Contacts of the helix formed by residues 417 - 434 (chain A) in PDB entry 3OY3
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 SER 417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A ILE* 3.7 25.6 - - - +
409A GLU* 4.7 3.3 + - - -
415A LYS 5.5 0.2 + - - -
416A PHE* 1.3 77.1 - - - +
418A ILE* 1.3 66.4 + - - +
419A LYS* 3.1 21.7 + - - +
420A SER* 2.7 26.8 + - - -
421A ASP* 3.2 5.5 + - - -
480A PRO* 5.1 1.9 - - - +
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Residues in contact with ILE 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A MET* 4.4 4.9 - - + +
354A LEU* 4.7 0.7 - - + -
355A GLU* 3.7 45.5 - - + +
359A PHE 3.9 16.4 - - - +
360A ILE* 4.0 6.7 - - + +
417A SER* 1.3 76.5 - - - +
419A LYS* 1.3 74.0 + - + +
421A ASP* 3.2 15.5 + - - +
422A VAL* 2.8 26.5 + - + +
486A PHE* 3.6 33.7 - - + -
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Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU* 5.1 1.2 + - - -
417A SER* 3.1 10.0 + - - +
418A ILE* 1.3 87.4 - - + +
420A SER* 1.3 63.9 + - - +
422A VAL* 3.1 9.2 + - + +
423A TRP 3.1 14.7 + - - -
480A PRO* 3.3 42.6 - - + +
481A SER* 4.6 8.3 - - - +
483A ARG* 2.9 45.0 + - + +
484A PRO 3.1 22.9 + - - +
485A SER* 3.5 13.7 - - - +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ILE* 5.0 0.2 - - - +
405A TRP 4.9 1.0 - - - +
407A ALA* 3.7 13.5 + - - +
409A GLU* 3.9 5.6 + - - -
410A SER* 3.4 23.8 - - - -
415A LYS 4.5 0.2 - - - -
416A PHE* 3.3 15.1 - - - +
417A SER* 2.7 39.6 + - - -
419A LYS* 1.3 74.2 - - - +
421A ASP* 1.3 67.0 + - - +
423A TRP* 3.2 4.7 + - - +
424A ALA* 3.1 19.8 + - - +
483A ARG* 3.8 8.6 - - - +
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Residues in contact with ASP 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A MET* 3.9 10.2 - - + +
360A ILE* 3.6 10.9 - - - +
361A HIS* 2.7 33.0 + - - +
362A ARG* 2.8 29.6 + - - -
363A ASP 4.5 0.7 + - - -
364A LEU* 4.1 6.2 + - + +
417A SER 3.2 9.3 + - - +
418A ILE* 3.2 16.2 + - - +
420A SER* 1.3 75.4 + - - +
422A VAL* 1.3 68.1 + - - +
424A ALA* 3.1 8.5 + - - +
425A PHE* 2.8 23.4 + - - +
486A PHE* 3.7 13.9 - - + -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 2.8 21.8 + - + +
419A LYS* 3.1 17.6 + - + +
421A ASP* 1.3 76.4 - - - +
423A TRP* 1.3 63.8 + - - +
425A PHE* 3.0 12.2 + - - +
426A GLY 3.1 9.5 + - - -
475A CYS* 3.5 33.1 - - - +
483A ARG* 4.0 9.4 - - + -
484A PRO* 3.6 27.4 - - + +
485A SER* 4.8 0.9 - - - -
486A PHE* 3.5 31.9 - - + +
489A ILE* 3.9 7.0 - - + -
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Residues in contact with TRP 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS 5.0 1.2 + - - -
405A TRP 3.6 19.1 + - - -
406A THR 3.8 8.7 + - - -
407A ALA* 3.7 19.7 - - + -
408A PRO* 3.6 29.2 - - + -
419A LYS 3.1 10.4 + - - +
420A SER 3.5 8.5 - - - +
421A ASP 3.1 0.4 - - - -
422A VAL* 1.3 75.5 - - - +
424A ALA* 1.3 63.4 + - - +
426A GLY 3.0 10.0 + - - -
427A VAL* 3.2 22.0 + - + +
440A TYR* 4.2 7.7 + - - -
452A LEU* 3.8 30.5 - - + +
457A ARG* 3.7 18.2 - - - -
475A CYS 3.4 15.2 + - - +
476A TRP* 3.1 57.9 + + + -
477A GLN 3.6 7.2 - - - -
483A ARG* 3.6 17.0 - - - +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.5 33.4 - - + +
405A TRP* 3.7 26.3 - - + +
420A SER 3.1 9.4 + - - +
421A ASP* 3.1 11.1 + - - +
423A TRP* 1.3 78.4 - - - +
425A PHE* 1.3 60.4 + - - +
427A VAL* 2.9 8.2 + - - +
428A LEU* 2.8 27.9 + - - +
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Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 4.1 4.7 - - - -
347A ILE* 3.5 35.9 - - + -
348A SER* 3.9 17.7 - - - -
351A MET* 4.8 0.2 - - + -
364A LEU* 3.9 12.7 - - + +
421A ASP 2.8 13.5 + - - +
422A VAL 3.0 8.7 + - - +
424A ALA* 1.3 76.7 - - - +
426A GLY* 1.3 59.2 + - - +
428A LEU* 3.3 7.8 + - + +
429A LEU* 2.8 65.3 + - + +
432A ILE* 6.2 0.4 - - + -
475A CYS* 4.0 12.8 - - - -
486A PHE* 3.7 23.6 - + + -
489A ILE* 3.5 30.3 - - + -
493A PHE* 4.0 5.2 - + - -
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Residues in contact with GLY 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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422A VAL 3.1 6.9 + - - -
