Contacts of the helix formed by residues 436 - 453 (chain B) in PDB entry 1OPL
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 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ILE* 3.8 7.8 - - - +
381B ARG* 6.2 0.2 - - - +
406B LEU* 4.1 9.6 - - - -
409B GLY 5.9 1.8 - - - -
410B ASP 3.7 16.2 - - - -
411B THR* 4.5 7.6 - - - -
428B GLU* 4.9 3.1 + - - -
435B PHE* 1.3 77.3 - - - +
437B ILE* 1.3 65.5 + - - +
438B LYS* 2.9 28.1 + - - +
439B SER* 2.8 21.9 + - - -
440B ASP* 3.3 7.8 + - - -
499B PRO* 5.0 2.4 - - - +
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Residues in contact with ILE 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET* 4.5 5.2 - - + -
373B LEU* 4.8 0.4 - - + -
374B GLU* 3.7 43.7 - - + +
378B PHE 3.8 21.1 - - - +
379B ILE* 3.7 11.3 - - + +
406B LEU* 4.9 1.0 - - - +
408B THR* 4.5 24.2 - - + +
409B GLY* 5.2 6.4 - - - +
436B SER* 1.3 76.2 - - - +
438B LYS* 1.3 75.4 + - + +
440B ASP* 3.1 18.9 + - - +
441B VAL* 3.0 25.8 + - + +
505B PHE* 3.8 17.9 - - + -
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Residues in contact with LYS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLU* 5.2 0.8 + - - -
436B SER* 2.9 12.3 + - - +
437B ILE* 1.3 91.2 - - + +
439B SER* 1.3 62.1 + - - +
441B VAL* 3.2 7.6 + - + +
442B TRP 3.2 13.3 + - - -
499B PRO* 3.4 44.9 - - + +
500B SER* 4.8 7.2 + - - +
502B ARG* 2.9 43.8 + - + +
503B PRO 3.6 17.5 + - - +
504B SER* 3.7 14.3 - - - +
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Residues in contact with SER 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG* 5.6 0.2 - - - +
424B TRP 4.9 1.4 - - - +
426B ALA* 3.8 13.6 + - - +
428B GLU* 3.8 6.5 + - - -
429B SER* 3.6 22.0 - - - -
435B PHE* 3.4 18.3 - - - +
436B SER* 2.8 34.5 + - - -
438B LYS* 1.3 78.2 - - - +
440B ASP* 1.3 64.8 + - - +
442B TRP* 3.3 4.3 + - - +
443B ALA* 3.1 20.6 + - - +
502B ARG* 3.9 7.8 - - - +
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B MET* 3.8 10.9 - - + +
379B ILE* 3.5 11.6 - - - +
380B HIS* 2.8 32.6 + - - +
381B ARG* 2.9 30.1 + - - +
382B ASN 4.7 0.2 + - - -
383B LEU* 3.8 7.1 - - + +
436B SER 3.3 8.3 + - - +
437B ILE* 3.1 15.7 + - + +
439B SER* 1.3 77.7 + - - +
441B VAL* 1.3 59.7 + - - +
443B ALA* 3.2 8.2 + - - +
444B PHE* 2.8 25.5 + - - +
505B PHE* 3.5 19.2 - - + -
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLU* 5.0 0.9 - - - +
437B ILE 3.0 19.1 + - - +
438B LYS* 3.4 16.8 - - + +
439B SER 3.2 0.4 - - - -
440B ASP* 1.3 77.9 - - - +
442B TRP* 1.3 63.4 + - - +
444B PHE* 3.1 11.3 + - - +
445B GLY 3.1 9.5 + - - -
494B CYS* 3.5 27.5 - - - +
502B ARG* 3.9 17.5 - - + -
503B PRO* 3.4 28.5 - - + +
504B SER* 4.7 1.3 - - - -
505B PHE* 3.6 32.1 - - + +
508B ILE* 3.9 5.8 - - + -
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Residues in contact with TRP 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS 4.9 1.2 + - - -
