Contacts of the helix formed by residues 456 - 474 (chain B) in PDB entry 3HN3
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 LEU 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B ALA 5.2 0.2 - - - +
415B PRO* 3.9 41.5 - - + -
418B PHE* 4.2 9.0 - - + -
453B ALA* 3.1 30.7 + - + +
454B SER 3.8 3.3 - - - +
455B HIS* 1.3 101.3 - - + +
457B GLU* 1.3 65.6 + - - +
458B SER* 4.1 6.5 - - - +
459B ALA* 3.1 12.2 + - + +
460B GLY* 2.9 17.7 + - - -
491B LYS* 4.1 1.6 - - - +
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Residues in contact with GLU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B HIS 3.7 3.0 + - - -
456B LEU* 1.3 70.5 - - - +
458B SER* 1.3 57.4 + - - +
460B GLY* 2.9 16.9 + - - +
461B TYR* 3.1 12.8 + - - +
491B LYS* 3.8 31.7 - - - +
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Residues in contact with SER 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 4.7 5.0 + - - +
418B PHE* 3.7 27.9 + - - +
456B LEU* 4.1 12.0 - - - +
457B GLU* 1.3 78.8 - - - +
459B ALA* 1.3 59.3 + - - +
461B TYR* 3.5 8.0 + - - +
462B TYR* 3.0 27.9 + - - +
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B PHE* 3.5 35.7 - - + -
453B ALA 3.2 26.7 - - - +
454B SER* 3.8 9.0 - - - -
456B LEU* 3.1 8.1 + - + +
458B SER* 1.3 78.1 + - - +
460B GLY* 1.3 59.4 + - - +
463B LEU* 2.8 40.5 + - + +
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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
----------------------------------------------------------
454B SER 4.6 0.4 + - - -
456B LEU 2.9 10.5 + - - -
457B GLU* 2.9 7.5 + - - -
459B ALA* 1.3 76.9 - - - +
461B TYR* 1.3 55.5 + - - +
463B LEU* 3.8 2.3 - - - +
464B LYS* 2.9 29.2 + - - +
491B LYS* 3.7 34.4 - - - +
492B GLY 4.5 1.1 - - - -
495B TYR* 4.0 8.3 - - - -
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Residues in contact with TYR 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASN* 5.5 6.5 - - - -
423B LEU* 4.0 17.1 - - + +
457B GLU 3.1 9.2 + - - +
458B SER* 3.9 8.7 - - - +
460B GLY* 1.3 71.5 - - - +
462B TYR* 1.3 72.1 + - + +
464B LYS* 3.2 13.5 + - + +
465B MET* 3.0 64.5 + - + +
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Residues in contact with TYR 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU* 4.2 6.6 - - - +
412B LEU* 3.8 23.7 - - + +
417B PHE 4.1 14.3 + - - -
418B PHE* 3.5 30.3 - + + -
419B ASN 4.2 3.1 - - - -
422B SER* 3.7 9.3 + - - -
423B LEU* 3.5 47.5 - - + +
426B HIS* 2.7 42.2 + + - +
458B SER 3.0 18.5 + - - +
459B ALA 3.6 3.1 - - - +
461B TYR* 1.3 83.6 - - + +
463B LEU* 1.3 71.9 + - + +
465B MET 3.3 0.5 + - - -
466B VAL* 3.1 33.3 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 5.6 0.2 - - + -
418B PHE* 5.2 0.2 - - + -
426B HIS* 5.7 0.7 - - + -
448B VAL* 4.5 9.0 - - + -
449B ALA* 4.2 16.6 - - + -
452B PRO* 4.0 22.2 - - + -
454B SER* 3.5 32.3 - - - -
459B ALA* 2.8 25.6 + - + +
460B GLY 3.8 2.7 - - - +
462B TYR* 1.3 85.8 - - + +
464B LYS* 1.3 68.5 + - - +
466B VAL* 3.4 3.0 + - + +
467B ILE* 2.9 35.9 + - + +
481B PHE* 3.8 25.1 - - + -
492B GLY* 4.1 12.8 - - - -
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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
----------------------------------------------------------
460B GLY 2.9 14.5 + - - +
461B TYR* 3.3 20.2 - - + +
463B LEU* 1.3 76.0 - - - +
465B MET* 1.3 78.5 + - + +
467B ILE* 3.9 1.6 - - - +
468B ALA* 3.0 31.6 + - + +
495B TYR* 3.7 57.3 + - + +
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Residues in contact with MET 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 4.3 14.8 - - + -
427B MET* 4.7 9.5 - - - +
461B TYR* 3.0 57.4 + - + +
462B TYR 3.8 3.8 - - - +
464B LYS* 1.3 111.1 - - + +
466B VAL* 1.3 62.3 + - - +
