Contacts of the helix formed by residues 418 - 432 (chain A) in PDB entry 2C0L
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 LEU 418 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ILE* 5.3 1.1 - - + -
413A PHE* 2.9 37.2 + - + +
414A THR* 4.5 0.6 + - - +
416A GLU* 3.6 32.3 - - + +
417A SER* 1.3 79.5 - - - +
419A GLN* 1.3 63.4 + - - +
420A ARG 3.5 1.8 - - - -
421A GLN* 3.6 33.6 + - - +
422A ALA* 3.1 23.6 + - - +
500A LEU* 5.1 0.7 - - - -
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Residues in contact with GLN 419 (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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417A SER 3.5 5.7 + - - +
418A LEU* 1.3 71.3 - - - +
420A ARG* 1.3 66.8 + - - +
421A GLN* 4.4 0.2 + - - -
422A ALA* 3.2 2.3 + - - +
423A CYS* 3.0 34.8 + - - -
464A SER* 3.4 24.5 + - - +
465A ASP* 4.7 6.2 + - - +
468A PHE* 3.6 28.4 - - - +
500A LEU* 4.1 41.3 + - + +
501A SER* 6.0 0.2 - - - -
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Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU 3.5 0.6 - - - -
419A GLN* 1.3 79.4 - - - +
421A GLN* 1.3 79.0 + - - +
423A CYS* 3.2 1.6 + - - -
424A GLU* 3.1 44.7 + - - +
461A SER 3.4 16.6 + - - -
462A LEU* 3.1 38.2 + - - +
464A SER* 4.0 26.0 + - - +
467A LEU* 3.6 15.0 - - + +
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Residues in contact with GLN 421 (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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413A PHE* 3.8 26.4 - - + -
418A LEU* 3.8 39.5 - - - +
419A GLN 3.3 0.2 - - - -
420A ARG* 1.3 99.4 + - - +
422A ALA* 1.3 58.2 + - - +
424A GLU* 3.4 15.0 + - - +
425A ILE* 3.1 33.4 + - - +
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Residues in contact with ALA 422 (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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410A ALA* 3.7 15.3 - - + +
413A PHE* 3.9 11.6 - - + -
414A THR* 3.7 24.0 - - - +
418A LEU 3.1 18.8 + - - +
419A GLN* 3.2 5.4 + - - +
421A GLN* 1.3 76.0 - - - +
423A CYS* 1.3 58.8 + - - +
425A ILE* 3.4 3.3 + - - +
426A LEU* 3.0 35.3 + - + +
500A LEU* 4.0 10.3 - - + -
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Residues in contact with CYS 423 (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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419A GLN* 3.0 23.8 + - - -
420A ARG* 3.6 7.9 - - - +
422A ALA* 1.3 73.6 - - - +
424A GLU* 1.3 61.2 + - - +
426A LEU* 3.3 7.6 + - - +
427A ARG* 2.9 23.6 + - - +
464A SER 5.2 0.4 - - - -
467A LEU* 3.8 18.2 - - + -
468A PHE* 3.7 43.5 - - - -
471A VAL* 3.3 19.5 - - + +
497A LEU* 3.9 10.8 - - - -
500A LEU* 4.2 3.1 - - - -
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Residues in contact with GLU 424 (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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420A ARG* 3.1 45.8 + - - +
421A GLN* 3.6 16.0 - - - +
423A CYS* 1.3 77.5 - - - +
425A ILE* 1.3 61.3 + - + +
427A ARG* 3.3 9.5 + - - +
428A ASP* 3.0 35.6 + - - +
461A SER* 4.6 5.3 - - - +
467A LEU* 3.7 16.4 - - + +
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Residues in contact with ILE 425 (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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396A LEU* 5.1 2.5 - - + -
406A LEU* 2.9 50.1 - - + +
409A LEU* 4.1 17.9 - - + -
410A ALA* 3.8 11.7 - - + +
413A PHE* 3.9 20.4 - - + -
421A GLN 3.1 18.4 + - - +
422A ALA 3.8 4.5 - - - +
423A CYS 3.3 0.2 - - - -
424A GLU* 1.3 78.2 - - + +
426A LEU* 1.3 58.2 + - - +
428A ASP* 3.4 12.6 + - - +
429A TRP* 2.9 26.3 + - - +
