Contacts of the helix formed by residues 414 - 431 (chain A) in PDB entry 2C0O
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 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ILE* 3.4 19.8 - - + +
406A GLU* 5.3 1.6 + - - -
412A SER* 3.7 12.4 + - - +
413A PHE* 1.3 80.8 - - - +
415A ILE* 1.3 65.1 + - - +
416A LYS* 3.0 25.2 + - - +
417A SER* 2.8 20.3 + - - -
418A ASP* 3.2 9.7 + - - +
477A PRO* 5.4 1.4 - - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A MET* 4.1 5.2 - - + -
351A ILE* 4.2 2.0 - - + -
352A GLU* 3.6 49.8 - - + +
356A TYR 3.5 23.3 - - - +
357A ILE* 3.5 6.4 - - + +
414A THR* 1.3 76.3 - - - +
416A LYS* 1.3 74.9 + - + +
417A SER 3.4 0.2 - - - -
418A ASP* 3.1 22.9 - - - +
419A VAL* 2.9 26.9 + - + +
483A PHE* 3.8 16.4 - - + -
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU* 5.1 1.8 + - - +
414A THR* 3.0 10.9 + - - +
415A ILE* 1.3 90.5 - - + +
417A SER* 1.3 64.5 + - - +
418A ASP 3.2 0.2 - - - -
419A VAL* 3.2 7.0 + - + +
420A TRP 3.2 13.9 + - - -
477A PRO* 3.4 41.3 - - + +
478A GLU* 4.5 11.8 + - - +
480A ARG* 2.7 48.9 + - + +
481A PRO 3.1 19.9 + - - +
482A THR* 3.8 15.8 - - - +
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Residues in contact with SER 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A THR* 6.0 0.2 - - - -
404A ALA* 3.6 22.7 + - - +
406A GLU* 3.8 9.1 + - - -
407A ALA* 4.4 8.7 - - - -
412A SER 4.3 5.6 - - - -
413A PHE* 3.3 14.0 - - - +
414A THR* 2.8 36.1 + - - -
416A LYS* 1.3 80.1 - - - +
418A ASP* 1.3 58.9 + - - +
420A TRP* 3.2 5.7 + - - +
421A SER* 2.8 26.4 + - - -
480A ARG* 3.6 8.0 - - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A MET* 3.8 7.5 - - + +
357A ILE* 3.3 11.8 - - - +
358A HIS* 2.5 32.1 + - - +
359A ARG* 2.9 27.4 + - - -
360A ASP 4.6 0.5 + - - -
361A LEU* 4.3 7.4 - - + +
414A THR 3.2 10.3 + - - -
415A ILE* 3.1 21.5 - - - +
416A LYS 3.2 0.2 - - - -
417A SER* 1.3 77.0 + - - +
419A VAL* 1.3 54.7 + - - +
421A SER* 3.1 10.1 + - - -
422A PHE* 2.8 27.5 + - - +
483A PHE* 3.7 15.6 - - + -
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Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU* 4.8 2.0 - - - +
415A ILE* 2.9 17.9 + - + +
416A LYS* 3.2 14.3 + - + +
418A ASP* 1.3 74.5 - - - +
420A TRP* 1.3 59.7 + - - +
422A PHE* 3.2 4.7 + - - +
423A GLY 3.0 22.0 + - - -
472A CYS* 3.4 25.2 - - + +
480A ARG* 3.9 22.7 - - + -
481A PRO* 3.4 23.6 - - + +
483A PHE* 3.7 32.5 - - + +
486A ILE* 4.3 5.6 - - + -
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Residues in contact with TRP 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS 4.8 1.8 + - - -
402A TRP 3.5 16.4 + - - -
403A THR 3.9 7.9 + - - -
404A ALA* 3.8 18.2 - - + -
405A PRO* 3.7 30.1 - - + -
416A LYS 3.2 5.7 + - - -
417A SER 3.3 10.1 - - - +
419A VAL* 1.3 74.8 - - - +
421A SER* 1.3 68.5 + - - +
423A GLY* 2.9 12.5 + - - -
424A ILE* 3.1 25.8 + - + +
437A TYR* 4.4 5.3 + - - -
449A LEU* 4.0 25.5 - - + +
454A ARG* 4.0 23.6 - - - -
472A CYS 3.8 8.7 + - - +
473A TRP* 3.4 47.5 + + + -
474A LYS 3.6 7.9 - - - -
475A ASN* 5.0 0.7 - - - -
480A ARG* 3.3 24.9 - - - +
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Residues in contact with SER 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG 5.7 1.4 + - - -
361A LEU* 3.7 33.2 + - - +
402A TRP* 3.0 27.8 + - - -
403A THR* 4.8 1.9 - - - -
417A SER 2.8 15.1 + - - -
418A ASP* 3.1 10.7 + - - -
420A TRP* 1.3 77.7 - - - +
422A PHE* 1.3 65.7 + - - +
424A ILE* 2.9 8.6 + - - +
425A LEU* 2.8 20.6 + - - +
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A SER* 3.8 19.7 - - - -
344A ILE* 3.6 22.7 - - + -
345A ALA* 3.5 33.4 - - + -
348A MET* 4.9 0.2 - - + -
361A LEU* 4.0 13.6 - - + +
418A ASP 2.8 13.5 + - - +
419A VAL 3.4 8.1 - - - +
421A SER* 1.3 77.1 - - - +
423A GLY* 1.3 63.5 + - - +
425A LEU* 2.9 17.9 + - + +
426A LEU* 3.0 39.3 + - + +
472A CYS* 4.4 1.1 - - - -
483A PHE* 3.7 22.0 - + + -
486A ILE* 3.5 31.0 - - + -
490A LEU* 3.9 7.9 - - + -
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Residues in contact with GLY 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL 3.0 7.7 + - - -