424B TRP 4.0 9.1 + - - -
425B THR 3.8 8.5 + - - +
426B ALA* 3.7 23.8 - - + -
427B PRO* 3.5 27.8 - - + -
438B LYS 3.2 9.8 + - - +
439B SER 3.5 9.4 - - - +
440B ASP 3.2 0.2 - - - -
441B VAL* 1.3 77.7 - - - +
443B ALA* 1.3 64.7 + - - +
445B GLY 3.0 10.6 + - - -
446B VAL* 3.3 19.5 + - + +
459B TYR* 4.4 7.0 + - - -
471B LEU* 3.8 29.8 - - + -
476B ARG* 3.8 18.6 - - - -
494B CYS 3.5 12.3 + - - +
495B TRP* 3.2 56.9 + + + -
496B GLN 3.6 7.4 - - - -
497B TRP 4.6 0.2 - - - -
502B ARG* 3.6 20.0 - - - +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ARG 6.3 0.9 - - - -
383B LEU* 3.7 32.0 - - + +
424B TRP* 3.5 25.8 - - + +
439B SER 3.1 12.0 + - - +
440B ASP* 3.2 10.7 + - - +
442B TRP* 1.3 77.7 - - - +
444B PHE* 1.3 58.7 + - - +
446B VAL* 3.0 8.4 + - - +
447B LEU* 2.8 28.0 + - - +
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA* 3.9 17.7 - - + -
366B ILE* 3.6 34.5 - - + -
367B SER* 4.0 14.4 - - - -
370B MET* 4.9 0.7 - - + -
383B LEU* 3.9 12.1 - - + +
440B ASP 2.8 14.6 + - - +
441B VAL* 3.1 8.5 + - - +
443B ALA* 1.3 77.5 - - - +
445B GLY* 1.3 59.1 + - - +
447B LEU* 3.2 11.0 + - + +
448B LEU* 2.8 43.7 + - + +
451B ILE* 6.0 0.9 - - + -
490B LEU* 6.3 0.2 - - + -
494B CYS* 4.2 15.0 - - - -
505B PHE* 3.6 22.0 - + + -
508B ILE* 3.8 13.0 - - + -
512B PHE* 3.7 29.6 - + - -
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Residues in contact with GLY 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B VAL 3.1 6.5 + - - -
442B TRP 3.0 10.1 + - - -
444B PHE* 1.3 77.4 - - - +
446B VAL* 1.3 60.2 + - - +
448B LEU* 3.3 8.6 + - - +
449B TRP* 3.1 17.0 + - - +
491B MET* 3.9 6.4 - - - +
494B CYS* 3.8 19.1 - - - -
495B TRP* 3.4 23.8 - - - -
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LYS 3.5 24.2 - - - +
424B TRP* 3.5 31.0 - - + +
442B TRP* 3.3 21.2 + - + +
443B ALA* 3.0 7.4 + - - +
445B GLY* 1.3 72.6 - - - +
447B LEU* 1.3 66.6 + - - +
449B TRP* 3.1 4.8 + - - +
450B GLU* 2.9 21.5 + - - +
458B PRO* 3.8 22.7 - - + -
459B TYR* 4.8 2.7 - - - +
477B MET* 4.3 7.6 - - + -
495B TRP* 3.6 22.7 - - + +
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Residues in contact with LEU 447 (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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342B LEU* 4.4 4.5 - - + -
366B ILE* 3.9 19.7 - - + -
383B LEU* 3.7 33.7 - - + -
384B ALA* 4.2 8.5 - - - -
385B ALA* 3.5 34.3 - - + +
388B CYS* 3.9 9.9 - - - -
424B TRP* 4.5 0.2 - - - -
443B ALA 2.8 12.9 + - - +
444B PHE* 3.4 12.6 - - + +
446B VAL* 1.3 78.2 - - - +
448B LEU* 1.3 57.2 + - - +
450B GLU* 3.0 12.8 + - - +
451B ILE* 2.9 44.5 + - + +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ALA* 4.2 16.8 - - + -
444B PHE* 2.8 30.6 + - + +
445B GLY* 3.4 10.3 - - - +
446B VAL 3.2 0.2 - - - -
447B LEU* 1.3 75.0 - - - +
449B TRP* 1.3 55.7 + - - +
451B ILE* 3.2 10.5 + - + +
452B ALA* 2.9 31.3 + - + +
