Contacts of the helix formed by residues 449 - 471 (chain B) in PDB entry 5OC9
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 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B GLN 3.2 5.2 + - - -
447B MET 3.7 0.4 - - - -
448B GLU* 1.4 80.2 - - - +
450B PHE* 1.3 64.3 + - - +
452B PRO* 3.5 6.7 - - - +
453B TYR* 2.8 38.3 + - - +
532B SER* 2.9 48.3 + - - -
535B LEU* 4.5 5.2 - - - -
536B LYS* 3.9 16.4 - - - -
540B VAL* 4.1 3.3 - - - +
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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
----------------------------------------------------------
445B GLN* 3.3 44.2 + - + +
446B ILE* 3.9 18.2 - - + -
449B SER* 1.3 81.9 + - - +
451B LEU* 1.3 61.5 + - - +
453B TYR* 3.9 7.3 - + - +
454B TRP* 3.2 24.3 + - - +
528B THR* 5.5 5.6 - - - -
532B SER* 4.2 20.0 - - - -
535B LEU* 4.3 15.9 - - + -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE* 2.8 34.9 + - + +
447B MET* 4.1 30.1 - - + +
450B PHE* 1.3 69.9 - - - +
452B PRO* 1.4 67.9 - - + +
454B TRP* 3.1 14.4 + - + +
455B LEU* 3.1 44.3 + - + +
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Residues in contact with PRO 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ILE 3.6 0.7 - - - +
447B MET 3.3 28.0 - - - +
448B GLU 3.6 11.0 - - - +
449B SER 3.4 13.2 - - - +
451B LEU* 1.4 92.5 - - + +
453B TYR* 1.4 54.3 + - - +
455B LEU* 3.5 11.3 + - + +
456B GLN* 2.9 30.1 + - - +
540B VAL* 3.7 23.3 - - + +
541B PHE* 6.4 0.4 - - + -
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Residues in contact with TYR 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B SER 2.8 23.9 + - - +
450B PHE* 3.9 5.2 - - - +
451B LEU 3.2 0.2 - - - -
452B PRO* 1.4 69.6 - - - +
454B TRP* 1.3 62.4 + + + +
456B GLN* 3.2 1.8 + - - +
457B ARG* 2.8 80.9 + - + +
535B LEU* 3.7 33.0 - - + -
539B ARG* 3.6 41.6 - - + -
540B VAL* 3.7 12.8 - - + +
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Residues in contact with TRP 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B PHE 3.2 12.3 + - - +
451B LEU* 3.1 17.4 + - + +
453B TYR* 1.3 84.8 - + + +
455B LEU* 1.4 63.2 + - + +
457B ARG* 3.5 5.2 + - - +
458B LYS* 3.1 59.4 + - + +
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 3.1 48.3 + - + +
452B PRO* 3.9 8.3 - - + +
454B TRP* 1.4 81.4 - - + +
456B GLN* 1.4 62.0 + - - +
458B LYS* 3.7 11.2 + - + +
459B HIS* 3.3 20.8 + - - +
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Residues in contact with GLN 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B PRO 2.9 18.5 + - - +
453B TYR* 3.8 3.6 - - - +
455B LEU* 1.4 72.4 - - - +
457B ARG* 1.4 60.7 + - - +
459B HIS* 3.4 24.2 + - - +
460B GLY* 2.9 27.6 + - - +
484B LEU* 4.6 7.1 - - - +
487B GLU 4.8 1.7 - - - +
488B MET* 3.6 45.9 - - + +
489B GLY 4.4 2.1 + - - -
539B ARG 3.5 24.7 - - - +
540B VAL* 3.8 16.2 - - + +
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Residues in contact with ARG 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B TYR* 2.8 61.9 + - + +
454B TRP* 3.7 6.3 - - - +
456B GLN* 1.4 71.2 - - - +
458B LYS* 1.4 58.3 + - + +
460B GLY* 3.1 3.3 + - - +
461B VAL* 3.0 47.4 + - + +
539B ARG* 5.4 1.8 + - - +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B TRP* 3.1 50.0 + - + +
455B LEU* 3.9 13.0 - - + +
456B GLN 3.4 0.2 - - - -
457B ARG* 1.4 75.3 - - + +
459B HIS* 1.3 59.5 + - - +
461B VAL* 3.7 6.8 + - - +
462B ARG* 3.3 48.2 + - - +
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Residues in contact with HIS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B LEU 3.3 12.2 + - - +
456B GLN* 3.7 29.4 + - - +
457B ARG 3.3 0.6 - - - -
458B LYS* 1.3 75.7 - - - +
460B GLY* 1.3 60.1 + - - +
462B ARG* 3.3 21.3 + - + +
463B VAL* 2.9 54.1 + - + +
483B ILE 5.2 0.4 - - - -
484B LEU* 4.7 10.2 - - + +
487B GLU* 4.0 32.6 + - + +
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Residues in contact with GLY 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B GLN* 2.9 17.0 + - - -
