.8 - - + +
362B VAL* 4.2 17.7 - - + +
365B ILE* 3.7 24.9 - - + -
366B ALA* 4.2 14.1 - - + -
371B GLY 2.9 22.1 + - - +
372B LYS* 3.5 6.1 - - - +
374B ALA* 1.3 67.0 - - - +
376B GLU* 1.3 68.6 + - - +
378B VAL* 3.1 7.5 + - - +
379B GLN* 2.9 23.2 + - - +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 4.6 5.5 + - + -
346B ARG* 3.1 30.7 + - - +
347B LEU* 4.3 8.9 - - + +
372B LYS* 2.9 45.0 + - + +
373B GLN* 3.6 21.7 + - - +
375B LEU* 1.3 73.7 - - - +
377B THR* 1.3 59.6 + - - +
379B GLN* 3.1 10.9 + - - +
380B ALA* 2.9 30.9 + - - +
406B LYS* 6.0 2.0 - - - -
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Residues in contact with THR 377 (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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373B GLN 2.7 22.3 + - - -
374B ALA 3.8 0.4 - - - -
376B GLU* 1.3 77.3 - - - +
378B VAL* 1.3 60.6 + - - +
380B ALA* 4.5 4.9 - - - +
381B LEU* 2.9 38.7 + - + +
406B LYS* 2.8 41.8 - - + +
409B LEU* 3.3 36.7 - - + +
410B GLU* 4.4 4.9 - - + -
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Residues in contact with VAL 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 4.0 21.8 - - + -
355B HIS* 5.8 0.9 - - + +
357B LEU* 4.5 12.3 - - + -
365B ILE* 3.9 25.4 - - + -
374B ALA 2.9 18.5 + - - +
375B LEU* 3.1 8.9 + - - +
377B THR* 1.3 74.0 - - - +
379B GLN* 1.3 67.2 + - - +
380B ALA 2.8 1.7 + - - -
382B LEU* 2.9 48.2 + - + +
396B VAL* 4.6 13.0 - - + -
397B VAL* 5.6 0.9 - - + -
400B ALA* 4.0 12.8 - - + -
409B LEU* 3.9 7.4 - - + +
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG* 5.7 2.3 + - - -
347B LEU* 4.0 18.1 - - + +
350B VAL* 3.9 15.9 - - + +
351B LEU* 3.3 31.0 - - + -
355B HIS* 3.6 23.4 + - - +
375B LEU 2.9 10.7 + - - +
376B GLU* 3.4 14.1 - - - +
378B VAL* 1.3 77.1 - - - +
380B ALA* 1.3 62.4 + - - +
383B PRO* 4.3 1.6 - - - +
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Residues in contact with ALA 380 (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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376B GLU 2.9 15.3 + - - +
377B THR* 3.9 6.3 - - - +
378B VAL 2.8 1.2 + - - -
379B GLN* 1.3 85.5 - - - +
381B LEU* 1.3 74.3 + - + +
383B PRO* 4.0 10.6 - - - +
384B VAL* 4.9 2.3 - - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B THR* 2.9 25.4 + - + +
380B ALA* 1.3 89.2 - - + +
382B LEU* 1.3 68.6 + - - +
383B PRO* 2.9 6.3 - - - -
384B VAL* 3.1 27.5 + - + +
385B LEU* 3.5 20.4 + - + +
409B LEU* 4.3 4.0 - - + -
410B GLU* 4.1 37.5 - - + +
413B GLN* 3.9 31.6 - - + +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B HIS* 3.7 33.9 - - + +
357B LEU* 5.0 9.6 - - + -
377B THR 4.3 0.2 + - - -
378B VAL* 2.9 35.4 + - + +
381B LEU* 1.3 75.3 - - - +
383B PRO* 1.3 74.5 - - + +
385B LEU* 3.8 3.8 + - - +
386B CYS* 3.2 34.5 + - - +
393B PRO* 4.7 17.0 - - + -
396B VAL* 3.1 42.8 - - + +
397B VAL* 6.0 2.0 - - + -
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Residues in contact with PRO 383 (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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355B HIS* 3.3 26.0 - - + +
379B GLN 4.3 2.5 - - - +
380B ALA 4.0 10.8 - - - +
381B LEU 2.9 3.8 - - - +
382B LEU* 1.3 100.8 - - + +
384B VAL* 1.3 67.8 + - + +
386B CYS* 3.0 9.3 + - + +
387B GLN* 3.0 31.4 + - + +
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Residues in contact with VAL 384 (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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380B ALA 4.9 1.6 - - - +
381B LEU* 3.2 27.6 - - + +
383B PRO* 1.3 76.0 - - + +
385B LEU* 1.3 62.2 + - - +
386B CYS 3.0 0.7 + - - -
387B GLN* 3.1 13.5 + - - +
388B ALA* 2.7 37.1 + - + -
389B HIS* 3.1 25.6 + - + +
413B GLN* 3.5 30.1 - - + +
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LEU* 3.5 28.6 + - + +
382B LEU 4.1 6.7 - - - +
383B PRO 3.4 0.6 - - - -
384B VAL* 1.3 79.2 - - - +
386B CYS* 1.3 56.5 + - - +
389B HIS* 3.2 19.7 - - + +
390B GLY 3.0 18.7 + - - -
391B LEU* 3.2 19.7 + - + +
396B VAL* 4.1 26.9 - - + -
399B ILE* 6.4 0.4 - - + -
409B LEU* 4.7 22.0 - - + +
412B VAL* 3.7 29.4 - - + -
413B GLN* 3.7 28.3 - - + -
416B LEU* 4.9 0.7 - - + -
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Residues in contact with CYS 386 (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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382B LEU* 3.2 28.7 + - - +
383B PRO* 3.0 4.6 + - + +
385B LEU* 1.3 79.7 - - - +
387B GLN* 1.3 61.0 + - + +
390B GLY* 3.1 18.9 - - - -
391B LEU 3.0 25.6 + - - +
392B THR 4.7 0.2 - - - -
393B PRO* 3.8 33.9 - - - -
396B VAL* 4.8 2.7 - - - -
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Residues in contact with GLN 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B PRO* 3.0 37.8 - - + +
384B VAL* 3.3 8.6 - - - +
386B CYS* 1.3 76.1 - - + +
388B ALA* 1.3 73.3 + - - +
389B HIS 3.0 5.7 + - - -
390B GLY* 3.2 9.9 + - - -
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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
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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