Contacts of the helix formed by residues 456 - 474 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413D ALA 5.4 0.2 - - - +
415D PRO* 3.9 39.9 - - + -
418D PHE* 4.3 6.1 - - + -
453D ALA* 3.1 31.3 + - + +
454D SER 3.7 3.6 - - - +
455D HIS* 1.3 103.0 - - + +
457D GLU* 1.3 65.0 + - - +
458D SER* 3.9 17.0 - - - +
459D ALA* 3.2 4.1 + - + +
460D GLY 3.1 17.2 + - - -
491D LYS* 3.8 2.2 - - - +
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Residues in contact with GLU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D HIS 3.8 1.5 + - - +
456D LEU* 1.3 69.1 - - - +
458D SER* 1.3 67.7 + - - +
460D GLY* 3.2 10.0 + - - -
461D TYR* 3.2 13.5 + - - +
491D LYS* 3.0 46.2 + - + +
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Residues in contact with SER 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D PRO* 4.8 3.6 + - - +
418D PHE* 3.8 26.9 + - - +
456D LEU* 3.9 15.4 - - - +
457D GLU* 1.3 81.2 - - - +
459D ALA* 1.3 57.4 + - - +
461D TYR* 3.4 7.5 + - - +
462D TYR* 3.0 27.8 + - - +
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Residues in contact with ALA 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D PHE* 3.5 32.1 - - + -
453D ALA 3.2 27.4 - - - +
454D SER* 3.8 8.7 - - - -
456D LEU* 3.2 10.2 + - + +
458D SER* 1.3 79.2 + - - +
460D GLY* 1.3 59.5 + - - +
462D TYR* 3.4 0.6 - - - +
463D LEU* 2.8 38.0 + - + +
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Residues in contact with GLY 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D SER 4.8 0.4 + - - -
456D LEU 3.1 10.7 + - - -
457D GLU 3.2 4.0 + - - -
459D ALA* 1.3 76.3 - - - +
461D TYR* 1.3 51.3 + - - +
463D LEU* 3.4 1.9 + - - +
464D LYS* 2.8 34.4 + - - +
491D LYS* 3.6 35.1 - - - +
492D GLY* 4.2 3.6 - - - -
495D TYR* 4.1 7.3 - - - -
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Residues in contact with TYR 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420D ASN* 6.1 0.2 - - - -
423D LEU* 3.9 17.6 - - + +
457D GLU 3.2 10.8 + - - +
458D SER* 3.7 9.4 - - - +
460D GLY* 1.3 71.9 - - - +
462D TYR* 1.3 72.1 + - - +
464D LYS* 3.1 24.5 + - - +
465D MET* 2.9 55.8 + - + +
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Residues in contact with TYR 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D LEU* 4.5 4.3 - - - +
412D LEU* 3.7 20.2 - - + +
417D PHE 4.1 5.8 + - - -
418D PHE* 3.7 26.7 - + + -
419D ASN 4.3 2.9 - - - -
422D SER* 3.5 27.7 + - - -
423D LEU* 3.5 33.9 - - + +
426D HIS* 2.6 48.6 + + + +
458D SER 3.0 17.3 + - - +
459D ALA* 3.4 7.6 - - - +
461D TYR* 1.3 83.3 - - + +
463D LEU* 1.3 70.2 + - + +
465D MET 3.2 0.5 + - - -
466D VAL* 3.0 37.8 + - + +
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Residues in contact with LEU 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D LEU* 5.9 0.2 - - + -
426D HIS* 5.6 1.1 - - + -
448D VAL* 4.1 15.0 - - + -
449D ALA* 4.1 25.8 - - + -
452D PRO* 4.0 14.8 - - + -
454D SER* 3.7 29.6 - - - -
459D ALA* 2.8 27.3 + - + +
460D GLY 4.0 2.2 - - - +
462D TYR* 1.3 84.6 - - + +
464D LYS* 1.3 67.7 + - - +
466D VAL* 4.1 3.5 - - + +
467D ILE* 3.0 38.2 + - + +
481D PHE* 4.0 19.7 - - + -
492D GLY* 4.2 11.4 - - - -
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Residues in contact with LYS 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D GLY 2.8 16.0 + - - +
461D TYR* 3.2 27.2 - - - +
463D LEU* 1.3 76.5 - - - +
465D MET* 1.3 96.1 + - + +
467D ILE* 3.9 2.1 - - - +
468D ALA* 3.0 24.4 + - + +
495D TYR* 3.3 57.4 - - + +
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Residues in contact with MET 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 4.2 16.6 - - + -
427D MET* 4.7 8.2 - - + +
461D TYR* 2.9 51.6 + - + +
462D TYR 3.8 3.6 - - - +
464D LYS* 1.3 120.1 - - + +
