Contacts of the helix formed by residues 442 - 459 (chain B) in PDB entry 1YOM
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 442 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B VAL* 3.4 18.4 - - - +
434B GLU* 4.6 3.5 + - - -
440B ARG* 3.2 11.2 + - + +
441B PHE* 1.3 76.7 - - - +
443B ILE* 1.3 65.5 + - - +
444B LYS* 3.3 15.2 + - - +
445B SER* 2.8 34.6 + - - -
446B ASP 3.1 4.3 + - - -
505B PRO* 4.9 4.2 - - + +
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B MET* 3.8 9.9 - - + +
379B VAL* 3.7 30.1 - - + -
380B GLU* 3.8 39.7 - - + +
384B TYR 3.9 11.2 - - - +
385B VAL* 3.7 7.2 - - + +
442B THR* 1.3 74.9 - - - +
444B LYS* 1.3 71.6 + - + +
446B ASP* 2.9 31.6 - - - +
447B VAL* 2.9 12.3 + - + +
511B PHE* 3.9 16.2 - - + -
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Residues in contact with LYS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 5.7 0.9 - - - +
442B THR* 3.1 11.6 - - - +
443B ILE* 1.3 86.1 - - + +
445B SER* 1.3 61.8 + - - +
447B VAL* 3.4 17.9 + - + +
448B TRP 3.4 3.3 + - - -
505B PRO* 3.2 27.6 - - + +
506B GLU* 3.9 18.5 + - - +
508B ARG* 2.3 60.0 + - + +
509B PRO* 3.8 0.2 - - - +
510B THR* 3.3 35.4 - - - +
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Residues in contact with SER 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 5.0 0.2 - - - +
432B ALA* 4.1 12.0 + - - +
434B GLU* 3.7 14.8 - - - -
435B ALA* 4.4 7.0 - - - -
440B ARG 4.1 5.6 - - - -
441B PHE* 3.4 19.2 - - - -
442B THR* 2.8 34.7 + - - -
444B LYS* 1.3 73.3 - - - +
446B ASP* 1.3 65.2 + - - +
448B TRP* 3.4 11.4 + - - +
449B SER* 3.2 15.1 + - - -
508B ARG* 3.7 9.8 - - - +
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Residues in contact with ASP 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B MET* 3.5 25.5 - - + +
385B VAL* 3.4 9.9 - - - +
386B HIS* 2.5 33.5 + - - +
387B ARG* 3.2 22.3 + - - -
389B LEU* 3.5 19.7 - - - +
442B THR 3.1 10.3 + - - -
443B ILE* 2.9 18.4 + - - +
445B SER* 1.3 80.3 + - - +
447B VAL* 1.3 58.6 + - - +
449B SER* 3.1 15.0 + - - -
450B PHE 3.1 8.7 + - - -
511B PHE* 3.9 4.0 - - + -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 5.0 0.4 - - - +
443B ILE* 2.9 14.7 + - + +
444B LYS* 3.5 19.7 - - + +
445B SER 3.3 0.6 - - - -
446B ASP* 1.3 74.6 - - - +
448B TRP* 1.3 62.7 + - - +
450B PHE* 3.1 11.8 + - - +
451B GLY 3.1 9.0 + - - -
500B CYS* 3.4 33.9 - - + +
508B ARG* 4.1 5.8 - - + -
509B PRO* 3.3 34.3 - - + +
510B THR* 4.8 1.3 - - - -
511B PHE* 3.3 33.2 - - + -
514B LEU* 3.8 4.7 - - + -
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Residues in contact with TRP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LYS 4.7 0.8 + - - -
430B TRP 3.7 7.3 + - - -
431B THR 3.4 13.8 + - - -
432B ALA* 3.4 30.7 - - + -
433B PRO* 3.5 25.6 - - + -
444B LYS 3.4 3.2 + - - -
445B SER 3.4 11.8 + - - +
446B ASP 3.2 0.2 - - - -
447B VAL* 1.3 79.6 - - - +
449B SER* 1.3 62.1 + - - +
451B GLY 3.2 2.1 + - - -
452B ILE* 3.3 16.3 + - + +
465B TYR* 4.2 12.7 + - - -
477B VAL* 3.5 27.4 - - + -
482B ARG* 3.8 19.3 - - - -
500B CYS 3.4 13.0 + - - +
501B TRP* 3.1 58.5 + + + -
502B ARG 4.7 0.9 - - - -
503B LYS* 5.0 1.1 - - - -
508B ARG* 3.2 31.2 - - - +
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Residues in contact with SER 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG 6.1 0.5 - - - -
389B LEU* 3.1 34.7 + - - +
430B TRP* 2.9 28.6 + - - -
431B THR* 4.4 5.0 - - - -
445B SER 3.2 14.0 + - - -
446B ASP* 3.1 10.5 + - - -
448B TRP* 1.3 73.1 - - - +
450B PHE* 1.3 55.8 + - - +
451B GLY 3.0 2.0 - - - -
452B ILE* 2.9 5.3 + - - +
453B LEU* 2.6 36.7 + - - +
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER* 3.2 35.7 - - - -
372B ILE* 3.9 18.8 - - + -
373B ALA* 3.8 17.9 - - + -
389B LEU* 4.1 8.7 - - + +
446B ASP 3.1 6.9 + - - +
447B VAL* 3.1 10.5 + - - +
449B SER* 1.3 76.8 - - - +
451B GLY* 1.3 59.5 + - - +
453B LEU* 3.2 13.5 + - + +
454B LEU* 2.9 44.3 + - + +
500B CYS* 4.4 1.1 - - - -
511B PHE* 3.6 27.8 - + + -
514B LEU* 3.9 26.2 - - + -
518B LEU* 3.6 25.4 - - + -
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Residues in contact with GLY 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B VAL 3.1 9.9 + - - -
