Contacts of the helix formed by residues 418 - 435 (chain A) in PDB entry 2OF2
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 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A ILE* 3.7 13.9 - - - +
392A ASN* 3.7 25.8 - - - +
393A GLU* 3.4 29.2 - - + +
410A GLU* 4.7 4.8 + - + +
416A THR* 5.2 1.8 - - - +
417A PHE* 1.3 80.8 - - - +
419A ILE* 1.3 61.0 + - - +
420A LYS* 2.9 28.2 + - - +
421A SER* 2.8 28.5 + - - +
422A ASP* 3.5 4.7 + - - -
481A PRO* 4.8 4.4 - - + +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A MET* 4.3 6.1 - - + -
356A GLU* 3.8 41.7 - - + +
360A TYR 3.7 21.5 - - - +
361A ILE* 3.6 10.6 - - + +
392A ASN 5.1 0.8 + - - -
418A THR* 1.3 76.6 - - - +
420A LYS* 1.3 76.2 + - + +
422A ASP* 3.1 20.8 + - - +
423A VAL* 3.0 24.8 + - + +
487A PHE* 3.9 25.4 - - + -
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Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 5.2 1.4 + - - -
418A THR* 2.9 14.9 + - - +
419A ILE* 1.3 87.4 - - + +
421A SER* 1.3 60.9 + - - +
422A ASP 3.3 0.2 - - - -
423A VAL* 3.4 8.4 + - + +
424A TRP 3.3 13.2 + - - -
481A PRO* 3.2 41.5 - - + +
482A GLU* 4.5 10.9 + - - +
484A ARG* 2.8 48.6 + - + +
485A PRO 3.3 19.6 + - - +
486A THR* 3.8 16.4 - - - +
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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
----------------------------------------------------------
407A THR* 6.2 0.2 - - - -
408A ALA* 3.9 14.2 + - - +
410A GLU* 3.1 21.6 + - - +
411A ALA* 4.5 1.5 - - - +
416A THR 3.7 4.5 + - - -
417A PHE* 3.4 26.6 - - - -
418A THR* 2.8 28.7 + - - -
420A LYS* 1.3 75.2 - - - +
422A ASP* 1.3 67.4 + - - +
424A TRP* 3.3 5.9 + - - +
425A SER* 3.2 23.6 + - - -
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Residues in contact with ASP 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A MET* 3.7 17.1 - - + +
361A ILE* 3.5 10.6 - - - +
362A HIS* 2.8 27.1 + - - +
363A ARG* 2.9 28.4 + - - +
364A ASP 4.7 0.2 + - - -
365A LEU* 3.5 11.3 - - + +
417A PHE* 5.7 0.2 - - - -
418A THR 3.5 5.1 + - - +
419A ILE* 3.1 13.8 + - - +
421A SER* 1.3 78.4 - - - +
423A VAL* 1.3 59.5 + - - +
425A SER* 3.0 9.9 + - - -
426A PHE 2.8 24.9 + - - -
487A PHE* 3.6 14.6 - - + -
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 5.1 0.7 - - - +
419A ILE* 3.0 15.7 + - + +
420A LYS* 3.5 16.4 - - + +
421A SER 3.2 0.2 - - - -
422A ASP* 1.3 78.0 - - - +
424A TRP* 1.3 62.6 + - - +
426A PHE* 3.0 12.6 + - - +
427A GLY 3.1 9.4 + - - -
476A CYS* 3.4 32.4 - - - +
484A ARG* 4.0 10.8 - - + -
485A PRO* 3.4 28.9 - - + +
486A THR* 5.1 0.7 - - - -
487A PHE* 3.5 30.1 - - + +
490A LEU* 4.1 7.2 - - + -
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Residues in contact with TRP 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LYS 4.9 1.6 + - - -
406A TRP 3.9 9.1 - - - -
407A THR 3.9 7.9 + - - -
408A ALA* 3.7 23.6 - - + -
409A PRO* 3.6 33.7 - - + -
420A LYS 3.3 7.6 + - - +
421A SER 3.5 9.2 - - - +
422A ASP 3.2 0.2 - - - -
423A VAL* 1.3 79.1 - - - +
425A SER* 1.3 64.6 + - - +
427A GLY 3.0 10.4 + - - -
428A ILE* 3.3 21.3 + - + +
441A TYR* 4.4 5.2 + - - -
453A LEU* 4.1 23.1 - - + -
458A ARG* 3.6 25.8 - - - -
476A CYS 3.4 12.8 + - - +
477A TRP* 3.2 54.6 + + + -
478A LYS 3.8 5.8 - - - -
479A GLU* 5.3 0.7 - - - -
484A ARG* 3.4 20.4 - - - +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ARG* 5.7 2.6 + - - -
365A LEU* 3.5 34.5 + - - +
406A TRP* 2.8 27.8 + - - +
407A THR* 4.5 3.1 - - - -
421A SER 3.2 12.1 + - - -
422A ASP* 3.0 12.9 + - - -
424A TRP* 1.3 75.5 - - - +
426A PHE* 1.3 60.2 + - - +
428A ILE* 3.1 6.8 + - - +
429A LEU* 2.9 27.2 + - - +
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Residues in contact with PHE 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA* 3.4 25.8 - - - -
348A ILE* 3.7 26.9 - - + -
349A ALA* 3.7 12.1 - - + -
365A LEU* 4.0 10.3 - - + +
422A ASP 2.8 12.8 + - - +
423A VAL 3.0 10.0 + - - +
425A SER* 1.3 75.8 - - - +
427A GLY* 1.3 58.6 + - - +
429A LEU* 3.0 13.9 + - + +
430A LEU* 2.9 56.3 + - + +
476A CYS* 4.3 3.1 - - - -
487A PHE* 3.7 19.5 - + + -
