Contacts of the helix formed by residues 56 - 74 (chain B) in PDB entry 4OL0
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 56 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ARG 3.5 1.3 - - - -
55B GLN* 1.3 101.3 + - - +
57B VAL* 1.3 62.8 + - - +
58B GLU* 4.0 13.2 - - + +
59B SER* 2.6 42.7 + - - -
60B CYS* 3.3 23.6 - - - -
100B LEU* 4.5 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.9 8.3 - - + -
56B ASP* 1.3 74.9 - - - +
58B GLU* 1.3 64.6 + - + +
60B CYS* 3.5 2.4 + - - +
61B TYR* 2.8 26.5 + - - +
100B LEU* 4.2 24.0 - - + +
101B SER* 3.7 30.1 - - - +
103B VAL* 4.5 7.9 - - + -
104B ILE* 3.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.7 7.9 - - + -
82A GLN* 2.7 27.4 - - - +
15B VAL* 4.5 7.3 - - + +
16B GLN* 5.3 2.1 - - - -
19B TYR* 3.4 31.4 - - + +
20B HIS* 3.0 32.4 + - - -
56B ASP* 3.3 12.1 - - + +
57B VAL* 1.3 81.7 - - + +
59B SER* 1.3 61.1 + - - +
61B TYR* 3.2 6.5 + - - +
62B PHE* 2.8 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.8 32.2 + - - -
15B VAL* 4.4 13.8 - - - +
50B LEU* 4.3 13.4 + - - +
53B ILE 5.4 0.2 + - - -
55B GLN* 3.7 11.4 + - - +
56B ASP* 2.6 30.0 + - - -
58B GLU* 1.3 75.3 - - - +
60B CYS* 1.3 66.8 + - - +
62B PHE* 3.4 3.3 + - - +
63B ALA* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU 4.2 5.2 - - - -
51B LEU* 3.7 5.1 - - - +
53B ILE 4.0 19.7 - - - -
54B ARG* 4.3 9.4 - - - -
56B ASP 3.3 18.8 + - - +
57B VAL 3.5 3.3 + - - +
58B GLU 3.2 0.2 - - - -
59B SER* 1.3 81.6 + - - +
61B TYR* 1.3 59.3 + - - +
63B ALA* 3.3 6.8 + - - +
64B ALA* 2.8 31.5 + - - +
97B LEU* 3.7 24.9 - - + -
100B LEU* 4.3 8.1 - - - -
104B ILE* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 2.7 35.0 + - - +
78A GLY* 4.1 6.5 - - - -
81A ILE* 3.6 32.1 - - + -
111A VAL* 3.1 35.2 - - + +
19B TYR* 3.9 17.5 - + - -
57B VAL 2.8 21.7 + - - +
58B GLU 3.6 4.0 - - - +
60B CYS* 1.3 72.6 - - - +
62B PHE* 1.3 59.3 + - - +
64B ALA* 3.8 2.9 - - - +
65B GLN* 2.8 35.8 + - + +
103B VAL* 3.9 26.7 - - + -
104B ILE* 3.9 10.1 - - + +
107B GLN* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.0 13.2 - - + -
78A GLY* 5.5 2.7 - - - -
11B VAL* 4.4 9.9 - - + -
15B VAL* 3.9 19.3 - - + -
18B LEU* 5.2 1.1 - - + -
19B TYR* 4.4 15.5 - + - +
34B LEU* 3.7 51.8 - - + -
37B LEU* 4.6 12.3 - - + -
38B GLN* 3.8 15.9 - - + -
46B ILE* 6.0 0.4 - - + -
47B SER* 6.5 0.2 - - - -
50B LEU* 4.3 13.2 - - + -
58B GLU 2.8 20.2 + - - +
59B SER* 3.7 4.3 - - - +
61B TYR* 1.3 79.0 - - - +
63B ALA* 1.3 53.3 + - - +
65B GLN* 3.8 7.5 - - - +
66B THR* 2.6 59.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER* 3.6 32.1 - - - +
50B LEU* 3.6 15.0 - - + -
51B LEU* 3.7 10.8 - - + +
59B SER 2.8 18.6 + - - +
60B CYS* 3.5 4.9 - - - +
62B PHE* 1.3 81.8 - - - +
64B ALA* 1.3 57.8 + - - +
66B THR* 3.1 4.6 + - - -
67B MET* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.0 5.8 - - + +
60B CYS 2.8 19.9 + - - +
61B TYR* 3.9 2.0 - - - +
63B ALA* 1.3 72.2 - - - +
65B GLN* 1.3 57.7 + - - +
67B MET* 3.2 8.3 + - - +
68B LYS* 2.9 30.5 + - - +
104B ILE* 4.1 9.4 - - + +
107B GLN* 3.6 22.8 - - + +
108B LEU* 3.8 28.3 - - + -
111B ALA* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.5 1.9 - - - +
76A ARG 4.0 5.7 - - - +
77A ASP* 3.8 24.5 + - + +
78A GLY* 3.8 25.4 - - - +
38B GLN* 3.2 21.3 + - - +
61B TYR* 2.8 24.7 + - + +
62B PHE* 3.8 8.7 - - - +
