Contacts of the helix formed by residues 441 - 448 (chain A) in PDB entry 6HBU
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 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A GLN 3.0 17.0 + - - -
438A CYS 3.0 12.1 + - - -
440A SER* 1.3 74.5 - - - +
442A VAL* 1.3 63.5 + - - +
443A SER 3.2 2.2 - - - -
444A ALA* 3.4 6.4 + - - +
482A ARG* 3.4 11.7 + - - +
517A ALA* 3.3 10.9 + - - +
520A ALA* 3.6 19.1 - - - +
521A SER* 3.1 22.0 + - - -
524A ALA* 3.3 21.8 - - - +
541A MET* 5.3 0.2 - - - -
545A PHE* 4.9 1.6 - - - -
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PHE* 3.4 18.6 - - + +
440A SER 3.2 1.2 - - - -
441A SER* 1.3 77.0 - - - +
443A SER* 1.3 59.7 + - - +
444A ALA 3.1 2.5 - - - -
445A VAL* 3.2 20.4 + - + +
446A GLU* 3.7 2.8 - - - +
538A THR* 3.7 31.2 - - + -
541A MET* 3.8 21.3 - - + -
542A THR* 4.0 22.4 - - + -
545A PHE* 3.7 24.2 - - + -
538B THR* 3.8 15.0 - - + +
542B THR* 4.4 7.4 - - + -
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLN* 4.6 0.2 + - - -
440A SER 3.3 5.8 + - - -
442A VAL* 1.3 77.8 - - - +
444A ALA* 1.3 55.5 + - - +
445A VAL 3.2 1.8 - - - -
446A GLU* 2.9 25.7 + - - +
447A LEU* 4.8 1.0 + - - +
477A ASP* 4.9 1.4 - - - +
481A MET* 4.2 8.0 - - - +
482A ARG* 2.5 31.9 + - - -
535B SER* 4.2 22.0 + - - -
538B THR* 4.4 5.4 - - - +
539B LEU* 3.7 30.1 - - - +
542B THR* 5.9 0.2 + - - -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A SER 3.6 10.5 - - - +
442A VAL 3.1 1.4 - - - -
443A SER* 1.3 74.1 - - - +
445A VAL* 1.3 63.0 + - - +
446A GLU 3.2 2.2 + - - -
447A LEU* 3.5 7.6 + - - +
477A ASP* 3.6 26.2 - - - +
482A ARG* 3.2 18.6 - - - +
521A SER* 4.1 13.5 - - - +
524A ALA* 3.9 10.7 - - + +
525A LEU* 3.3 25.1 - - + +
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A VAL* 3.2 19.6 + - + +
444A ALA* 1.3 77.9 - - - +
446A GLU* 1.3 58.8 + - - +
447A LEU 3.2 5.3 + - - -
448A PHE 4.2 1.7 + - - -
449A VAL* 3.3 17.3 - - - +
524A ALA* 3.8 30.1 - - + +
525A LEU* 5.5 0.3 - - - +
527A ILE* 6.2 0.2 - - + -
528A ALA* 3.4 19.7 - - + +
534A VAL* 3.7 20.2 - - + -
537A ALA* 3.7 29.4 - - + +
538A THR* 3.8 14.1 - - - +
541A MET* 4.3 8.7 - - + -
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Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A VAL 3.7 0.9 - - - +
443A SER* 2.9 36.0 + - - +
444A ALA 3.2 0.4 - - - -
445A VAL* 1.3 79.3 - - - +
447A LEU* 1.3 61.3 + - - +
448A PHE 3.5 0.9 - - - -
449A VAL* 4.1 3.4 - - - -
450A VAL* 3.3 33.5 + - + +
534A VAL* 3.7 22.6 - - + +
538A THR* 4.2 8.3 + - - -
534B VAL* 3.4 40.6 - - + +
535B SER* 4.3 16.1 - - - +
538B THR* 3.5 16.0 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A SER 4.8 0.4 + - - -
444A ALA* 3.5 16.8 + - - +
445A VAL 3.2 3.2 - - - -
446A GLU* 1.3 78.9 - - - +
448A PHE* 1.3 77.0 + - + +
450A VAL* 4.8 1.9 + - - +
451A GLU* 4.8 5.2 + - - +
473A LYS* 3.5 58.5 + - + +
474A LEU* 4.6 2.7 - - - +
476A SER* 5.3 2.9 - - - +
477A ASP* 3.7 33.0 - - + +
525A LEU* 3.8 24.2 - - + -
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A VAL 4.2 2.6 + - - +
447A LEU* 1.3 92.1 - - + +
449A VAL* 1.3 62.0 + - + +
451A GLU 4.3 4.0 - - - -
452A LYS* 3.8 20.1 + - - +
455A PHE* 5.9 0.9 - - - +
469A TYR* 4.3 19.7 + + + -
470A PHE* 3.5 46.7 - + - -
473A LYS* 3.5 30.1 - - + -
474A LEU* 5.1 1.6 - - + -
525A LEU* 3.8 28.2 - - + +
528A ALA* 4.5 3.6 - - + +
529A ALA* 4.1 25.4 - - + -
530A GLY 4.7 4.0 + - - +
531A GLN 4.7 1.2 - - - +
648A LEU* 3.8 27.7 - - + +
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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