487B VAL* 3.9 27.6 - - + +
490B LEU* 4.4 3.8 - - + -
491B MET* 3.6 29.8 - - + +
494B CYS* 5.8 0.7 - - - -
512B PHE* 3.7 36.6 - - + -
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Residues in contact with TRP 449 (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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445B GLY 3.1 11.8 + - - +
446B VAL 3.1 8.8 + - - +
448B LEU* 1.3 73.8 - - - +
450B GLU* 1.3 70.2 + - - +
452B ALA* 3.3 0.9 + - - -
453B THR* 3.0 46.7 + - + +
456B MET* 3.5 46.2 - - + -
457B SER 3.5 18.6 - - - -
458B PRO* 3.6 14.8 - - + -
459B TYR 4.6 2.0 - - - -
460B PRO* 5.1 6.5 - - + -
477B MET* 3.5 43.2 - - + +
478B GLU 3.3 22.3 + - - -
480B PRO* 3.5 24.5 - - + +
488B TYR* 5.5 0.2 - + - -
491B MET* 3.9 19.5 - - - +
495B TRP* 4.2 2.2 - + + -
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Residues in contact with GLU 450 (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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343B LEU* 3.8 17.3 - - - +
346B LEU* 4.0 1.6 - - - +
384B ALA* 5.2 0.2 - - - +
385B ALA* 2.9 41.0 + - + +
386B ARG 4.9 0.5 + - - -
424B TRP* 2.8 42.9 + - - +
446B VAL 2.9 17.5 + - - +
447B LEU* 3.0 12.2 + - - +
449B TRP* 1.3 77.7 - - + +
451B ILE* 1.3 62.1 + - - +
453B THR* 3.2 8.7 + - - -
455B GLY* 2.7 32.0 + - - -
456B MET 4.3 9.7 - - - +
458B PRO* 4.3 14.7 - - + +
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Residues in contact with ILE 451 (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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342B LEU* 4.1 14.1 - - + -
346B LEU* 3.8 11.2 - - + +
359B LEU* 3.8 51.0 - - + +
362B MET* 4.8 3.6 - - + -
363B ALA* 4.0 24.5 - - + +
366B ILE* 3.9 28.0 - - + -
385B ALA* 5.6 0.2 - - + -
444B PHE* 6.0 1.3 - - + -
447B LEU* 2.9 29.3 + - + +
448B LEU* 3.5 14.1 - - + +
449B TRP 3.2 0.2 - - - -
450B GLU* 1.3 77.5 - - - +
452B ALA* 1.3 58.4 + - + +
454B TYR* 3.1 19.8 + - - -
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 4.7 8.2 - - - +
448B LEU* 2.9 17.5 + - + +
449B TRP 3.3 3.8 + - - +
451B ILE* 1.3 77.9 - - - +
453B THR* 1.3 60.0 + - - +
454B TYR* 3.4 9.0 - - - -
480B PRO* 4.0 25.2 - - + +
481B GLU 4.8 6.4 - - - +
483B CYS* 4.3 12.4 - - + +
487B VAL* 5.3 3.4 - - + -
491B MET* 4.1 11.2 - - + -
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Residues in contact with THR 453 (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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351B ARG* 4.7 5.7 + - - -
449B TRP* 3.0 40.4 + - + +
450B GLU* 3.2 5.9 + - - -
452B ALA* 1.3 77.1 - - - +
454B TYR* 1.3 71.4 + - - +
456B MET* 3.0 51.1 + - - +
480B PRO* 3.6 28.5 - - + -
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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
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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