Contacts of the helix formed by residues 456 - 474 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415E PRO* 3.9 40.6 - - + -
418E PHE* 4.3 6.1 - - + -
453E ALA* 3.1 27.9 + - + +
454E SER 3.8 0.3 - - - +
455E HIS* 1.3 102.6 - - + +
457E GLU* 1.3 65.3 + - - +
458E SER* 3.8 17.7 - - - +
459E ALA* 3.0 14.6 + - - +
460E GLY 3.0 10.0 + - - -
491E LYS* 3.8 4.6 - - - +
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Residues in contact with GLU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E HIS 3.8 1.4 + - - +
456E LEU* 1.3 71.3 - - - +
458E SER* 1.3 62.0 + - - +
460E GLY* 3.3 2.1 + - - -
461E TYR* 3.2 21.3 + - - +
491E LYS* 3.6 37.9 + - - +
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Residues in contact with SER 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415E PRO* 4.9 3.3 + - - +
418E PHE* 3.7 27.7 - - - +
456E LEU* 3.8 15.6 - - - +
457E GLU* 1.3 78.8 - - - +
459E ALA* 1.3 57.4 + - - +
461E TYR* 3.3 8.5 + - - +
462E TYR* 3.0 28.7 + - - +
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Residues in contact with ALA 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E PHE* 3.7 31.6 - - + -
452E PRO* 5.5 0.2 - - + -
453E ALA 3.3 26.5 - - - +
454E SER* 3.8 10.3 - - - -
456E LEU* 3.0 9.5 + - + +
458E SER* 1.3 77.7 + - - +
460E GLY* 1.3 61.5 + - - +
462E TYR* 3.4 0.4 - - - +
463E LEU* 2.8 39.3 + - + +
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Residues in contact with GLY 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454E SER 4.7 0.4 + - - -
456E LEU 3.0 10.3 + - - -
457E GLU 3.3 2.4 + - - -
458E SER 3.3 0.4 - - - -
459E ALA* 1.3 76.3 - - - +
461E TYR* 1.3 56.3 + - - +
463E LEU* 3.9 1.7 - - - +
464E LYS* 3.0 28.8 + - - +
491E LYS* 3.6 36.7 - - - +
492E GLY* 4.2 2.9 - - - -
495E TYR* 3.9 8.3 - - - -
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Residues in contact with TYR 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E ASN* 5.7 2.3 + - - -
423E LEU* 3.8 16.8 - - + +
457E GLU 3.2 12.2 + - - +
458E SER* 3.8 9.2 - - - +
459E ALA 3.3 0.2 - - - -
460E GLY* 1.3 72.8 - - - +
462E TYR* 1.3 69.6 + - + +
464E LYS* 3.2 10.1 + - + +
465E MET* 3.1 72.0 + - + +
495E TYR* 6.0 0.2 - - - -
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Residues in contact with TYR 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E LEU* 4.3 5.9 - - - +
412E LEU* 3.9 21.6 - - + +
417E PHE 4.0 13.5 - - - -
418E PHE* 3.7 31.6 - + + -
419E ASN 4.3 2.5 - - - -
422E SER* 3.6 9.7 + - - -
423E LEU* 3.4 51.5 - - + +
426E HIS* 2.6 49.5 + + + +
458E SER 3.0 17.3 + - - +
459E ALA 3.4 4.0 - - - +
461E TYR* 1.3 81.3 - - + +
463E LEU* 1.3 71.4 + - + +
465E MET 3.3 2.1 + - - -
466E VAL* 3.1 24.7 + - + +
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Residues in contact with LEU 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E PHE* 5.5 0.4 - - + -
426E HIS* 5.6 0.7 - - + -
448E VAL* 4.2 14.6 - - + +
449E ALA* 4.1 26.0 - - + -
452E PRO* 4.0 19.3 - - + -
454E SER* 4.0 11.7 - - - -
459E ALA* 2.8 25.5 + - + +
460E GLY 4.0 2.0 - - - +
462E TYR* 1.3 86.0 - - + +
464E LYS* 1.3 67.2 + - - +
466E VAL* 3.3 3.7 + - + +
467E ILE* 2.9 40.1 + - + +
481E PHE* 3.9 30.5 - - + -
492E GLY* 4.2 12.8 - - - -
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Residues in contact with LYS 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E MRD 4.4 10.1 - - - +
460E GLY 3.0 14.0 + - - +
461E TYR* 3.2 16.1 + - + +
463E LEU* 1.3 75.7 - - - +
465E MET* 1.3 82.9 + - + +
467E ILE* 3.7 2.1 - - - +
468E ALA* 2.9 30.7 + - + +
495E TYR* 3.5 57.3 + - + +
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Residues in contact with MET 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 4.0 15.9 - - + -
427E MET* 4.8 8.7 - - - +
461E TYR* 3.1 56.8 + - + +
462E TYR 3.6 6.1 - - - +
