Contacts of the helix formed by residues 73 - 88 (chain D) in PDB entry 2BKU
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 73 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 4.2 13.2 - - + +
71D SER* 3.2 4.4 + - - +
72D LYS* 1.3 78.3 - - - +
74D SER* 1.3 54.1 + - - +
75D VAL* 2.5 42.8 + - - +
76D LYS* 2.9 36.4 + - + +
77D THR* 2.6 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LYS 3.7 4.3 + - - -
73D ASP* 1.3 72.1 + - - +
75D VAL* 1.3 71.0 + - - +
77D THR* 3.6 10.2 - - - -
78D GLN* 3.4 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ASP* 2.5 18.2 + - - +
74D SER* 1.3 76.9 + - - +
76D LYS* 1.3 59.8 + - + +
78D GLN* 3.0 17.2 + - - +
79D GLN* 2.9 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C GLU* 3.3 37.9 + - - +
71C LYS* 6.1 1.8 - - - +
76C ARG* 4.8 5.5 - - - +
30D LYS* 6.1 1.2 - - - +
71D SER* 3.7 14.1 - - - +
73D ASP* 2.9 26.2 + - + +
75D VAL* 1.3 77.3 - - + +
77D THR* 1.3 51.9 + - - +
79D GLN* 3.7 21.6 - - - +
80D PHE* 2.7 66.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU 4.6 2.1 - - - +
70D VAL* 4.7 17.5 - - + +
71D SER* 3.1 26.0 + - - +
73D ASP 2.6 25.5 + - - -
74D SER* 3.6 11.1 - - - -
75D VAL 3.2 0.2 - - - -
76D LYS* 1.3 76.8 - - - +
78D GLN* 1.3 59.1 + - + +
80D PHE* 3.9 4.3 - - - +
81D ALA* 3.1 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D SER* 3.5 17.7 + - - +
75D VAL* 3.0 17.9 + - - +
77D THR* 1.3 75.2 - - + +
79D GLN* 1.3 66.8 + - + +
81D ALA* 3.3 6.4 + - - +
82D GLN* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D VAL* 2.9 29.5 + - + +
76D LYS* 3.5 33.9 - - - +
78D GLN* 1.3 77.9 - - + +
80D PHE* 1.3 64.3 + - + +
82D GLN* 3.3 6.8 + - - +
83D ARG* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LYS* 5.7 2.7 - - - -
37D PHE* 5.8 0.2 - - - -
67D ASN 3.2 24.9 - - - -
68D GLU* 3.5 34.2 - - - +
69D LEU* 3.3 25.8 - - - +
70D VAL 3.8 11.0 - - - -
71D SER* 4.1 10.8 - - - -
76D LYS* 2.7 54.1 + - + +
77D THR 3.9 2.0 - - - +
79D GLN* 1.3 76.2 - - + +
81D ALA* 1.3 66.4 + - - +
83D ARG* 3.4 28.3 + - - +
84D TRP* 3.1 24.4 + - - +
125D ILE* 4.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU 4.3 0.6 + - - -
77D THR* 3.1 19.9 + - + +
78D GLN* 3.6 8.1 - - - +
79D GLN 3.3 0.2 - - - -
80D PHE* 1.3 76.7 - - - +
82D GLN* 1.3 62.2 + - - +
84D TRP 3.5 0.2 + - - -
85D ILE* 3.2 31.8 + - + +
125D ILE* 3.6 35.5 - - + +
129D HIS* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D GLN 2.9 17.1 + - - +
79D GLN* 3.7 6.6 + - - +
81D ALA* 1.3 74.7 - - - +
83D ARG* 1.3 64.3 + - - +
85D ILE* 3.3 9.1 + - + +
86D THR* 2.7 56.4 + - + +
87D GLN* 4.7 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER 3.9 17.6 + - - -
34D ASN* 5.0 7.9 + - - +
37D PHE* 3.7 34.8 - - + -
68D GLU* 2.9 54.6 + - - +
79D GLN 2.9 17.3 + - - +
80D PHE* 3.4 25.1 + - - +
82D GLN* 1.3 80.1 - - - +
84D TRP* 1.3 55.3 + - - +
86D THR* 3.8 4.7 - - - -
87D GLN* 2.7 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 4.3 6.1 - + + -
41D ALA* 4.6 5.8 - - + -
65D LEU* 5.2 0.9 - - + -
69D LEU* 3.4 32.1 - - + -
80D PHE 3.1 13.9 + - - +
81D ALA 3.8 3.4 - - - +
83D ARG* 1.3 79.5 - - - +
85D ILE* 1.3 65.1 + - + +
86D THR 3.5 0.2 + - - -
88D VAL* 3.4 33.8 - - + +
93D LYS* 3.1 40.2 + - + +
96D ILE* 3.9 45.1 - - + -
97D LYS* 4.5 5.8 - - + -
122D ILE* 3.7 27.9 - - + +
125D ILE* 3.6 31.4 - - + -
126D GLU* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ALA* 3.2 24.2 + - + +
82D GLN* 3.8 8.3 - - + +
83D ARG 3.3 0.2 - - - -
84D TRP* 1.3 83.2 - - + +
86D THR* 1.3 69.7 + - + +
88D VAL 4.2 1.0 - - - +
93D LYS* 3.2 21.9 + - - +
125D ILE* 4.0 19.1 - - + +
126D GLU* 5.7 3.8 - - + -
129D HIS* 4.5 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLN* 2.7 42.9 + - + +
83D ARG 3.4 0.5 + - - -
85D ILE* 1.3 87.5 - - + +
87D GLN* 1.3 88.8 + - - +
88D VAL 4.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 4.6 15.0 - - + -
38D LEU* 3.9 19.2 - - + +
82D GLN* 4.7 4.4 - - - +
83D ARG* 2.7 44.9 + - + +
86D THR* 1.3 96.5 + - - +
88D VAL* 1.3 63.4 + - + +
89D SER* 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.9 24.0 - - + -
38D LEU* 3.7 9.6 - - + -
41D ALA* 4.7 6.3 - - + -
84D TRP* 3.4 40.5 + - + +
85D ILE 4.2 2.6 - - - +
86D THR 4.6 2.0 - - - +
87D GLN* 1.3 75.4 - - - +
89D SER* 1.3 61.7 + - - +
90D PRO* 3.8 1.2 - - - +
92D ALA* 3.8 10.5 - - + -
93D LYS* 2.8 61.7 + - + +
96D ILE* 4.3 8.1 - - + -
----------------------------------------------------------
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