Contacts of the helix formed by residues 54 - 65 (chain B) in PDB entry 1DGB
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 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.2 11.4 - - - +
42B ILE* 2.9 33.7 + - + +
50B LEU* 4.7 4.0 - - + -
51B LEU* 3.2 14.5 + - - +
52B VAL 3.0 4.3 + - - +
53B GLN* 1.3 74.0 - - - +
55B VAL* 1.3 58.9 + - - +
56B VAL 3.5 0.7 + - - -
57B PHE* 2.9 26.8 + - + +
58B THR* 3.3 19.9 + - - -
431D ARG* 2.7 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 5.9 3.1 - - + -
52B VAL 4.1 9.0 - - - +
53B GLN 2.7 20.3 + - - +
54B ASP* 1.3 70.0 - - - +
56B VAL* 1.3 67.0 + - + +
57B PHE 3.1 2.2 - - - -
58B THR* 4.2 8.3 - - - -
59B ASP* 2.6 40.0 + - + +
337C SER* 3.6 41.3 - - - +
355C LEU* 4.4 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 4.2 20.9 - - + -
34B PRO 5.8 0.9 - - - +
35B VAL* 3.9 35.9 - - + -
37B ASP 4.9 0.7 - - - +
38B LYS* 4.1 9.6 - - + -
54B ASP* 3.2 7.2 - - - +
55B VAL* 1.3 83.3 - - + +
57B PHE* 1.3 64.8 + - - +
59B ASP* 3.8 5.8 - - - +
60B GLU* 3.2 20.7 + - + +
420C GLU* 4.2 8.7 - - - +
159D ILE* 4.1 16.3 - - + +
431D ARG* 3.7 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 6.0 3.1 - - + -
41B VAL* 3.8 16.4 - - + -
50B LEU* 4.2 22.9 - - + -
51B LEU 6.0 0.7 - - - -
54B ASP* 2.9 31.6 + - + +
56B VAL* 1.3 80.0 - - - +
58B THR* 1.3 80.3 + - - +
60B GLU* 3.1 1.9 + - - +
61B MET* 2.9 55.0 + - + +
158D PRO* 3.4 33.0 - - + -
159D ILE* 3.7 26.9 - - + +
353D GLY* 3.9 17.0 - - - -
356D PHE* 4.6 11.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 6.0 2.3 - - - +
52B VAL* 4.5 7.3 + - - +
54B ASP 3.3 12.0 + - - -
55B VAL* 3.2 11.2 + - - -
57B PHE* 1.3 87.6 - - - +
59B ASP* 1.3 55.7 + - - +
61B MET* 4.5 3.6 - - - -
62B ALA* 2.7 37.6 + - - +
356C PHE* 5.1 13.0 - - + +
359C PRO* 6.2 0.9 - - + -
363C ARG* 4.7 13.7 - - - +
356D PHE* 3.8 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B THR* 3.5 11.3 - - + +
30B GLY* 2.9 33.7 + - - -
55B VAL* 2.6 24.0 + - + +
56B VAL* 3.8 6.5 - - - +
58B THR* 1.3 76.2 - - - +
60B GLU* 1.3 63.8 + - - +
62B ALA* 3.9 2.3 - - - +
63B HIS* 3.4 17.5 + - - +
363C ARG* 4.3 17.1 + - - +
371C LEU* 4.8 8.0 - - - +
387C GLN* 3.1 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.7 49.0 + - + +
56B VAL* 3.2 13.2 + - + +
57B PHE* 3.1 4.4 + - + +
59B ASP* 1.3 75.7 - - - +
61B MET* 1.3 68.2 + - - +
63B HIS* 3.2 6.2 + - - +
64B PHE* 2.9 18.9 + - - +
386C TYR* 4.1 19.2 + - - +
387C GLN* 3.6 27.2 - - + +
159D ILE* 3.3 16.5 - - - +
162D PRO* 4.3 20.1 - - + +
163D SER* 4.3 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PHE* 2.9 49.5 + - + +
58B THR 3.9 2.0 - - - +
60B GLU* 1.3 75.5 - - - +
62B ALA* 1.3 54.2 + - - +
64B PHE* 2.8 21.0 + - - +
65B ASP* 2.7 61.9 + - - +
158D PRO* 3.7 16.4 - - + +
159D ILE* 5.3 0.2 - - - -
162D PRO* 3.9 16.1 - - + +
356D PHE* 4.0 15.9 - - + -
357D ALA* 4.1 7.9 - - + -
1203D HEM 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR 2.7 23.2 + - - +
59B ASP 3.9 1.6 - - - +
61B MET* 1.3 73.2 - - - +
63B HIS* 1.3 61.9 + - - +
65B ASP 3.4 5.9 + - - -
66B ARG* 2.8 30.6 + - - +
363C ARG* 3.3 41.3 - - - +
356D PHE* 4.2 6.0 - - + -
360D ASP* 3.6 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP 3.4 5.4 + - - +
60B GLU 3.2 8.4 + - - +
61B MET 3.1 0.8 - - - -
62B ALA* 1.3 76.4 - - - +
64B PHE* 1.3 68.7 + - - +
66B ARG* 2.8 17.6 + - + +
67B GLU* 3.3 9.5 + - + +
363C ARG* 5.3 0.4 - - - +
368C PRO* 4.5 10.8 + - + +
369C ASN* 2.9 34.2 + - - -
372C HIS* 5.5 1.1 - - - -
387C GLN* 3.6 31.8 + - + +
388C ARG* 3.0 42.2 + - - -
389C ASP 3.2 11.4 + - - -
390C GLY* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU 2.9 13.0 + - - +
61B MET* 2.8 18.5 + - - +
63B HIS* 1.3 76.6 - - - +
65B ASP* 1.3 71.0 + - - +
66B ARG 2.9 5.9 + - - -
67B GLU* 3.2 40.2 + - - +
68B ARG* 5.8 0.4 - - - -
73D VAL* 3.5 41.1 - - + +
74D VAL* 4.2 3.1 - - + -
161D PHE* 3.8 21.1 - + - -
162D PRO* 3.6 39.7 - - + -
165D ILE* 3.7 38.6 - - + -
166D HIS* 4.3 3.6 - + - -
1203D HEM 4.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B MET* 2.7 33.6 + - - +
62B ALA 3.5 5.2 - - - +
63B HIS 3.1 0.2 - - - -
64B PHE* 1.3 85.3 - - - +
66B ARG* 1.3 59.4 + - - +
67B GLU 3.7 0.7 - - - -
68B ARG 5.5 0.2 + - - -
73D VAL* 5.0 6.5 - - - +
356D PHE* 3.8 1.6 - - - -
357D ALA* 3.5 31.9 - - - +
360D ASP* 2.6 30.3 - - - +
361D THR* 2.9 34.8 + - - -
364D HIS* 3.6 11.6 - - - -
1203D HEM 4.0 6.8 - - - +
----------------------------------------------------------
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