Contacts of the helix formed by residues 336 - 353 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ASP 3.3 12.1 + - - -
334A HIS* 4.7 0.4 - - - -
335A ASP* 1.3 75.4 - - - +
337A GLY* 1.3 68.1 + - - +
338A LYS 3.4 1.1 - - - -
339A GLN* 3.3 14.2 + - - +
340A ALA* 3.4 12.0 + - - +
370A GLY 5.8 0.2 + - - -
4I C 3.7 41.2 - - - +
5I C 4.2 2.4 + - - -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP 5.1 0.2 + - - -
302A GLY* 5.9 0.8 - - - -
306A ALA* 3.9 11.9 - - - +
331A ILE 4.2 5.2 - - - -
332A ALA* 3.7 27.8 - - - -
334A HIS 3.3 7.8 + - - -
336A GLY* 1.3 74.8 - - - +
338A LYS* 1.3 65.0 + - - +
339A GLN 3.0 0.5 + - - -
340A ALA* 3.0 4.1 + - - +
341A LEU* 2.9 29.7 + - - +
4I C 4.9 0.4 + - - -
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN* 3.7 37.2 - - + +
306A ALA* 4.0 8.9 - - - +
308A GLU* 4.8 5.6 - - - +
309A THR* 3.1 31.4 - - - +
312A ARG* 4.7 5.4 - - - +
336A GLY 3.4 0.4 - - - -
337A GLY* 1.3 71.3 - - - +
339A GLN* 1.3 79.9 + - - +
341A LEU* 3.5 0.7 + - - +
342A GLU* 3.0 59.0 + - - +
4I C 4.2 12.7 + - - +
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLY 3.3 3.9 + - - +
337A GLY 3.2 1.2 - - - -
338A LYS* 1.3 108.0 - - - +
340A ALA* 1.3 58.7 + - - +
342A GLU* 3.9 9.0 + - - +
343A THR* 2.9 35.2 + - - -
346A ARG* 5.9 0.2 + - - -
372A LYS* 2.8 38.3 + - + +
4I C 3.4 32.0 + - - +
5I C 3.4 34.3 - - - +
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 3.8 24.7 - - + +
336A GLY 3.4 8.3 + - - +
337A GLY* 3.0 6.1 + - - +
339A GLN* 1.3 75.7 - - - +
341A LEU* 1.3 66.3 + - - +
343A THR* 3.4 1.3 + - - -
344A VAL* 2.9 28.9 + - - +
366A ALA* 3.8 17.9 - - + +
368A HIS 5.0 2.0 - - - +
371A GLY* 4.2 5.4 - - - +
372A LYS* 4.1 20.6 - - - +
375A LEU* 4.2 0.4 - - - +
5I C 5.2 0.2 + - - -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ALA 4.3 0.7 - - - +
309A THR* 3.6 28.3 - - + -
310A VAL* 3.7 34.8 - - + +
313A LEU* 4.4 11.2 - - + -
317A LEU* 4.1 23.0 - - + +
328A VAL* 3.9 14.4 - - + +
331A ILE* 3.6 30.5 - - + -
332A ALA* 4.2 6.7 - - + +
337A GLY 2.9 20.0 + - - +
338A LYS 3.8 2.9 - - - +
340A ALA* 1.3 74.5 - - - +
342A GLU* 1.3 65.7 + - - +
344A VAL* 2.8 17.1 + - + +
345A GLN* 2.9 13.0 + - - +
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Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 4.4 1.8 - - + -
312A ARG* 3.0 31.8 + - - +
313A LEU* 4.2 15.7 - - + -
338A LYS* 3.0 49.0 + - - +
339A GLN* 4.1 10.1 + - - +
341A LEU* 1.3 75.6 - - - +
343A THR* 1.3 57.7 + - - +
345A GLN* 3.3 16.0 + - - +
346A ARG* 3.0 37.9 + - - +
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN 2.9 16.0 + - - -
340A ALA 3.8 2.7 - - - -
342A GLU* 1.3 77.2 - - - +
344A VAL* 1.3 57.6 + - - +
346A ARG* 3.2 20.5 + - - +
347A LEU* 2.9 52.2 + - + +
372A LYS* 2.9 40.2 - - + +
375A LEU* 3.5 23.7 - - + +
376A GLU* 4.1 1.5 + - + -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 4.0 19.5 - - + -
323A LEU* 4.6 11.4 - - + -
331A ILE* 4.0 12.8 - - + -
340A ALA 2.9 16.7 + - - +
341A LEU* 2.8 9.7 + - - +
343A THR* 1.3 75.2 - - - +
345A GLN* 1.3 68.3 + - - +
347A LEU* 5.2 0.2 - - - -
348A LEU* 2.9 52.4 + - + +
362A VAL* 4.6 8.5 - - + -
