Contacts of the helix formed by residues 409 - 416 (chain A) in PDB entry 2HHT
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 ASP 409 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A PHE* 3.4 15.2 - - - -
407A VAL* 3.7 5.0 - - - +
408A ASP* 1.3 88.9 - - - +
410A VAL* 1.3 65.0 + - - +
411A ALA* 3.9 6.2 - - - +
412A ALA* 3.0 29.7 + - - +
413A ALA 3.3 8.5 + - - -
424A PRO* 3.1 15.1 - - - +
425A ASP* 3.1 48.2 + - + +
426A GLU 4.8 0.7 + - - -
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Residues in contact with VAL 410 (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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371A PHE* 3.6 39.2 - - + -
394A LEU* 4.4 10.3 - - + -
409A ASP* 1.3 73.7 - - - +
411A ALA* 1.3 57.3 + - - +
413A ALA* 3.2 3.7 + - - +
414A ALA* 2.8 27.1 + - + +
422A VAL* 4.5 4.9 - - + -
423A ARG 6.1 0.2 - - - +
425A ASP* 5.0 1.2 + - - -
450A LYS* 4.0 46.6 - - + +
453A ALA* 3.8 29.2 - - + -
454A ILE* 4.3 8.3 - - + -
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Residues in contact with ALA 411 (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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409A ASP* 3.2 4.3 - - - +
410A VAL* 1.3 79.3 - - - +
412A ALA* 1.3 57.0 + - - +
414A ALA* 3.4 1.9 + - - +
415A LYS* 3.0 29.2 + - - +
419A TYR 4.7 1.0 - - - +
420A GLU* 6.1 0.2 - - - +
422A VAL* 3.9 22.3 - - + +
423A ARG 3.7 9.0 + - - +
424A PRO* 3.6 41.1 - - + -
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Residues in contact with ALA 412 (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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405A GLN* 5.2 3.9 - - + +
406A GLY 5.3 0.7 - - - +
407A VAL* 4.1 26.2 - - + +
408A ASP* 4.4 2.5 - - - +
409A ASP* 3.0 24.5 + - - +
411A ALA* 1.3 75.5 - - - +
413A ALA* 1.3 64.3 + - - +
415A LYS* 3.5 17.6 + - - +
416A MET* 3.7 10.4 + - - +
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Residues in contact with ALA 413 (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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371A PHE* 4.3 2.0 - - + -
394A LEU* 3.9 29.8 - - + -
398A ALA* 4.1 10.5 - - + -
407A VAL* 3.7 25.0 - - + +
409A ASP 3.3 4.4 + - - +
410A VAL 3.2 7.0 + - - +
412A ALA* 1.3 77.8 - - - +
414A ALA* 1.3 64.9 + - - +
416A MET* 3.0 25.4 + - - +
461A PHE* 3.5 11.1 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A VAL 2.8 18.1 + - - +
411A ALA 3.8 3.8 - - - +
413A ALA* 1.3 76.0 - - - +
415A LYS* 1.3 62.9 + - - +
417A LYS* 3.1 8.8 + - - +
419A TYR* 3.0 49.3 + - + +
422A VAL* 4.3 8.7 - - + -
453A ALA* 4.7 1.6 - - + -
457A LEU* 3.4 29.5 - - + +
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Residues in contact with LYS 415 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A ALA 3.0 17.9 + - - +
412A ALA* 3.6 10.5 - - - +
413A ALA 3.2 0.4 - - - -
414A ALA* 1.3 77.9 - - - +
416A MET* 1.3 61.8 + - - +
418A GLN* 3.1 21.2 + - - +
419A TYR 3.6 8.3 + - - +
420A GLU* 4.0 31.0 - - + +
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Residues in contact with MET 416 (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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398A ALA* 4.0 28.5 - - - +
401A LEU* 4.0 34.8 - - + -
402A ASP* 4.5 14.1 - - + -
405A GLN* 4.5 16.6 - - + +
407A VAL* 4.1 11.9 - - - -
412A ALA 3.9 7.6 - - - +
413A ALA 3.0 17.6 + - - +
415A LYS* 1.3 79.3 - - - +
417A LYS* 1.3 65.7 + - + +
418A GLN* 3.5 8.2 + - - -
461A PHE* 4.1 9.4 - - + -
464A GLU* 5.5 2.0 - - - +
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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