Contacts of the helix formed by residues 409 - 416 (chain D) in PDB entry 2HHW
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371D PHE* 3.4 19.2 - - - -
407D VAL* 3.7 0.7 - - - +
408D ASP* 1.3 86.2 - - - +
410D VAL* 1.3 64.0 + - - +
411D ALA* 3.9 5.8 - - - -
412D ALA* 2.8 30.9 + - - +
413D ALA 3.3 8.3 + - - -
424D PRO* 3.3 13.7 - - - +
425D ASP* 3.0 48.3 + - + +
426D GLU 4.7 0.9 + - - -
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Residues in contact with VAL 410 (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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371D PHE* 3.5 42.0 - - + -
394D LEU* 4.4 9.4 - - + +
409D ASP* 1.3 73.5 - - - +
411D ALA* 1.3 62.8 + - - +
413D ALA* 3.1 4.3 + - - +
414D ALA* 2.9 20.9 + - + +
422D VAL* 4.5 6.1 - - + -
425D ASP* 4.9 1.8 + - - -
450D LYS* 4.0 43.4 - - + +
453D ALA* 3.8 28.9 - - + -
454D ILE* 4.4 7.6 - - + -
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Residues in contact with ALA 411 (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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409D ASP* 3.2 3.4 + - - +
410D VAL* 1.3 78.9 - - - +
412D ALA* 1.3 62.5 + - - +
414D ALA* 3.2 1.9 + - - +
415D LYS* 2.9 26.9 + - - +
419D TYR 4.7 0.7 - - - +
422D VAL* 3.9 20.6 - - + +
423D ARG 3.7 9.4 + - - +
424D PRO* 3.6 42.8 - - + -
450D LYS* 5.7 0.4 - - - +
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Residues in contact with ALA 412 (chain D).
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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405D GLN* 5.6 2.3 - - - +
406D GLY 5.3 0.4 - - - +
407D VAL* 4.1 27.1 - - + +
408D ASP* 4.2 5.6 - - - +
409D ASP* 2.8 26.6 + - - +
411D ALA* 1.3 75.5 - - - +
413D ALA* 1.3 64.7 + - - +
415D LYS* 3.4 21.1 + - - +
416D MET* 3.7 9.7 + - - +
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Residues in contact with ALA 413 (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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371D PHE* 4.3 2.2 - - + -
394D LEU* 3.8 31.2 - - + -
398D ALA* 4.1 9.6 - - + -
407D VAL* 3.7 24.1 - - + +
409D ASP 3.3 4.4 + - - +
410D VAL 3.1 7.9 + - - +
412D ALA* 1.3 78.7 - - - +
414D ALA* 1.3 64.0 + - - +
416D MET* 3.0 25.9 + - - +
461D PHE* 3.4 10.4 - - + -
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Residues in contact with ALA 414 (chain D).
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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410D VAL 2.9 16.6 + - - +
411D ALA 3.6 4.0 - - - +
413D ALA* 1.3 76.8 - - - +
415D LYS* 1.3 64.0 + - - +
417D LYS* 2.9 13.2 + - - +
419D TYR* 3.0 45.1 + - + +
422D VAL* 4.2 10.1 - - + -
453D ALA* 4.8 1.1 - - + -
457D LEU* 3.6 28.9 - - + +
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Residues in contact with LYS 415 (chain D).
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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411D ALA 2.9 17.8 + - - +
412D ALA* 3.6 12.1 - - - +
413D ALA 3.2 0.4 - - - -
414D ALA* 1.3 76.8 - - - +
416D MET* 1.3 62.8 + - - +
417D LYS 3.2 0.7 + - - -
418D GLN* 3.2 21.5 + - - +
419D TYR 3.5 7.1 + - - +
420D GLU* 3.9 26.5 - - + +
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Residues in contact with MET 416 (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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398D ALA* 4.0 25.6 - - - +
401D LEU* 3.7 40.4 - - + -
402D ASP* 5.2 5.8 - - + +
405D GLN* 4.5 22.9 - - + +
407D VAL* 4.0 14.4 - - + -
412D ALA 4.0 6.7 - - - +
413D ALA 3.0 15.3 + - - +
415D LYS* 1.3 78.9 - - - +
417D LYS* 1.3 65.3 + - + +
418D GLN* 3.5 4.7 + - - +
461D PHE* 3.9 10.1 - - + -
464D GLU* 5.1 3.6 - - - +
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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