448B TRP 3.2 0.4 + - - -
449B SER 3.0 0.4 - - - -
450B PHE* 1.3 75.7 - - - +
452B ILE* 1.3 62.7 + - - +
454B LEU* 3.1 23.7 + - - +
455B THR* 3.5 4.3 + - - +
497B MET* 4.1 3.2 - - - +
500B CYS* 3.9 17.0 - - - +
501B TRP* 3.2 31.6 - - - -
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Residues in contact with ILE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B LYS 3.8 10.1 - - - +
430B TRP* 3.3 31.4 - - + +
448B TRP* 3.3 24.4 + - + +
449B SER* 2.9 7.3 + - - +
451B GLY* 1.3 76.3 - - - +
453B LEU* 1.3 56.9 + - - +
455B THR* 2.8 31.1 + - - -
456B GLU* 3.2 4.9 + - - +
464B PRO* 3.6 23.3 - - + -
465B TYR* 3.1 30.1 - - + +
483B MET* 3.4 20.0 - - + -
501B TRP* 3.8 15.3 - - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.2 13.2 - - + -
372B ILE* 3.8 32.8 - - + -
389B LEU* 4.6 13.0 - - + -
390B ARG* 4.4 9.9 - - - -
391B ALA* 4.3 6.5 - - + +
394B ILE* 4.5 9.4 - - + -
430B TRP* 5.0 0.2 - - - +
449B SER 2.6 20.2 + - - +
450B PHE* 3.6 16.4 - - + +
451B GLY 3.2 0.2 - - - -
452B ILE* 1.3 74.0 - - - +
454B LEU* 1.3 57.5 + - + +
456B GLU* 3.2 24.9 + - + +
457B LEU* 3.0 46.7 + - + +
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Residues in contact with LEU 454 (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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366B VAL* 6.2 0.2 - - - -
369B SER* 3.7 32.1 - - - +
450B PHE* 2.9 39.7 + - + +
451B GLY* 3.1 15.7 + - - +
453B LEU* 1.3 77.7 - - - +
455B THR* 1.3 55.4 + - - +
457B LEU* 3.8 7.5 - - + +
458B THR* 3.0 32.4 + - + +
493B LEU* 4.5 21.1 - - + -
496B LEU* 4.0 22.9 - - + -
497B MET* 3.8 29.4 - - + +
500B CYS* 5.0 0.9 - - - -
518B LEU* 4.7 1.3 - - + -
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Residues in contact with THR 455 (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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451B GLY 3.5 2.2 + - - +
452B ILE 2.8 17.7 + - - +
454B LEU* 1.3 74.4 - - - +
456B GLU* 1.3 57.0 + - - +
458B THR* 3.5 8.1 - - - -
459B THR* 2.5 46.4 + - - +
462B ARG 4.9 1.4 + - - -
464B PRO* 4.1 18.9 - - - +
483B MET* 3.8 32.4 - - + -
486B PRO* 5.4 5.8 - - + -
497B MET* 4.0 11.4 - - + -
501B TRP* 3.9 18.2 - - + -
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Residues in contact with GLU 456 (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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349B LEU* 3.7 17.8 - - - +
352B LEU* 3.4 8.1 - - + +
390B ARG* 4.9 0.2 - - - +
391B ALA* 2.9 48.3 + - + +
430B TRP* 3.1 40.7 + - + +
452B ILE 3.2 9.1 + - - +
453B LEU* 3.2 15.6 + - + +
455B THR* 1.3 83.7 + - - +
457B LEU* 1.3 57.4 + - - +
459B THR* 3.8 4.3 - - - -
460B LYS 3.0 9.5 + - - -
461B GLY* 2.9 30.7 + - - +
462B ARG 4.2 16.3 - - - +
464B PRO* 5.0 2.2 - - + -
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.4 37.0 - - + -
352B LEU* 3.9 14.1 - - + -
365B LEU* 2.8 46.9 - - + +
368B MET* 4.5 11.9 - - + -
369B SER* 3.2 40.8 - - - -
372B ILE* 4.7 1.3 - - + -
453B LEU* 3.0 27.8 + - + +
454B LEU* 3.8 15.0 - - + +
456B GLU* 1.3 76.0 - - - +
458B THR* 1.3 62.8 + - + +
459B THR 3.6 0.2 + - - -
460B LYS 3.9 3.8 + - - -
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Residues in contact with THR 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LEU* 4.2 11.0 - - + -
365B LEU* 4.3 6.7 - - + -
454B LEU* 3.0 26.1 + - + +
455B THR* 3.5 8.1 + - - -
457B LEU* 1.3 81.0 - - + +
459B THR* 1.3 60.1 + - - +
460B LYS* 3.5 3.3 + - - +
486B PRO* 3.3 29.1 - - - +
487B PRO 5.2 0.9 - - - +
489B CYS* 4.3 7.6 - - - -
493B LEU* 3.2 34.3 - - + -
497B MET* 3.5 4.3 - - + +
535B LEU* 3.8 23.9 - - - +
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Residues in contact with THR 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B THR* 2.5 32.3 + - - +
456B GLU* 3.6 1.0 + - - -
457B LEU 3.3 0.2 - - - -
458B THR* 1.3 79.7 - - - +
460B LYS* 1.3 75.7 + - - +
461B GLY 3.2 0.5 + - - -
462B ARG* 3.3 46.1 + - + +
486B PRO* 4.0 23.1 - - + -
487B PRO* 5.6 3.4 - - + -
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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