Contacts of the helix formed by residues 369 - 387 (chain A) in PDB entry 4CBS
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 THR 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A GLN* 4.6 4.0 - - - +
294A ALA* 4.4 3.5 - - - +
363A LEU* 4.9 0.8 - - - +
366A CYS 3.3 26.5 - - - +
367A ASN* 2.9 8.2 + - - -
368A ALA* 1.3 76.2 - - - +
370A ARG* 1.3 63.8 + - - +
371A GLU* 3.6 8.4 + - - +
372A ASN* 3.1 35.2 + - - +
373A VAL* 3.2 17.1 + - - +
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Residues in contact with ARG 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU 6.0 1.1 - - - +
294A ALA* 5.0 7.8 - - + +
297A TYR* 3.7 68.0 + - + +
369A THR* 1.3 72.5 - - - +
371A GLU* 1.3 59.3 + - - +
373A VAL* 2.8 23.6 + - - +
374A ASP* 3.0 13.1 + - - +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A THR* 3.2 8.0 + - - +
370A ARG* 1.3 80.2 - - - +
372A ASN* 1.3 63.4 + - - +
374A ASP* 3.3 14.4 + - + +
375A ARG* 3.2 50.2 + - + +
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Residues in contact with ASN 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.8 30.5 - - - +
26A LEU* 3.7 23.0 - - + +
363A LEU* 5.3 3.8 - - + -
367A ASN* 3.1 36.2 + - - +
369A THR* 3.1 22.2 + - - +
371A GLU* 1.3 76.2 - - - +
373A VAL* 1.3 60.4 + - - +
375A ARG* 3.3 12.7 + - - +
376A VAL* 3.0 29.5 + - - +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 4.0 12.3 - - + +
297A TYR* 3.6 17.9 - - + -
298A LEU* 3.4 44.0 - - + -
301A ARG* 4.2 4.3 - - - -
363A LEU* 4.2 16.4 - - + -
369A THR 3.2 15.7 + - - +
370A ARG* 2.8 15.8 + - - +
372A ASN* 1.3 77.0 - - - +
374A ASP* 1.3 57.4 + - - +
376A VAL* 3.6 6.4 + - - +
377A THR* 2.5 42.7 + - - +
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Residues in contact with ASP 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TYR* 2.4 34.9 + - - -
301A ARG* 2.7 22.8 + - - +
370A ARG* 3.0 17.5 + - - +
371A GLU* 3.3 18.0 + - + +
372A ASN 3.2 0.2 - - - -
373A VAL* 1.3 76.9 - - - +
375A ARG* 1.3 59.3 + - + +
377A THR* 3.3 1.6 + - - -
378A GLU* 3.0 41.1 + - - +
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.8 21.8 - - + -
343A PHE* 5.2 1.6 - - - -
345A ILE* 3.9 16.6 - - + +
371A GLU* 3.2 41.1 + - + +
372A ASN* 3.6 14.4 + - - +
374A ASP* 1.3 79.0 - - + +
376A VAL* 1.3 56.7 + - - +
378A GLU* 3.9 4.8 - - - +
379A ALA* 3.0 30.0 + - - +
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Residues in contact with VAL 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.9 17.9 - - + -
298A LEU* 4.1 23.1 - - + -
339A VAL* 5.3 0.7 - - + -
345A ILE* 4.2 9.4 - - + +
347A ILE* 3.8 30.3 - - + -
361A ILE* 4.2 16.6 - - + -
363A LEU* 6.4 0.9 - - + -
372A ASN 3.0 14.9 + - - +
373A VAL* 3.8 10.3 - - - +
375A ARG* 1.3 73.9 - - - +
377A THR* 1.3 65.9 + - - +
379A ALA* 3.8 4.9 - - + +
380A LEU* 2.9 45.2 + - + +
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Residues in contact with THR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.8 2.6 - - - +
301A ARG* 3.4 58.1 - - + +
302A LEU* 5.1 2.8 - - + +
305A LEU* 3.5 26.1 - - + +
373A VAL* 2.5 25.9 + - - +
374A ASP 3.6 4.7 - - - -
376A VAL* 1.3 82.7 - - - +
