Contacts of the helix formed by residues 67 - 89 (chain E) in PDB entry 1B06
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 LEU 67 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C VAL* 5.0 2.9 - - + +
125C GLU* 3.9 26.0 - - + +
126C SER* 3.6 40.6 - - - +
129C SER* 4.3 9.4 - - - +
52E LEU* 4.8 8.1 - - + -
55E LEU* 3.8 29.2 - - + -
65E TYR* 3.6 14.0 - - + -
66E ASP* 1.3 71.2 - - - +
68E GLN* 1.3 58.9 - - - +
70E ILE* 2.9 13.3 + - + +
71E LEU* 2.8 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C SER* 3.0 48.4 + - - +
131C PRO* 3.8 20.9 - - + +
151C THR* 3.2 28.9 + - - +
153C GLU* 4.4 7.6 - - - +
158C ASN* 5.7 0.5 + - - -
69D GLY* 4.4 14.1 - - - +
72D ARG* 4.6 6.7 + - + -
66E ASP 3.1 1.4 + - - -
67E LEU* 1.3 77.4 - - - +
69E GLY* 1.3 57.2 + - - +
71E LEU* 4.2 6.6 - - - +
72E ARG* 3.0 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASP* 4.1 10.8 - - - -
68D GLN* 4.4 11.0 - - - +
69D GLY* 3.6 24.9 - - - -
48E LEU* 4.6 4.2 - - - +
66E ASP 2.7 18.3 + - - -
68E GLN* 1.3 75.2 - - - +
70E ILE* 1.3 59.0 + - - -
72E ARG* 4.8 0.8 - - - +
73E GLY* 3.3 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ASP* 3.6 30.7 - - - +
48E LEU* 4.0 32.8 - - + +
51E ARG* 4.2 19.7 - - + +
52E LEU* 4.3 15.7 - - + +
55E LEU* 4.2 18.8 - - + -
60E LEU* 5.2 0.7 - - + -
65E TYR* 4.1 20.0 - - + -
66E ASP 3.4 2.4 + - - +
67E LEU* 2.9 12.6 + - + +
69E GLY* 1.3 74.8 - - - +
71E LEU* 1.3 66.8 + - + +
73E GLY* 3.3 2.1 + - - -
74E LEU* 3.0 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C SER* 4.0 30.3 - - - +
129C SER* 4.3 0.9 - - - +
148C GLN* 4.7 1.6 - - - +
149C ILE* 3.9 25.4 - - + +
150C MET* 3.4 13.3 - - + +
151C THR* 4.0 31.9 - - + +
52E LEU* 5.2 9.2 - - + -
67E LEU* 2.8 37.2 + - + +
68E GLN* 4.2 11.0 - - - +
70E ILE* 1.3 73.8 - - + +
72E ARG* 1.3 61.3 + - - +
74E LEU* 3.0 26.9 + - + +
75E THR* 3.3 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C MET* 5.3 0.9 - - - -
153C GLU* 3.9 8.1 + - - -
158C ASN* 4.3 9.9 + - - +
68D GLN* 4.7 5.2 + - + -
72D ARG* 3.3 54.6 - - - +
68E GLN* 3.0 27.3 + - - +
69E GLY* 4.8 1.3 - - - +
71E LEU* 1.3 76.5 - - - +
73E GLY* 1.3 61.5 + - - +
75E THR* 3.4 10.7 + - - +
76E PHE* 3.3 22.2 + - - +
156E PHE* 3.6 35.7 - - + -
157E MET* 5.1 5.5 - - - +
131F PRO* 4.4 11.1 - - - +
153F GLU* 2.8 41.4 + - - -
157F MET* 5.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LEU* 3.4 15.7 - - - -
69E GLY 3.3 19.8 + - - -
70E ILE 3.7 1.6 - - - -
71E LEU 3.2 1.0 - - - -
72E ARG* 1.3 77.1 - - - +
74E LEU* 1.3 57.1 + - - +
76E PHE* 3.7 5.8 + - - +
77E ASN* 3.0 36.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLN* 3.7 24.7 - - - +
150C MET* 4.3 5.8 - - + -
45E ALA* 3.8 14.1 - - - +
48E LEU* 3.7 24.7 - - + -
49E LEU* 4.2 11.7 - - + +
52E LEU* 3.9 20.6 - - + -
70E ILE* 3.0 28.5 + - + +
71E LEU* 3.0 13.6 + - + +
73E GLY* 1.3 76.2 - - - +
75E THR* 1.3 59.9 + - - +
76E PHE 3.2 0.2 - - - -
77E ASN* 4.9 0.7 - - - -
78E ILE* 2.8 59.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C MET* 3.7 16.5 - - - +
