Contacts of the helix formed by residues 440 - 449 (chain A) in PDB entry 1DGH
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 VAL 440 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.8 20.9 - - + -
438A ASP* 2.9 10.4 + - - +
439A ASN* 1.3 92.1 - - + +
441A THR* 1.3 68.7 + - - +
442A GLN 3.5 2.0 - - - -
443A VAL* 3.1 9.5 + - - +
444A ARG* 2.9 34.9 + - - +
484A GLU* 4.2 37.5 - - + +
485A VAL* 4.0 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A PHE* 4.1 18.8 - - + -
438A ASP* 2.7 37.6 + - - -
440A VAL* 1.3 73.3 - - - +
442A GLN* 1.3 64.3 + - + +
444A ARG* 3.2 33.2 + - - +
445A ALA* 3.2 12.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 3.4 16.0 - - + +
292A PHE* 4.6 1.6 - - - -
294A PHE* 3.8 33.7 - - + -
301A LYS* 3.3 21.8 - - + +
302A VAL* 2.8 58.2 + - - +
304A PRO* 4.7 8.5 - - - +
438A ASP* 4.5 1.4 + - - -
440A VAL 3.5 0.2 - - - -
441A THR* 1.3 77.5 - - + +
443A VAL* 1.3 62.1 + - + +
445A ALA* 3.3 4.9 + - - -
446A PHE* 3.1 14.7 + - - +
3000A NDP 3.0 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.8 10.1 - - + +
194A HIS* 3.6 37.0 - - + +
197A SER* 3.5 26.7 - - - +
439A ASN 3.4 26.5 - - - +
440A VAL* 3.1 10.3 + - - +
442A GLN* 1.3 76.7 - - + +
444A ARG* 1.3 58.8 + - - +
446A PHE* 3.1 6.6 + - + +
447A TYR* 2.9 26.7 + - - +
485A VAL* 3.8 23.1 - - + -
489A TYR* 4.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 2.9 18.0 + - - +
441A THR* 3.4 33.8 + - - +
443A VAL* 1.3 74.2 - - - +
445A ALA* 1.3 59.4 + - - +
447A TYR* 4.4 2.2 - - - +
448A VAL* 2.8 50.0 + - + +
484A GLU 3.2 16.2 + - - -
485A VAL* 2.8 46.1 + - - +
486A HIS* 4.5 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A THR* 3.2 10.1 + - + +
442A GLN* 3.6 11.7 - - - +
443A VAL 3.3 0.2 - - - -
444A ARG* 1.3 79.7 - - - +
446A PHE* 1.3 58.8 + - - +
448A VAL* 5.0 0.2 - - - -
449A ASN* 3.1 40.7 + - - +
450A VAL* 3.3 11.3 + - - +
3000A NDP 4.0 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A HIS* 4.6 0.7 - + - +
197A SER* 3.6 40.8 - - - -
198A PHE* 3.5 35.9 - + + -
201A SER* 4.4 0.9 - - - -
442A GLN 3.1 5.8 + - - +
443A VAL* 3.1 12.9 + - + +
445A ALA* 1.3 75.6 - - - +
447A TYR* 1.3 68.0 + - + +
450A VAL* 3.3 27.0 + - + +
451A LEU* 3.1 48.8 + - + +
459A LEU* 4.9 2.0 - - + -
3000A NDP 3.4 61.0 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL 2.9 15.2 + - - +
444A ARG* 3.8 6.3 - - - +
446A PHE* 1.3 85.5 - - + +
448A VAL* 1.3 64.7 + - + +
451A LEU* 3.8 10.0 - - + +
453A GLU* 5.1 0.5 + - - -
456A ARG* 2.8 66.9 + - + +
459A LEU* 4.2 11.0 - - + -
460A CYS* 4.4 7.7 - - - -
485A VAL* 4.8 0.9 - - + -
486A HIS* 4.1 31.4 - + + -
488A ASP* 3.2 27.6 + - - -
489A TYR* 3.7 58.4 - + + -
492A HIS* 5.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A ARG* 2.8 33.7 + - + +
445A ALA* 5.0 0.2 - - - -
447A TYR* 1.3 80.8 - - + +
449A ASN* 1.3 79.2 + - - +
451A LEU 3.5 0.7 - - - +
456A ARG* 2.8 28.0 + - - +
486A HIS* 3.9 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ALA* 3.1 26.5 + - - +
448A VAL* 1.3 96.4 + - - +
450A VAL* 1.3 68.6 + - + +
451A LEU 4.1 2.6 - - - +
3000A NDP 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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