Contacts of the helix formed by residues 443 - 454 (chain K) in PDB entry 3HX0
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 ILE 443 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403K ALA* 5.1 3.6 - - + +
406K PHE* 4.0 17.9 - - + -
407K ASN* 4.7 6.1 - - + +
410K LEU* 4.0 27.4 - - + -
432K ILE* 5.3 2.7 - - + -
439K SER 3.6 17.3 - - - +
440K HIS* 3.2 22.2 + - - +
441K ARG 4.2 1.6 - - - +
442K GLY* 1.3 79.6 - - - +
444K PHE* 1.3 70.8 + - - +
445K SER 3.1 2.9 + - - -
446K ARG* 3.2 27.6 + - - +
447K LEU* 2.8 42.1 + - + +
471K GLN* 5.2 0.2 + - - -
493K VAL* 5.0 9.9 - - + -
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Residues in contact with PHE 444 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440K HIS 4.7 0.2 + - - -
442K GLY* 3.8 0.6 - - - -
443K ILE* 1.3 79.3 - - - +
445K SER* 1.3 70.3 + - - +
447K LEU* 3.3 5.0 + - + +
448K LEU* 3.1 48.0 + - + +
463K SER 3.9 3.1 - - - -
464K GLN* 3.7 32.3 - - + -
471K GLN* 3.0 66.0 + - + +
472K LYS 3.3 22.4 - - - -
473K TYR* 3.7 20.0 - - + -
491K ILE* 4.3 7.9 - - + -
493K VAL* 4.1 20.1 - - + +
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Residues in contact with SER 445 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A HIS* 5.9 7.4 - - - -
442K GLY* 4.9 4.0 - - - -
443K ILE 3.3 1.4 - - - +
444K PHE* 1.3 85.1 - - - +
446K ARG* 1.3 68.3 + - - +
447K LEU 3.0 1.0 + - - -
448K LEU* 3.0 7.6 + - - +
449K ASP* 2.9 24.4 + - - +
464K GLN* 5.1 4.9 + - - -
471K GLN* 5.2 2.9 + - - -
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Residues in contact with ARG 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406K PHE* 3.4 63.5 + - + +
442K GLY 3.5 18.4 + - - +
443K ILE* 3.2 19.1 + - - +
445K SER* 1.3 83.1 - - - +
447K LEU* 1.3 56.6 + - - +
449K ASP* 4.0 7.3 - - - +
450K SER* 3.1 28.2 + - - -
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Residues in contact with LEU 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399K VAL* 3.9 10.5 - - + +
402K ALA* 3.7 16.6 - - + +
403K ALA* 3.5 36.1 - - + +
406K PHE* 4.3 6.0 - - + -
432K ILE* 3.5 32.3 - - + -
443K ILE* 2.8 28.3 + - + +
444K PHE* 3.5 5.4 - - + +
446K ARG* 1.3 74.8 - - - +
448K LEU* 1.3 61.4 + - + +
450K SER* 3.3 2.8 + - - -
451K LEU* 3.0 43.0 + - + +
491K ILE* 4.3 13.5 - - + -
493K VAL* 5.2 3.8 - - + -
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Residues in contact with LEU 448 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K PHE* 3.1 49.2 + - + +
445K SER* 3.0 7.9 + - - +
447K LEU* 1.3 76.5 - - + +
449K ASP* 1.3 68.1 + - - +
451K LEU* 3.3 1.7 + - + -
452K ARG* 2.8 42.6 + - - +
457K LEU* 3.8 14.8 - - + +
463K SER* 3.7 15.5 - - - +
473K TYR* 3.6 37.9 - - + -
491K ILE* 4.1 17.3 - - + -
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Residues in contact with ASP 449 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A HIS* 3.0 50.6 + - - +
291A LYS* 4.8 3.1 - - - +
445K SER 2.9 16.6 + - - +
446K ARG* 4.0 8.3 - - - +
448K LEU* 1.3 76.0 - - - +
450K SER* 1.3 59.9 + - - +
452K ARG* 3.3 16.6 + - - +
453K GLN* 2.9 48.5 + - - +
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Residues in contact with SER 450 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402K ALA* 4.3 10.0 + - - +
406K PHE* 4.0 19.9 - - - -
446K ARG 3.1 21.2 + - - -
447K LEU* 3.3 5.8 - - - -
448K LEU 3.1 0.2 - - - -
449K ASP* 1.3 78.1 + - - +
451K LEU* 1.3 64.4 + - - +
453K GLN* 3.0 17.7 + - - +
454K GLU* 3.2 25.3 + - - +
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Residues in contact with LEU 451 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398K THR* 4.3 13.9 - - + +
399K VAL* 4.0 13.9 - - + -
402K ALA* 3.5 27.6 - - + -
447K LEU* 3.0 27.3 + - + +
448K LEU* 5.0 0.7 - - - -
450K SER* 1.3 78.5 + - - +
452K ARG* 1.3 58.4 + - - +
454K GLU* 3.4 13.8 - - - +
456K PHE* 3.0 50.7 + - + +
457K LEU* 3.3 22.5 + - + -
491K ILE* 3.8 29.2 - - + -
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Residues in contact with ARG 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A HIS* 6.2 0.8 - - - +
448K LEU* 2.8 37.9 + - - +
449K ASP* 3.5 29.4 + - - +
451K LEU* 1.3 76.3 - - - +
453K GLN* 1.3 68.0 + - + +
455K GLY* 3.0 14.4 + - - -
457K LEU* 3.9 28.6 - - + +
460K ASP* 3.1 34.8 + - - +
463K SER* 4.5 8.7 + - - -
473K TYR* 4.7 2.0 - - - -
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Residues in contact with GLN 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A HIS* 3.0 45.8 + - + +
449K ASP* 2.9 40.1 + - - +
450K SER* 3.0 6.7 + - - +
452K ARG* 1.3 76.0 - - - +
454K GLU* 1.3 58.5 + - - +
455K GLY* 3.0 10.4 + - - -
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Residues in contact with GLU 454 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398K THR* 4.8 7.4 - - - +
402K ALA* 4.3 5.2 - - - +
450K SER* 3.2 29.1 + - - +
451K LEU* 3.4 29.8 - - - +
453K GLN* 1.3 75.8 - - - +
455K GLY* 1.3 60.0 + - - +
456K PHE* 3.3 10.2 + - + +
480K PRO* 6.1 1.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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