457B ARG* 3.1 5.3 + - - -
459B HIS* 1.3 73.2 - - - +
461B VAL* 1.4 61.7 + - - +
463B VAL* 3.3 2.6 + - - +
464B LYS* 3.2 24.4 + - - +
484B LEU* 3.7 23.3 - - - +
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Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ARG* 3.0 34.1 + - + +
458B LYS* 4.1 6.5 - - - +
460B GLY* 1.4 74.4 - - - +
462B ARG* 1.3 56.9 + - - +
464B LYS* 3.5 5.6 + - - +
465B ARG* 3.1 66.4 + - + +
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Residues in contact with ARG 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LYS* 3.3 50.9 + - - +
459B HIS* 3.3 29.0 + - + +
461B VAL* 1.3 79.6 - - - +
463B VAL* 1.4 60.6 + - + +
465B ARG* 3.7 7.2 + - - +
466B LYS* 3.1 52.7 + - + +
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Residues in contact with VAL 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B HIS* 2.9 49.9 + - + +
460B GLY 3.3 0.6 + - - -
462B ARG* 1.4 73.7 - - + +
464B LYS* 1.4 63.4 + - - +
466B LYS* 3.2 20.8 + - + +
467B VAL* 3.2 20.8 + - + +
480B GLU* 4.2 22.2 - - + +
483B ILE* 4.6 20.0 - - + -
484B LEU* 3.8 24.7 - - + -
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Residues in contact with LYS 464 (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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460B GLY 3.2 15.9 + - - +
461B VAL* 3.9 6.1 - - - +
462B ARG 3.5 0.2 - - - -
463B VAL* 1.4 75.7 - - - +
465B ARG* 1.3 61.1 + - + +
467B VAL* 3.6 2.6 + - - +
468B GLN* 3.2 26.7 + - - +
480B GLU* 3.4 27.7 + - - +
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Residues in contact with ARG 465 (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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461B VAL* 3.1 44.2 + - + +
462B ARG* 4.0 6.7 - - - +
464B LYS* 1.3 74.7 - - + +
466B LYS* 1.3 63.6 + - - +
468B GLN* 3.7 6.3 + - - +
469B ALA* 3.4 22.0 + - - +
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B ARG* 3.1 47.2 + - + +
463B VAL* 3.2 15.2 + - + +
465B ARG* 1.3 76.6 - - - +
467B VAL* 1.4 63.9 + - + +
469B ALA* 3.5 18.5 + - - +
470B LEU* 3.6 13.6 + - - +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B VAL* 3.2 21.0 + - + +
464B LYS 4.1 0.7 - - - +
466B LYS* 1.4 72.9 - - + +
468B GLN* 1.4 64.6 + - - +
469B ALA 3.2 0.4 - - - -
470B LEU* 3.2 36.4 + - + +
471B LYS 3.8 3.1 + - - -
472B ALA* 5.2 1.0 + - - +
476B ALA* 4.4 25.8 - - + +
479B TYR* 5.1 11.9 - - + -
480B GLU* 3.8 38.1 - - + +
483B ILE* 6.3 2.0 - - + -
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Residues in contact with GLN 468 (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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464B LYS 3.2 19.1 + - - +
465B ARG* 3.9 7.9 - - - +
466B LYS 3.4 0.2 - - - -
467B VAL* 1.4 75.7 - - - +
469B ALA* 1.3 59.5 + - - +
470B LEU 3.5 0.5 + - - -
471B LYS* 3.4 28.3 + - - +
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Residues in contact with ALA 469 (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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465B ARG 3.4 11.6 + - - +
466B LYS* 3.5 13.5 - - - +
467B VAL 3.2 0.4 - - - -
468B GLN* 1.3 75.7 - - - +
470B LEU* 1.4 63.0 + - - +
471B LYS* 3.5 14.1 + - - +
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Residues in contact with LEU 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.9 32.1 - - + -
466B LYS 3.6 9.6 - - - +
467B VAL* 3.2 34.3 + - + +
469B ALA* 1.4 78.5 - - - +
471B LYS* 1.4 68.8 - - - +
472B ALA* 4.4 10.2 - - + +
479B TYR* 5.4 2.7 - - + -
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Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL 3.8 3.4 + - - -
468B GLN 3.4 24.0 + - - +
469B ALA* 3.5 12.0 + - - +
470B LEU* 1.4 80.2 - - - +
472B ALA* 1.3 65.7 + - - +
473B ASP* 3.8 1.0 + - - -
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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