463E LEU 3.2 0.2 - - - -
464E LYS* 1.3 122.4 - - + +
466E VAL* 1.3 59.6 + - - +
468E ALA* 3.3 8.7 + - + +
469E HIS* 2.9 30.9 + - - +
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Residues in contact with VAL 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 3.6 17.9 - - + -
426E HIS* 3.7 30.5 - - + +
427E MET* 4.4 7.4 - - + -
430E MET* 3.6 22.2 - - + +
448E VAL* 3.6 30.3 - - + -
462E TYR* 3.1 24.5 + - + +
463E LEU* 4.0 4.3 - - + +
465E MET* 1.3 74.2 - - - +
467E ILE* 1.3 57.6 + - - +
469E HIS* 3.4 6.3 + - - +
470E THR* 2.8 32.6 + - - -
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Residues in contact with ILE 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E VAL* 4.0 13.9 - - + -
463E LEU* 2.9 24.4 + - + +
464E LYS* 3.7 4.3 - - - +
466E VAL* 1.3 73.6 - - - +
468E ALA* 1.3 66.6 + - - +
470E THR* 3.2 3.5 + - - -
471E LYS* 3.0 34.7 + - + +
479E VAL* 3.9 36.1 - - + +
480E THR 5.0 0.4 - - - -
481E PHE* 4.5 10.5 - - + -
492E GLY 4.9 0.4 - - - +
495E TYR* 3.6 39.9 - - + +
496E VAL* 4.0 21.5 - - + -
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Residues in contact with ALA 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464E LYS* 2.9 21.2 + - + +
465E MET* 3.7 11.4 - - + +
467E ILE* 1.3 76.7 - - - +
469E HIS* 1.3 63.4 + - - +
471E LYS* 3.3 8.7 + - - +
472E SER* 3.0 22.3 + - - -
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Residues in contact with HIS 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E MET* 3.4 48.2 + - + +
430E MET* 5.0 2.5 - - + -
431E GLU* 2.7 38.9 + - + +
465E MET 2.9 17.8 + - - +
466E VAL 3.6 4.9 - - - +
467E ILE 3.2 0.2 - - - -
468E ALA* 1.3 76.4 - - - +
470E THR* 1.3 62.2 + - - +
472E SER* 2.6 31.6 + - - -
473E LEU* 3.2 22.5 - - + +
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Residues in contact with THR 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E MET* 3.5 35.1 - - + +
434E VAL* 4.4 4.7 - - + -
446E TRP* 3.6 33.4 - - + +
448E VAL* 3.6 6.8 - - - +
466E VAL 2.8 18.3 + - - -
467E ILE 3.2 8.3 + - - -
469E HIS* 1.3 75.6 - - - +
471E LYS* 1.3 62.1 + - - +
473E LEU* 3.0 22.5 + - - +
474E ASP* 3.0 12.3 + - - +
479E VAL* 3.8 15.7 - - + -
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Residues in contact with LYS 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E ILE* 3.0 28.8 + - + +
468E ALA* 3.8 10.1 - - - +
470E THR* 1.3 75.9 - - - +
472E SER* 1.3 61.4 + - - +
473E LEU 3.4 0.2 + - - -
474E ASP 3.5 23.9 + - - +
475E PRO* 3.9 6.7 - - + +
477E ARG 5.2 3.4 - - - +
479E VAL* 3.8 17.0 - - + -
495E TYR 4.9 3.4 + - - -
497E ASP* 2.7 41.8 + - - -
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Residues in contact with SER 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468E ALA 3.0 12.9 + - - -
469E HIS* 2.6 32.5 + - - -
471E LYS* 1.3 77.1 - - - +
473E LEU* 1.3 65.2 + - - +
475E PRO* 5.4 1.8 - - - +
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Residues in contact with LEU 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430E MET 4.1 6.7 - - - +
431E GLU* 3.6 49.8 - - + +
434E VAL* 4.1 23.1 - - + +
469E HIS* 3.2 27.6 - - + +
470E THR* 3.0 10.8 + - - +
472E SER* 1.3 86.8 - - - +
474E ASP* 1.3 59.0 - - - +
475E PRO* 4.2 4.2 - - - +
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Residues in contact with ASP 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434E VAL* 4.0 12.6 - - + -
438E LYS* 5.5 3.3 - - + +
446E TRP* 2.9 32.1 + - - +
470E THR 3.0 8.7 + - - +
471E LYS* 3.5 17.3 - - - +
472E SER 3.5 0.4 - - - -
473E LEU* 1.3 81.6 - - - +
475E PRO* 1.3 67.3 - - - +
476E SER* 2.7 27.3 + - - -
477E ARG* 3.0 37.6 + - - +
479E VAL* 5.8 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
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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