490A LEU* 3.7 29.4 - - + -
494A LEU* 3.6 23.3 - - + -
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Residues in contact with GLY 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL 3.1 6.9 + - - -
424A TRP 3.0 9.1 + - - -
426A PHE* 1.3 76.3 - - - +
428A ILE* 1.3 60.8 + - - +
430A LEU* 3.3 22.7 + - - +
431A THR* 3.5 4.7 + - - +
473A MET* 4.0 4.0 - - - +
476A CYS* 3.8 18.3 - - - +
477A TRP* 3.5 26.2 - - - -
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Residues in contact with ILE 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LYS 3.5 22.7 - - - +
406A TRP* 3.4 34.8 - - + +
424A TRP* 3.6 20.6 - - + +
425A SER 3.1 6.5 + - - +
427A GLY* 1.3 73.0 - - - +
429A LEU* 1.3 64.4 + - - +
431A THR* 2.5 27.2 + - - -
432A GLU* 3.2 4.5 + - - +
440A PRO* 3.7 24.0 - - + -
441A TYR* 3.7 19.3 - - - +
459A MET* 3.8 13.9 - - + -
477A TRP* 3.5 19.3 - - + +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.7 4.0 - - + -
348A ILE* 3.9 18.2 - - + -
365A LEU* 3.6 32.3 - - + -
366A ARG* 3.8 17.5 - - - -
367A ALA* 3.7 13.9 - - + +
370A ILE* 3.9 11.0 - - + -
406A TRP* 4.6 0.4 - - - -
425A SER 2.9 13.3 + - - +
426A PHE* 3.0 17.9 + - + +
428A ILE* 1.3 76.5 - - - +
430A LEU* 1.3 57.9 + - - +
432A GLU* 2.8 30.3 + - - +
433A ILE* 3.0 38.2 + - + -
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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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345A ALA* 3.6 31.0 - - + -
426A PHE* 2.9 47.7 + - + +
427A GLY* 3.4 11.4 - - - +
428A ILE 3.2 0.2 - - - -
429A LEU* 1.3 78.7 - - - +
431A THR* 1.3 61.1 + - - +
433A ILE* 3.2 12.1 + - + +
434A VAL* 3.1 19.8 + - - +
469A LEU* 4.1 25.0 - - + +
472A LEU* 4.6 11.7 - - + -
473A MET* 3.7 38.8 - - + +
476A CYS* 5.0 1.6 - - - -
494A LEU* 4.5 1.1 - - + -
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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 GLY 3.6 14.1 - - - +
428A ILE 2.5 18.2 + - - +
430A LEU* 1.3 77.6 - - - +
432A GLU* 1.3 60.1 + - - +
434A VAL* 3.5 3.7 - - - +
435A THR* 2.8 33.4 + - - +
438A ARG 5.3 1.2 + - - -
440A PRO* 4.1 9.8 - - - +
459A MET* 3.7 35.9 - - + +
462A PRO* 4.2 10.3 - - + -
473A MET* 3.7 24.7 - - + -
477A TRP* 3.9 9.4 - - + -
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Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL* 4.1 11.3 - - - +
328A LEU* 3.7 3.9 - - - +
366A ARG* 4.8 1.2 + - - +
367A ALA* 3.0 43.7 + - + +
368A ALA* 4.6 1.7 + - - +
406A TRP* 2.8 44.7 + - + +
428A ILE 3.8 7.4 - - - +
429A LEU* 2.8 18.0 + - - +
431A THR* 1.3 85.0 + - - +
433A ILE* 1.3 59.7 + - - +
435A THR* 3.6 4.7 + - - -
436A HIS 3.3 2.1 + - - -
437A GLY* 2.7 32.3 + - - +
438A ARG 4.0 17.3 - - - +
440A PRO* 4.7 2.2 - - + -
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Residues in contact with ILE 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.1 15.3 - - + -
328A LEU* 3.8 11.1 - - + +
341A LEU* 3.6 49.8 - - + +
344A MET* 4.8 3.4 - - + -
345A ALA* 3.9 34.1 - - + +
348A ILE* 4.1 8.3 - - + -
429A LEU* 3.0 38.7 + - + +
430A LEU* 3.2 12.1 + - + +
432A GLU* 1.3 77.9 - - + +
434A VAL* 1.3 59.3 + - + +
436A HIS* 3.0 19.6 + - - -
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ILE* 4.3 13.2 - - + -
341A LEU* 4.2 8.7 - - + +
430A LEU 3.1 11.9 + - - +
431A THR* 3.5 14.4 - - - +
433A ILE* 1.3 79.2 - - - +
435A THR* 1.3 69.2 + - + +
436A HIS* 3.3 10.4 + - - -
462A PRO* 4.0 14.8 - - + -
463A ASP 4.6 6.0 - - - +
464A ASN* 4.1 6.6 - - - +
465A CYS* 3.9 34.3 - - + +
466A PRO* 4.0 13.2 - - + -
469A LEU* 4.3 10.5 - - + -
473A MET* 4.3 0.4 - - + -
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Residues in contact with THR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A THR* 2.8 23.0 + - - +
432A GLU 3.6 1.6 + - - -
433A ILE 3.2 0.2 - - - -
434A VAL* 1.3 79.0 - - + +
436A HIS* 1.3 70.8 + - - +
437A GLY 3.4 0.2 + - - -
438A ARG* 3.1 52.9 + - + +
462A PRO* 3.6 31.2 - - + -
463A ASP* 5.0 6.1 - - + +
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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