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Residues in contact with LEU 426 (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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407A MET* 4.0 13.9 - - + -
410A ALA* 3.7 17.5 - - + -
422A ALA 3.0 24.0 + - - +
423A CYS 3.7 4.9 - - - +
424A GLU 3.2 0.2 - - - -
425A ILE* 1.3 75.2 - - - +
427A ARG* 1.3 63.7 + - - +
429A TRP* 3.4 5.6 + - + +
430A LEU 3.2 16.6 + - - -
471A VAL* 4.0 5.4 - - + -
475A PHE* 3.2 33.4 - - + -
493A GLY* 3.9 27.4 - - - +
496A VAL* 4.1 17.7 - - + -
497A LEU* 3.7 32.3 - - + -
500A LEU* 4.9 1.6 - - + -
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Residues in contact with ARG 427 (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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423A CYS 2.9 16.5 + - - +
424A GLU* 3.3 9.4 + - - +
426A LEU* 1.3 76.4 - - - +
428A ASP* 1.3 60.5 + - - +
430A LEU* 3.3 7.0 + - - +
431A ARG* 3.0 38.1 + - - +
440A VAL* 3.2 35.0 + - + +
457A ARG* 3.0 31.6 - - - +
461A SER* 6.4 0.9 - - - -
467A LEU* 4.9 9.6 - - - -
470A GLU* 2.8 32.1 + - - -
471A VAL* 3.9 16.7 - - + +
474A LEU* 3.7 21.3 - - + +
475A PHE* 5.1 0.2 - - - -
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Residues in contact with ASP 428 (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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406A LEU* 4.1 14.6 - - + +
424A GLU* 3.0 23.6 + - - +
425A ILE* 3.7 13.9 - - - +
426A LEU 3.3 0.2 - - - -
427A ARG* 1.3 78.8 - - - +
429A TRP* 1.3 63.1 + - - +
431A ARG* 2.9 37.4 + - - +
432A TYR* 3.0 41.0 + - + -
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Residues in contact with TRP 429 (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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403A GLN* 3.2 44.3 + - + +
406A LEU* 3.7 13.0 - - + +
407A MET* 3.8 28.9 - - + +
425A ILE 2.9 18.4 + - - +
426A LEU* 3.5 11.9 - - + +
427A ARG 3.3 0.2 - - - -
428A ASP* 1.3 74.8 - - - +
430A LEU* 1.3 100.0 + - + +
432A TYR* 3.3 2.4 + - - +
433A THR* 2.8 54.5 + - + -
436A TYR* 4.6 2.2 - + - -
475A PHE* 3.5 22.4 - + - -
487A ASP* 4.9 1.3 - - - -
489A ASP* 3.5 27.5 - - + +
490A VAL* 3.7 30.7 - - + -
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Residues in contact with LEU 430 (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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426A LEU 3.2 12.2 + - - +
427A ARG* 3.6 6.3 - - - +
429A TRP* 1.3 106.3 - - + +
431A ARG* 1.3 60.8 + - - +
432A TYR 3.2 1.3 + - - -
433A THR* 3.4 11.1 + - - +
436A TYR* 3.5 44.9 - - + +
439A LEU* 4.5 4.7 - - + -
440A VAL* 4.2 11.9 - - + -
474A LEU* 3.5 45.5 - - + +
475A PHE* 3.7 17.9 - - + -
478A ALA* 4.0 16.2 - - + -
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Residues in contact with ARG 431 (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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427A ARG* 3.0 22.3 + - - +
428A ASP* 2.9 40.5 + - - +
430A LEU* 1.3 76.0 - - - +
432A TYR* 1.3 88.9 + - + +
433A THR 3.5 0.4 - - - -
437A ALA* 3.3 28.7 - - - +
440A VAL* 3.5 36.1 - - + +
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Residues in contact with TYR 432 (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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400A PRO* 3.5 31.2 - - + +
401A ASP* 3.5 41.4 - - + +
403A GLN* 3.0 19.3 + - + -
406A LEU* 3.9 9.2 - - + -
428A ASP* 3.0 34.1 + - + +
429A TRP 3.7 3.8 - - - +
430A LEU 3.2 0.2 - - - -
431A ARG* 1.3 109.9 + - + +
433A THR* 1.3 59.4 + - - +
434A PRO* 3.2 6.7 - - - +
437A ALA* 5.2 0.7 - - - -
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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