468B ALA* 3.4 9.2 + - + +
469B HIS* 2.9 30.1 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 3.4 21.3 - - + -
426B HIS* 3.8 37.0 - - + +
427B MET* 4.3 6.5 - - + -
430B MET* 3.8 12.8 - - + -
448B VAL* 3.7 26.5 - - + -
462B TYR* 3.1 24.5 + - + +
463B LEU* 4.0 5.4 - - + +
465B MET* 1.3 75.9 - - - +
467B ILE* 1.3 53.9 + - - +
469B HIS* 3.6 6.0 - - + +
470B THR* 2.7 37.1 + - - -
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Residues in contact with ILE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 3.9 18.4 - - + -
463B LEU* 2.9 25.1 + - + +
464B LYS 3.9 3.4 - - - +
466B VAL* 1.3 76.5 - - - +
468B ALA* 1.3 58.1 + - - +
470B THR* 3.3 3.6 + - - -
471B LYS* 2.9 44.4 + - + +
479B VAL* 4.0 21.0 - - + +
480B THR 4.9 0.4 - - - +
481B PHE* 4.0 13.5 - - + -
492B GLY 4.3 3.1 - - - +
495B TYR* 3.4 37.5 - - + +
496B VAL* 3.9 27.8 - - + -
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Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B LYS* 3.0 20.1 + - + +
465B MET* 3.8 12.8 - - + +
467B ILE* 1.3 76.5 - - - +
469B HIS* 1.3 64.3 + - - +
471B LYS* 3.3 10.6 + - - +
472B SER* 3.0 24.0 + - - -
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Residues in contact with HIS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B MET* 3.6 47.8 + - + +
430B MET* 5.0 2.0 - - + -
431B GLU* 2.6 32.9 + - - +
465B MET 2.9 18.6 + - - +
466B VAL* 3.6 7.9 - - + +
468B ALA* 1.3 74.5 - - - +
470B THR* 1.3 63.3 + - - +
472B SER* 2.7 28.6 + - - -
473B LEU* 3.0 32.4 + - + +
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Residues in contact with THR 470 (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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430B MET* 3.6 34.1 - - + +
434B VAL* 4.5 6.5 - - + -
446B TRP* 4.0 17.5 - - + -
448B VAL* 3.5 11.6 - - - +
466B VAL 2.7 22.9 + - - -
467B ILE 3.5 4.9 - - - -
468B ALA 3.2 0.2 - - - -
469B HIS* 1.3 77.1 - - - +
471B LYS* 1.3 62.3 + - - +
473B LEU* 3.0 22.1 + - - +
474B ASP* 3.1 12.5 + - - +
479B VAL* 3.7 24.2 - - + -
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Residues in contact with LYS 471 (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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467B ILE* 2.9 34.1 + - + +
468B ALA* 3.3 9.2 + - - +
470B THR* 1.3 76.2 - - - +
472B SER* 1.3 61.5 + - - +
474B ASP 3.2 4.8 - - - +
475B PRO* 3.2 29.4 - - + +
477B ARG 5.4 1.8 - - - +
479B VAL* 3.5 19.1 - - + -
495B TYR* 3.2 19.1 + - - +
497B ASP* 3.1 39.3 + - - +
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Residues in contact with SER 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ALA 3.0 12.7 + - - -
469B HIS* 2.7 29.6 + - - -
471B LYS* 1.3 77.2 - - - +
473B LEU* 1.3 62.5 + - - +
475B PRO* 3.9 10.9 - - - +
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Residues in contact with LEU 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B MET* 4.2 6.1 - - + +
431B GLU* 3.7 52.0 - - + +
434B VAL* 4.1 22.7 - - + +
469B HIS* 3.0 32.8 + - + +
470B THR* 3.4 13.5 - - - +
472B SER* 1.3 82.6 + - - +
474B ASP* 1.3 58.9 + - - +
475B PRO* 3.9 2.7 - - - +
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Residues in contact with ASP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 4.1 14.4 - - + -
438B LYS* 5.6 2.5 - - + -
446B TRP* 2.8 32.5 + - - +
470B THR 3.1 9.4 + - - +
471B LYS* 3.2 8.1 - - - +
473B LEU* 1.3 81.6 - - - +
475B PRO* 1.3 64.3 - - - +
476B SER* 2.5 27.6 + - - -
477B ARG* 2.9 41.8 + - - +
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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
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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