420A TRP 2.9 9.4 + - - -
422A PHE* 1.3 77.1 - - - +
424A ILE* 1.3 60.0 + - - +
426A LEU* 3.2 10.6 - - - +
427A MET* 3.2 15.4 + - - +
469A MET* 4.1 4.8 - - - +
472A CYS* 3.8 19.1 - - - -
473A TRP* 3.4 25.0 - - - -
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Residues in contact with ILE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LYS 3.8 17.0 - - - +
402A TRP* 3.5 25.4 - - + -
420A TRP* 3.6 25.6 - - + +
421A SER 2.9 7.4 + - - +
423A GLY* 1.3 74.3 - - - +
425A LEU* 1.3 61.2 + - - +
427A MET* 3.1 3.5 + - - +
428A GLU* 2.8 26.2 + - - +
436A PRO* 3.5 34.3 - - + -
437A TYR* 4.0 14.4 - - + +
455A MET* 4.1 9.0 - - + -
473A TRP* 3.3 29.8 - - + +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.8 2.5 - - + -
344A ILE* 4.4 11.2 - - + -
361A LEU* 4.2 21.5 - - + -
362A ARG* 3.8 27.8 - - - +
363A ALA* 3.4 36.8 - - + +
366A ILE* 4.2 12.8 - - + -
402A TRP* 4.5 0.8 - - - +
421A SER 2.8 10.6 + - - +
422A PHE* 3.3 13.5 - - + +
424A ILE* 1.3 74.7 - - - +
426A LEU* 1.3 55.0 + - - +
428A GLU* 3.0 8.2 + - + +
429A ILE* 2.7 52.0 + - + +
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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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338A ILE* 5.9 0.4 - - + -
341A SER* 2.7 35.2 - - - +
422A PHE* 3.0 39.5 + - + +
423A GLY* 3.2 13.9 - - - +
425A LEU* 1.3 74.1 - - - +
427A MET* 1.3 65.6 + - - +
429A ILE* 3.1 7.7 + - + +
430A VAL* 2.9 27.0 + - + +
465A LEU* 3.8 29.2 - - + -
468A ILE* 4.0 22.2 - - + -
469A MET* 4.1 22.9 - - + +
472A CYS* 5.1 0.2 - - - -
490A LEU* 4.7 1.8 - - + -
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Residues in contact with MET 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 GLY 3.2 8.1 + - - +
424A ILE 3.1 9.0 + - - +
426A LEU* 1.3 80.2 - - - +
428A GLU* 1.3 59.0 + - - +
430A VAL* 3.4 2.2 + - - +
431A THR* 2.8 34.4 + - + +
434A ARG* 4.2 12.8 - - - +
436A PRO* 5.9 1.3 - - + -
455A MET* 3.4 40.6 - - + +
456A PRO 3.8 19.1 - - - +
458A PRO* 3.4 31.9 - - + -
466A TYR* 4.3 4.0 - - + -
469A MET* 3.6 27.1 - - - +
473A TRP* 3.8 14.6 - - + -
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Residues in contact with GLU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.4 26.7 - - - +
324A LEU* 4.6 0.7 - - - -
363A ALA* 2.9 31.3 + - + +
364A ALA* 4.7 1.7 + - - +
402A TRP* 2.6 42.2 + - + +
424A ILE 2.8 14.9 + - - +
425A LEU* 3.2 15.0 - - + +
427A MET* 1.3 74.5 - - - +
429A ILE* 1.3 60.7 - - - +
431A THR* 3.2 5.7 + - - -
432A TYR 3.1 4.5 + - - -
433A GLY* 2.9 29.2 + - - +
434A ARG 4.1 17.4 - - - +
435A ILE* 6.0 0.2 - - - -
436A PRO* 4.3 9.2 - - + +
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Residues in contact with ILE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.0 20.4 - - + -
324A LEU* 3.6 15.0 - - + +
337A LEU* 3.5 50.6 - - + +
340A PHE* 4.5 4.3 - - + -
341A SER* 3.8 25.8 - - - +
344A ILE* 3.9 26.5 - - + -
422A PHE* 6.5 0.4 - - + -
425A LEU* 2.7 33.1 + - + +
426A LEU* 3.6 5.4 - - + +
428A GLU* 1.3 72.5 - - - +
430A VAL* 1.3 64.8 + - + +
432A TYR* 3.1 13.5 + - - -
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 4.6 19.1 - - + -
337A LEU* 4.2 10.1 - - + -
338A ILE* 6.1 1.3 - - + -
426A LEU* 2.9 14.1 + - + +
427A MET* 3.7 8.3 - - - +
429A ILE* 1.3 78.8 - - + +
431A THR* 1.3 58.6 + - - +
432A TYR* 3.5 5.8 - - - -
458A PRO* 3.6 29.8 - - + -
460A ASN* 2.9 29.4 + - - +
461A CYS* 4.1 16.4 - - + -
462A PRO* 5.1 0.2 - - + -
465A LEU* 3.6 29.2 - - + -
469A MET* 4.4 4.9 - - + -
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Residues in contact with THR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A MET* 2.8 24.4 + - - +
428A GLU* 3.2 7.4 + - - -
429A ILE 3.1 0.2 - - - -
430A VAL* 1.3 79.4 - - - +
432A TYR* 1.3 72.4 + - - +
433A GLY 3.0 1.3 + - - -
434A ARG* 3.2 53.3 + - - +
458A PRO* 3.8 32.1 - - + -
460A ASN* 5.6 0.2 - - - +
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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