Contacts of the helix formed by residues 417 - 434 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 3.3 24.1 - - - +
409B GLU* 4.7 3.1 + - - -
415B LYS 5.7 0.2 - - - -
416B PHE* 1.3 75.8 - - - +
418B ILE* 1.3 68.4 + - - +
419B LYS* 3.0 22.7 + - - +
420B SER* 2.8 26.3 + - - -
421B ASP 3.1 5.5 + - - -
480B PRO* 5.3 0.9 - - - +
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Residues in contact with ILE 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B MET* 4.4 4.3 - - + +
354B LEU* 4.9 1.1 - - + -
355B GLU* 3.9 39.9 - - + +
359B PHE 4.1 13.9 - - - +
360B ILE* 3.9 7.3 - - + +
417B SER* 1.3 76.2 - - - +
419B LYS* 1.3 69.8 + - + +
421B ASP* 3.1 21.7 + - - +
422B VAL* 3.1 26.5 + - + +
486B PHE* 3.3 35.9 - - + -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 5.4 1.2 + - - +
417B SER* 3.0 11.2 + - - +
418B ILE* 1.3 86.7 - - + +
420B SER* 1.3 58.9 + - - +
422B VAL* 3.4 6.2 + - + +
423B TRP 3.3 13.2 + - - -
480B PRO* 3.2 41.5 - - + +
481B SER* 4.7 6.7 - - - +
483B ARG* 2.6 57.0 + - + +
484B PRO 2.8 24.1 + - - +
485B SER* 3.5 10.5 - - - +
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Residues in contact with SER 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 5.1 0.5 - - - +
362B ARG* 6.1 0.2 - - - -
405B TRP 5.1 0.9 - - - +
407B ALA* 3.7 14.9 + - - +
409B GLU* 3.8 6.4 + - - -
410B SER* 3.4 22.4 + - - -
416B PHE* 3.4 14.7 - - - -
417B SER* 2.8 35.7 + - - -
419B LYS* 1.3 79.4 - - - +
421B ASP* 1.3 63.6 + - - +
422B VAL 3.2 0.2 - - - -
423B TRP* 3.5 3.9 + - - +
424B ALA* 3.1 21.1 + - - +
483B ARG* 3.7 6.4 - - - +
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Residues in contact with ASP 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B MET* 3.7 6.8 - - + +
360B ILE* 3.5 6.7 - - - +
361B HIS* 2.6 35.4 + - - +
362B ARG* 3.0 26.0 + - - -
363B ASP 4.7 0.5 + - - -
364B LEU* 3.7 7.2 + - + +
417B SER 3.1 13.4 + - - +
418B ILE* 3.1 24.7 + - + +
420B SER* 1.3 76.2 + - - +
422B VAL* 1.3 58.8 + - - +
424B ALA* 3.8 5.1 - - - +
425B PHE* 2.9 23.0 + - - +
486B PHE* 3.3 21.6 - - + -
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 5.2 0.7 - - - +
418B ILE* 3.1 16.7 + - + +
419B LYS* 3.6 14.8 - - + +
420B SER 3.2 0.8 - - - -
421B ASP* 1.3 73.8 - - - +
423B TRP* 1.3 66.9 + - - +
425B PHE* 3.3 3.6 + - - +
426B GLY 3.0 17.7 + - - -
475B CYS* 3.4 34.8 - - + +
483B ARG* 4.3 7.9 - - + -
484B PRO* 3.6 24.0 - - + +
485B SER* 4.9 0.7 - - - -
486B PHE* 3.6 29.4 - - + +
489B ILE* 3.6 14.1 - - + -
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Residues in contact with TRP 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS 5.1 1.0 + - - -
405B TRP 3.5 18.8 + - - -
406B THR 3.8 9.1 + - - -
407B ALA* 3.6 18.4 - - + -
408B PRO* 3.5 29.2 - - + -
419B LYS 3.3 8.6 + - - +
420B SER 3.5 8.5 - - - +
422B VAL* 1.3 78.6 - - - +
424B ALA* 1.3 63.1 + - - +
426B GLY 3.1 9.9 + - - -
427B VAL* 3.2 21.0 + - + +
440B TYR* 4.3 6.5 + - - -
452B LEU* 3.8 28.9 - - + +
457B ARG* 3.8 24.5 - - - -
475B CYS 3.4 12.4 + - - +
476B TRP* 3.3 50.1 + + + -
477B GLN 3.6 7.2 - - - -
483B ARG* 3.6 20.0 - - - +
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.7 32.8 - - + +
405B TRP* 3.7 25.0 - - + +
420B SER 3.1 13.9 + - - +
421B ASP* 3.8 7.0 - - - +
422B VAL 3.3 0.2 - - - -
423B TRP* 1.3 76.0 - - - +
425B PHE* 1.3 60.3 + - - +
427B VAL* 2.9 9.4 + - - +
428B LEU* 2.8 26.9 + - - +
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Residues in contact with PHE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ALA* 4.1 7.6 - - - -
347B ILE* 3.9 22.9 - - + -
348B SER* 3.9 28.0 - - - -
364B LEU* 3.5 15.8 - - + +
421B ASP 2.9 18.5 + - - +
422B VAL 3.5 3.8 - - - +
423B TRP 3.3 0.2 - - - -
424B ALA* 1.3 75.4 - - - +
426B GLY* 1.3 54.4 + - - +
428B LEU* 3.1 9.3 + - + +
429B LEU* 2.7 69.5 + - + +
432B ILE* 6.4 0.4 - - + -