64B ALA* 1.3 76.4 - - - +
66B THR* 1.3 57.6 + - - +
68B LYS* 3.8 2.8 - - - +
69B MET* 2.8 60.4 + - - +
107B GLN* 3.4 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 5.4 0.4 - - + -
38B GLN* 3.1 36.2 + - + +
43B ALA* 4.0 24.5 - - + +
47B SER* 4.2 10.8 - - - +
62B PHE* 2.6 40.3 + - + -
63B ALA* 3.1 8.5 + - - -
65B GLN* 1.3 77.7 + - - +
67B MET* 1.3 55.3 + - - +
69B MET* 3.2 2.8 + - - +
70B LYS* 2.6 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.7 35.9 - - + +
47B SER* 3.0 29.4 - - - +
48B ASP* 4.7 4.5 - - - -
51B LEU* 4.0 18.4 - - + -
63B ALA 2.8 16.5 + - - +
64B ALA* 3.2 9.8 + - - +
66B THR* 1.3 72.6 - - - +
68B LYS* 1.3 64.3 + - - +
70B LYS* 3.0 4.4 + - - +
71B ILE* 2.9 35.5 + - + +
86B LEU* 3.5 32.3 - - + -
90B LEU* 4.0 12.1 - - + -
93B HIS* 6.3 0.7 - - - -
108B LEU* 5.5 1.6 - - + -
111B ALA* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 2.4 39.6 + - - +
64B ALA 2.9 20.1 + - - +
65B GLN* 3.8 7.8 - - - +
67B MET* 1.3 71.5 - - - +
69B MET* 1.3 76.6 + - - +
71B ILE* 3.1 18.5 - - - +
72B GLN* 3.3 27.7 - - - +
107B GLN* 3.3 27.8 + - - +
110B LEU* 3.4 38.4 - - + +
111B ALA* 3.7 14.2 - - + +
114B ASP* 3.7 15.2 - - - +
153B GLU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 4.9 4.0 - - - +
76A ARG* 3.7 38.4 - - + +
77A ASP* 4.5 6.7 - - - +
38B GLN* 3.8 21.5 - - + +
65B GLN* 2.8 41.7 + - - +
66B THR* 3.5 6.5 - - - +
68B LYS* 1.3 75.6 - - - +
70B LYS* 1.3 51.9 + - - +
72B GLN* 3.2 27.6 - - - +
73B THR* 2.7 57.4 + - + +
158B SER* 5.6 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 4.7 1.6 - - + -
39B ARG* 4.2 15.2 - - - +
40B SER 2.6 42.0 + - - +
41B VAL 3.9 3.6 - - - +
43B ALA* 3.4 39.4 - - + +
44B TRP* 3.6 35.9 - - + +
47B SER* 6.0 0.2 - - - +
66B THR* 2.6 24.3 + - + +
67B MET* 3.0 6.5 + - - +
69B MET* 1.3 72.6 - - - +
71B ILE* 1.3 56.9 + - - +
72B GLN 3.1 4.5 - - - -
73B THR* 3.9 7.6 - - + -
74B SER* 2.9 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TRP* 3.4 31.0 - - + -
67B MET* 2.9 20.5 + - + +
68B LYS 3.1 15.9 - - - +
70B LYS* 1.3 75.1 - - - +
72B GLN* 1.3 57.1 + - - +
74B SER 4.7 1.1 - - - -
75B PHE* 3.4 18.0 - - + +
86B LEU* 3.7 19.7 - - + -
90B LEU* 5.0 2.2 - - + -
111B ALA* 2.8 42.2 - - + +
114B ASP* 3.8 9.4 - - + -
115B LEU* 3.5 22.4 - - + +
118B GLN* 3.1 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LYS* 3.3 24.9 + - - +
69B MET* 3.2 41.4 - - - +
70B LYS 3.1 0.4 - - - -
71B ILE* 1.3 79.8 - - + +
73B THR* 1.3 59.4 + - - +
74B SER 3.4 1.6 - - - -
75B PHE* 5.0 1.8 + - - +
114B ASP* 3.0 27.3 - - + +
118B GLN* 4.5 8.8 + - - +
153B GLU* 4.3 2.8 - - - +
158B SER* 3.2 50.6 + - - +
159B LEU* 3.8 14.3 - - + +
160B ARG* 4.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 6.4 0.4 - - + -
39B ARG* 5.4 13.2 - - - +
69B MET* 2.7 45.1 + - + +
70B LYS* 3.9 11.7 - - + -
72B GLN* 1.3 73.7 - - - +
74B SER* 1.3 68.1 + - - +
75B PHE 4.2 0.2 - - - -
160B ARG* 5.7 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG* 6.5 1.6 - - - -
40B SER 5.6 0.9 - - - -
44B TRP* 3.4 15.9 - - - -
70B LYS* 2.9 44.5 + - - +
72B GLN 3.4 0.4 - - - -
73B THR* 1.3 85.8 - - - +
75B PHE* 1.3 61.7 + - - +
76B TYR* 3.5 11.2 - - - +
77B GLU* 3.7 26.6 - - - +
160B ARG* 6.3 0.7 - - - +
----------------------------------------------------------
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