423A TRP 3.0 9.5 + - - -
425A PHE* 1.3 77.6 - - - +
427A VAL* 1.3 63.1 + - - +
429A LEU* 3.1 12.2 + - - +
430A TRP 3.1 15.4 + - - -
472A MET* 3.9 5.2 - - - +
475A CYS* 3.8 18.6 - - - -
476A TRP* 3.5 22.3 - - - -
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Residues in contact with VAL 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LYS 3.6 24.7 - - - +
405A TRP* 3.5 31.2 - - + +
423A TRP* 3.2 25.1 + - + +
424A ALA* 2.9 7.4 + - - +
426A GLY* 1.3 77.1 - - - +
428A LEU* 1.3 56.6 + - - +
430A TRP* 2.9 19.9 + - - +
431A GLU* 3.0 12.5 + - - +
439A PRO* 3.8 22.7 - - + -
440A TYR* 5.1 2.0 - - - +
458A MET* 4.1 8.3 - - + -
476A TRP* 3.7 20.0 - - + +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.4 3.6 - - + -
347A ILE* 3.9 19.5 - - + -
364A LEU* 3.6 35.7 - - + -
365A ALA* 4.2 8.3 - - - +
366A ALA* 3.4 35.0 - - + +
369A CYS* 4.0 10.5 - - - -
405A TRP* 4.5 0.4 - - - +
424A ALA 2.8 13.2 + - - +
425A PHE* 3.5 11.7 - - + +
427A VAL* 1.3 72.1 - - - +
429A LEU* 1.3 59.3 + - - +
431A GLU* 3.2 13.3 + - - +
432A ILE* 2.9 44.3 + - + +
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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
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344A ALA* 3.6 22.2 - - + -
425A PHE* 2.8 46.9 + - + +
426A GLY* 3.1 10.7 + - - +
428A LEU* 1.3 73.1 - - - +
430A TRP* 1.3 57.8 + - - +
432A ILE* 3.3 10.5 + - + +
433A ALA* 2.9 29.1 + - - +
468A VAL* 4.5 14.4 - - + +
471A LEU* 4.8 3.4 - - + -
472A MET* 3.9 33.8 - - + +
475A CYS* 5.1 0.7 - - - -
493A PHE* 3.5 33.2 - - + -
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Residues in contact with TRP 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 GLY 3.1 10.0 + - - +
427A VAL 2.9 13.7 + - - +
429A LEU* 1.3 74.3 - - - +
431A GLU* 1.3 65.3 + - - +
433A ALA* 3.3 2.7 + - - +
434A THR* 2.9 42.7 + - + +
437A MET* 3.4 49.8 - - + -
438A SER 3.5 19.3 - - - -
439A PRO* 3.5 13.2 - - + -
441A PRO* 3.9 15.9 - - + -
458A MET* 3.4 42.3 - - + +
459A GLU* 3.5 17.0 + - - +
461A PRO* 3.5 23.7 - - + +
472A MET* 4.0 19.9 - - - +
476A TRP* 4.3 0.7 - + + -
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Residues in contact with GLU 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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324A LEU* 3.7 16.8 - - - +
327A LEU* 4.3 1.3 - - - -
366A ALA* 2.9 43.2 + - + +
367A ARG* 4.8 1.0 + - - -
405A TRP* 2.9 44.9 + - + +
427A VAL 3.0 15.0 + - - +
428A LEU* 3.3 13.5 - - - +
430A TRP* 1.3 79.6 - - + +
432A ILE* 1.3 61.1 + - - +
434A THR* 3.2 6.1 + - - -
435A TYR 3.2 2.8 + - - -
436A GLY* 2.8 31.8 + - - +
437A MET 4.3 14.3 - - - +
439A PRO* 4.6 5.3 - - + +
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU* 4.4 6.5 - - + -
327A LEU* 3.8 15.9 - - + +
340A LEU* 3.6 53.8 - - + +
343A MET* 4.1 8.7 - - + -
344A ALA* 4.2 22.2 - - + +
347A ILE* 3.8 28.9 - - + -
425A PHE* 6.2 0.4 - - + -
428A LEU* 2.9 32.5 + - + +
429A LEU* 3.7 11.7 - - + +
431A GLU* 1.3 76.0 - - - +
433A ALA* 1.3 62.0 + - - +
435A TYR* 3.0 14.4 + - - -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.7 8.8 - - - +
429A LEU 2.9 17.0 + - - +
430A TRP* 3.8 5.8 - - - +
431A GLU 3.3 0.2 - - - -
432A ILE* 1.3 77.8 - - - +
434A THR* 1.3 59.1 + - - +
435A TYR* 3.3 10.3 + - - -
461A PRO* 3.9 23.5 - - + +
462A GLU 4.7 7.1 - - - +
463A GLY 6.1 0.2 - - - -
464A CYS* 4.2 25.0 + - + -
468A VAL* 6.0 1.3 - - + -
472A MET* 4.9 1.1 - - + -
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Residues in contact with THR 434 (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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332A ARG* 4.5 3.5 + - - -
430A TRP* 2.9 40.0 + - + +
431A GLU* 3.2 5.0 + - - -
433A ALA* 1.3 76.5 - - - +
435A TYR* 1.3 71.6 + - - +
436A GLY 3.3 0.2 + - - -
437A MET* 3.1 48.6 + - - +
461A PRO* 3.5 30.5 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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