471B LEU* 4.3 1.6 - - + -
475B CYS* 4.1 13.9 - - - -
486B PHE* 3.7 17.7 - + + -
489B ILE* 3.6 30.5 - - + -
493B PHE* 4.0 6.1 - + - -
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Residues in contact with GLY 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B VAL 3.0 10.5 + - - -
423B TRP 3.1 6.4 + - - -
425B PHE* 1.3 77.6 - - - +
427B VAL* 1.3 61.1 + - - +
429B LEU* 3.3 11.3 + - - +
430B TRP 3.3 13.3 + - - -
472B MET* 3.9 3.9 - - - +
475B CYS* 3.8 18.6 - - - -
476B TRP* 3.2 25.7 - - - -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS 3.6 20.4 - - - +
405B TRP* 3.6 29.8 - - + +
423B TRP* 3.2 20.3 + - + +
424B ALA 2.9 8.2 + - - +
426B GLY* 1.3 76.4 - - - +
428B LEU* 1.3 58.1 + - - +
430B TRP* 3.0 5.6 + - - +
431B GLU* 3.0 24.4 + - - +
439B PRO* 3.8 26.7 - - + -
440B TYR* 4.7 3.6 - - - +
458B MET* 4.1 8.1 - - + -
476B TRP* 3.7 22.9 - - + +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 4.2 4.9 - - + -
347B ILE* 4.0 24.0 - - + -
364B LEU* 3.4 36.3 - - + -
365B ALA* 3.9 13.9 - - - +
366B ALA* 3.7 31.0 - - + +
369B CYS* 4.1 3.4 - - - -
405B TRP* 4.6 0.6 - - - +
424B ALA 2.8 12.6 + - - +
425B PHE* 3.3 12.3 - - + +
427B VAL* 1.3 74.0 - - - +
429B LEU* 1.3 67.0 + - - +
431B GLU* 3.1 12.7 + - - +
432B ILE* 3.0 38.8 + - + +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B ALA* 3.8 19.7 - - + -
425B PHE* 2.7 47.4 + - + +
426B GLY* 3.4 9.4 - - - +
428B LEU* 1.3 72.4 - - + +
430B TRP* 1.3 58.6 + - - +
432B ILE* 3.2 9.6 + - + +
433B ALA* 2.9 29.8 + - - +
468B VAL* 4.5 10.0 - - + +
471B LEU* 4.0 11.2 - - + -
472B MET* 3.8 32.2 - - + +
475B CYS* 5.0 0.4 - - - -
493B PHE* 3.3 33.2 - - + -
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Residues in contact with TRP 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLY 3.3 7.7 + - - +
427B VAL 3.0 12.6 + - - +
429B LEU* 1.3 79.4 - - - +
431B GLU* 1.3 60.1 + - - +
433B ALA* 3.5 1.0 + - - +
434B THR* 3.0 50.8 + - + +
437B MET* 3.6 28.9 - - + -
438B SER 3.6 25.1 - - - -
439B PRO* 3.7 12.1 - - + -
441B PRO* 4.0 21.3 - - + -
458B MET* 3.5 44.3 - - + +
459B GLU* 3.5 19.5 + - + -
461B PRO* 3.5 25.0 - - + +
472B MET* 3.6 19.9 - - + +
476B TRP* 4.3 0.7 - + + -
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Residues in contact with GLU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 3.8 17.2 - - - +
327B LEU* 3.5 1.9 - - - +
365B ALA* 3.7 0.3 - - - +
366B ALA* 3.0 44.0 + - + +
367B ARG* 4.8 0.9 + - - +
405B TRP* 2.9 43.7 + - + +
427B VAL 3.0 14.7 + - - +
428B LEU* 3.1 13.9 + - - +
430B TRP* 1.3 75.9 - - + +
432B ILE* 1.3 63.1 + - - +
434B THR* 3.4 5.9 + - - -
435B TYR 3.2 2.3 + - - -
436B GLY* 2.6 35.2 + - - +
437B MET 4.2 13.8 - - - +
439B PRO* 4.6 5.3 - - + +
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Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU* 4.3 13.2 - - + -
327B LEU* 3.7 10.7 - - + +
340B LEU* 3.7 53.4 - - + +
343B MET* 4.4 7.4 - - + -
344B ALA* 4.4 21.5 - - + +
347B ILE* 3.9 19.7 - - + -
425B PHE* 6.4 0.9 - - + -
428B LEU* 3.0 35.4 + - + +
429B LEU* 3.6 11.2 - - + +
431B GLU* 1.3 75.2 - - - +
433B ALA* 1.3 59.8 + - - +
435B TYR* 2.9 19.8 + - - -
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B LEU* 4.4 12.8 - - - +
429B LEU 2.9 16.3 + - - +
430B TRP 4.0 4.3 - - - +
432B ILE* 1.3 77.0 - - - +
434B THR* 1.3 60.2 + - - +
435B TYR* 3.4 6.3 + - - -
461B PRO* 4.0 22.8 - - + +
462B GLU 4.5 8.7 - - - +
464B CYS* 4.3 16.7 - - + +
468B VAL* 5.9 2.0 - - + -
472B MET* 4.3 9.0 - - + -
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 4.6 3.6 + - - -
430B TRP* 3.0 43.7 + - + +
431B GLU* 3.4 3.5 + - - -
432B ILE 3.1 0.4 - - - -
433B ALA* 1.3 76.6 - - - +
435B TYR* 1.3 72.7 + - - +
437B MET* 3.2 49.3 + - - +
461B PRO* 3.6 25.8 - - + -
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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