466D VAL* 1.3 60.0 + - - +
468D ALA* 3.7 17.6 - - + +
469D HIS* 2.9 29.8 + - - +
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Residues in contact with VAL 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.5 18.6 - - + -
426D HIS* 3.6 43.5 - - + +
427D MET* 4.4 7.2 - - + +
430D MET* 3.8 13.0 - - + -
448D VAL* 3.7 23.3 - - + -
462D TYR* 3.0 23.9 + - + +
463D LEU* 4.1 5.8 - - + +
465D MET* 1.3 73.6 - - - +
467D ILE* 1.3 61.9 + - - +
469D HIS* 3.3 7.0 + - - +
470D THR* 2.9 28.5 + - - -
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Residues in contact with ILE 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D VAL* 3.9 19.1 - - + -
463D LEU* 3.0 25.1 + - + +
464D LYS* 3.9 3.6 - - - +
466D VAL* 1.3 76.6 - - - +
468D ALA* 1.3 57.3 + - - +
470D THR* 3.2 3.0 + - - -
471D LYS* 2.9 44.0 + - + +
479D VAL* 4.0 24.7 - - + +
480D THR 4.8 2.5 - - - -
481D PHE* 4.2 11.7 - - + -
492D GLY 4.8 0.2 - - - +
495D TYR* 3.6 33.4 - - + +
496D VAL* 4.0 28.5 - - + -
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Residues in contact with ALA 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D LYS* 3.0 19.7 + - + +
465D MET* 3.7 19.3 - - + +
467D ILE* 1.3 77.4 - - - +
469D HIS* 1.3 63.6 + - - +
471D LYS* 3.3 9.8 + - - +
472D SER* 3.0 24.1 + - - -
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Residues in contact with HIS 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D MET* 3.2 60.6 + - + +
430D MET* 5.0 3.1 - - + -
431D GLU* 2.8 35.6 + - - +
465D MET 2.9 18.9 + - - +
466D VAL* 3.5 5.6 - - - +
468D ALA* 1.3 76.8 - - - +
470D THR* 1.3 62.3 + - - +
472D SER* 2.7 26.9 + - - -
473D LEU* 3.1 29.4 + - + +
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Residues in contact with THR 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D MET* 3.3 43.6 - - + +
434D VAL* 4.4 6.5 - - + -
446D TRP* 3.7 27.8 - - + +
448D VAL* 3.8 4.2 - - - +
466D VAL 2.9 14.7 + - - -
467D ILE 3.2 7.2 + - - -
469D HIS* 1.3 75.5 - - - +
471D LYS* 1.3 64.7 + - - +
473D LEU* 2.9 23.1 + - - +
474D ASP* 3.2 11.7 + - - +
479D VAL* 3.8 14.6 - - + -
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Residues in contact with LYS 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D ILE* 2.9 36.0 + - + +
468D ALA* 3.7 8.5 - - - +
469D HIS 3.3 0.2 - - - -
470D THR* 1.3 76.0 - - - +
472D SER* 1.3 60.1 + - - +
474D ASP 3.2 24.1 + - - +
475D PRO* 4.0 4.7 - - - +
477D ARG 5.4 3.4 - - - +
479D VAL* 3.7 16.2 - - + -
495D TYR 4.2 8.1 + - - -
497D ASP* 2.7 42.2 + - - -
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Residues in contact with SER 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ALA 3.0 12.8 + - - -
469D HIS* 2.7 28.3 + - - -
471D LYS* 1.3 76.4 - - - +
473D LEU* 1.3 64.8 + - - +
474D ASP 3.5 0.2 - - - -
475D PRO* 5.5 1.4 - - - +
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Residues in contact with LEU 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D MET 4.6 0.4 - - - -
431D GLU* 3.3 55.0 - - + +
434D VAL* 4.3 23.1 - - + +
469D HIS* 3.3 29.4 - - + +
470D THR* 2.9 13.9 + - - +
472D SER* 1.3 83.5 - - - +
474D ASP* 1.3 59.5 + - - +
475D PRO* 4.2 5.7 - - - +
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Residues in contact with ASP 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D THR* 5.0 3.5 - - - +
434D VAL* 4.2 15.0 - - + -
438D LYS* 5.5 2.9 - - + -
446D TRP* 3.0 27.5 + - - +
470D THR 3.2 7.3 + - - +
471D LYS* 3.2 16.2 + - - +
473D LEU* 1.3 79.7 - - - +
475D PRO* 1.3 68.5 - - - +
476D SER* 2.5 29.6 + - - -
477D ARG* 2.8 40.0 + - - +
479D VAL* 6.0 0.2 - - - +
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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