378A GLU* 1.3 57.5 + - - +
380A LEU* 4.7 2.7 - - - -
381A ARG* 2.9 30.9 + - - +
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 5.1 8.2 + - - +
343A PHE* 4.2 7.6 - - + -
374A ASP* 3.0 25.6 + - - +
375A ARG* 4.0 4.2 - - - +
377A THR* 1.3 77.9 - - - +
379A ALA* 1.3 65.6 + - - +
381A ARG* 3.2 36.1 + - - +
382A ALA* 3.0 24.9 + - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 4.6 0.2 - - - -
339A VAL* 3.9 23.5 - - + +
343A PHE* 3.6 44.8 - - + -
345A ILE* 4.1 5.2 - - + -
375A ARG 3.0 18.6 + - - +
376A VAL* 3.8 4.3 - - - +
378A GLU* 1.3 77.4 - - - +
380A LEU* 1.3 61.1 + - - +
382A ALA* 3.5 2.9 + - - +
383A ALA* 3.0 21.1 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.8 27.8 - - + -
305A LEU* 4.3 7.0 - - + -
307A LEU* 4.7 7.9 - - + -
335A ILE* 3.9 20.0 - - + -
339A VAL* 4.3 4.5 - - + -
347A ILE* 3.8 26.5 - - + -
359A LEU* 4.2 9.9 - - + -
361A ILE* 4.2 17.0 - - + -
376A VAL* 2.9 33.3 + - + +
377A THR* 3.8 4.0 - - - +
379A ALA* 1.3 73.8 - - - +
381A ARG* 1.3 56.0 + - - +
383A ALA* 3.1 5.6 + - - +
384A LEU* 2.7 45.1 + - + +
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Residues in contact with ARG 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ARG* 3.8 24.4 - - - +
305A LEU* 3.7 29.9 - - + +
377A THR* 2.9 22.2 + - - +
378A GLU* 3.5 40.9 + - - +
380A LEU* 1.3 76.1 - - - +
382A ALA* 1.3 59.2 + - - +
384A LEU* 3.1 9.6 + - + +
385A GLN* 2.9 50.0 + - - +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 3.9 8.1 - - + +
343A PHE* 3.7 26.7 - - + -
378A GLU 3.0 16.0 + - - +
379A ALA 3.7 0.4 - - - +
381A ARG* 1.3 75.9 - - - +
383A ALA* 1.3 63.9 + - - +
385A GLN* 3.1 14.2 + - - +
386A HIS* 3.0 37.9 + - + +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TYR* 5.1 0.2 - - - -
335A ILE* 4.1 26.7 - - + +
338A TYR* 3.5 30.6 - - + -
339A VAL* 4.3 2.0 - - + -
379A ALA 3.0 15.8 + - - +
380A LEU* 3.2 12.8 - - - +
382A ALA* 1.3 77.2 - - - +
384A LEU* 1.3 63.5 + - - +
387A CYS* 2.9 32.0 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 4.6 17.5 - - + +
307A LEU* 4.3 28.7 - - + -
327A PRO* 4.4 8.1 - - + -
330A TYR* 2.6 63.9 + - + +
335A ILE* 4.2 16.2 - - + -
380A LEU* 2.7 33.3 + - + +
381A ARG* 3.3 11.2 - - + +
383A ALA* 1.3 72.9 - - + +
385A GLN* 1.3 64.1 + - + +
387A CYS 4.1 2.4 - - - +
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A ARG* 2.9 43.9 + - + +
382A ALA* 3.1 13.0 + - - +
384A LEU* 1.3 79.7 - - + +
386A HIS* 1.3 85.9 + - + +
387A CYS 4.7 1.6 - - - +
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TYR* 2.7 38.3 + - + +
382A ALA* 3.0 21.4 + - + +
385A GLN* 1.3 104.7 + - + +
387A CYS* 1.3 64.9 + - - +
388A PRO* 3.5 5.0 - - - +
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Residues in contact with CYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 3.6 27.9 - - + -
331A ASP 6.2 0.4 - - - +
334A ASP* 4.0 28.0 - - + -
335A ILE* 4.0 5.8 - - + -
338A TYR* 3.9 34.3 - - - -
383A ALA 2.9 21.4 + - - +
384A LEU 4.1 2.8 - - - +
385A GLN 4.7 1.4 - - - +
386A HIS* 1.3 77.1 - - - +
388A PRO* 1.3 75.2 - - + +
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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