363A VAL* 5.8 0.4 - - + -
366A ALA* 3.4 28.5 - - + -
375A LEU* 3.6 9.2 - - + -
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Residues in contact with GLN 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 5.1 2.4 - - - +
313A LEU* 3.3 34.8 - - + +
316A VAL* 3.7 22.5 - - + +
317A LEU* 4.0 20.8 - - + +
321A HIS* 3.8 28.0 - - - +
341A LEU 2.9 9.7 + - - +
342A GLU* 3.6 16.7 + - - +
344A VAL* 1.3 78.8 - - - +
346A ARG* 1.3 64.8 + - + +
349A PRO* 3.9 3.5 - - - +
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Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLN* 5.9 0.2 + - - -
342A GLU* 3.0 17.3 + - - +
343A THR* 3.2 31.8 + - - +
344A VAL 3.0 0.4 - - - -
345A GLN* 1.3 83.4 - - + +
347A LEU* 1.3 85.7 + - + +
349A PRO* 3.7 8.8 - - - +
350A VAL* 4.0 7.1 - - - +
372A LYS* 5.1 6.3 - - - +
376A GLU* 3.6 20.6 + - - +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A THR* 2.9 40.9 + - + +
344A VAL* 5.2 0.7 - - - -
346A ARG* 1.3 92.5 - - + +
348A LEU* 1.3 65.0 + - - +
349A PRO* 3.4 3.1 - - - -
350A VAL* 3.1 15.0 + - + +
351A LEU* 2.9 40.6 + - + +
375A LEU* 4.4 5.8 - - + +
376A GLU* 3.8 27.4 - - + +
379A GLN* 3.2 39.3 - - + +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A HIS* 3.4 48.5 - - + +
323A LEU* 4.6 13.9 - - + -
344A VAL* 2.9 29.5 + - + +
347A LEU* 1.3 75.7 - - - +
349A PRO* 1.3 63.5 - - + +
351A LEU* 4.0 1.9 - - - +
352A CYS* 2.8 45.6 + - + +
359A PRO* 4.4 13.2 - - + +
362A VAL* 3.5 40.8 - - + -
363A VAL 5.3 0.4 - - - +
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Residues in contact with PRO 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A HIS* 3.9 20.4 - - + +
345A GLN 3.9 8.5 - - - +
346A ARG 3.7 11.4 - - - +
347A LEU 3.4 3.4 - - - -
348A LEU* 1.3 95.2 - - + +
350A VAL* 1.3 57.4 + - + +
352A CYS* 3.1 3.4 + - + -
353A GLN* 2.6 54.2 + - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ARG 4.0 7.2 - - - +
347A LEU* 3.1 35.9 - - + +
349A PRO* 1.3 78.1 - - + +
351A LEU* 1.3 57.7 + - + +
353A GLN* 4.7 1.6 - - - -
354A ALA* 3.0 40.9 + - + +
355A HIS* 3.2 15.4 + - + +
379A GLN* 4.3 18.8 - - + +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 2.9 33.6 + - + +
348A LEU 4.1 0.7 - - - +
350A VAL* 1.3 76.6 - - + +
352A CYS* 1.3 64.9 + - - +
355A HIS* 3.1 30.7 + - + +
357A LEU* 3.1 24.4 + - + +
362A VAL* 4.0 26.7 - - + -
365A ILE* 6.5 0.4 - - + -
375A LEU* 3.9 30.7 - - + +
378A VAL* 4.1 14.4 - - + -
379A GLN* 3.6 40.8 - - + +
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Residues in contact with CYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 2.8 27.6 + - - +
349A PRO* 3.7 2.2 - - + +
351A LEU* 1.3 77.8 - - - +
353A GLN* 1.3 66.4 + - + +
356A GLY* 3.2 18.0 - - - -
357A LEU 3.2 23.4 + - - +
358A THR 3.8 2.2 - - - -
359A PRO* 3.5 39.0 - - + -
362A VAL* 4.3 8.1 - - - -
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PRO* 2.6 33.8 + - + +
350A VAL* 4.7 1.2 - - - -
352A CYS* 1.3 77.8 - - + +
354A ALA* 1.3 61.5 - - + +
355A HIS 2.9 8.0 + - - -
356A GLY* 3.0 7.4 + - - -
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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