158C ASN* 2.6 47.6 - - + +
159C HIS 3.8 0.7 - - - +
160C ILE* 4.1 9.0 - - + -
71E LEU 3.3 9.4 + - - -
72E ARG* 3.4 15.8 + - - +
74E LEU* 1.3 76.9 - - - +
76E PHE* 1.3 62.6 + - - +
78E ILE* 4.9 1.6 - - - -
79E ASN* 3.0 47.2 + - - +
156E PHE* 3.9 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 4.0 21.8 - + - -
72E ARG 3.3 14.8 + - - +
73E GLY* 3.7 5.6 - - - +
75E THR* 1.3 80.1 - - - +
77E ASN* 1.3 80.8 + - - +
80E GLY* 3.0 24.8 + - - -
154E ASN* 3.3 27.4 - - - -
155E HIS* 3.6 19.2 - + - +
156E PHE* 3.7 22.2 - + + -
172E PHE* 5.3 0.4 - + - -
131F PRO* 3.7 31.0 - - + -
132F GLY* 3.7 20.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLY 4.1 1.6 - - - +
41E TYR* 3.6 44.8 - - - +
44E GLY* 3.8 11.0 - - - -
45E ALA* 3.6 20.2 - - + +
48E LEU* 3.6 16.0 - - - +
73E GLY* 3.0 23.2 + - - +
74E LEU 4.3 0.4 - - - +
76E PHE* 1.3 93.3 - - - +
78E ILE* 1.3 61.2 + - - +
81E HIS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLN* 4.1 15.9 - - + +
160C ILE* 3.9 29.8 - - + -
163C LEU* 5.7 0.4 - - + -
9E TYR* 3.9 36.1 - - + +
45E ALA* 4.2 12.1 - - + -
49E LEU* 5.5 0.9 - - + -
74E LEU* 2.8 47.2 + - + +
75E THR 4.6 0.7 - - - +
77E ASN* 1.3 72.3 - - - +
79E ASN* 1.3 57.2 + - - +
81E HIS* 3.3 6.3 + - + +
82E LYS* 2.9 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C HIS 2.9 25.0 + - - -
160C ILE* 3.7 7.4 - - - +
161C ALA* 3.0 34.1 + - - +
75E THR* 3.0 35.7 + - - +
78E ILE* 1.3 74.4 - - - +
80E GLY* 1.3 65.3 + - - +
82E LYS* 4.5 4.2 - - - +
83E LEU* 2.9 31.2 + - + +
155E HIS* 3.3 27.1 - - + +
156E PHE* 3.5 7.3 - - - +
159E HIS* 3.7 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 3.8 13.9 - - - -
76E PHE 3.0 19.0 + - - -
77E ASN 3.6 2.5 - - - -
78E ILE 3.2 0.4 - - - -
79E ASN* 1.3 79.1 - - - +
81E HIS* 1.3 60.7 + - - +
83E LEU* 4.4 0.4 - - - +
84E HIS* 2.6 31.7 + - - -
155E HIS* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLU* 2.8 35.2 + - - -
9E TYR* 3.9 23.9 - + + +
10E GLU 3.8 19.4 + - - -
12E PRO* 3.9 15.3 - - + -
38E HIS* 3.0 31.0 + - - -
41E TYR* 3.8 5.7 - - + +
42E VAL* 3.6 21.8 - - + +
45E ALA* 5.9 1.6 - - + -
77E ASN 3.0 16.1 + - - +
78E ILE* 3.7 4.9 - - - +
80E GLY* 1.3 74.4 - - - +
82E LYS* 1.3 77.8 + - + +
84E HIS 3.2 2.4 + - - -
85E ALA* 3.0 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ASP* 2.8 34.8 + - - -
142C ASN* 5.2 2.2 - - - +
143C GLU* 2.8 37.7 + - - +
160C ILE* 4.2 16.8 - - + -
161C ALA* 4.5 13.5 - - + +
162C GLU* 6.1 2.0 - - - +
163C LEU* 4.4 7.2 - - + +
9E TYR* 4.4 1.8 - - - -
78E ILE* 2.9 39.2 + - + +
79E ASN* 4.1 5.4 - - - +
81E HIS* 1.3 81.8 - - + +
83E LEU* 1.3 66.3 + - + +
85E ALA* 3.4 6.7 + - - +
86E ILE* 3.2 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ALA* 4.0 24.0 - - + -
79E ASN* 2.9 27.3 + - - +
82E LYS* 1.3 72.8 - - + +
84E HIS* 1.3 61.0 + - - +
86E ILE* 3.4 15.2 + - + +
87E TYR* 3.0 26.9 + - - +
135E TRP* 3.6 50.6 - - + +
137E VAL* 5.7 0.9 - - + -
155E HIS* 3.6 24.0 - - + +
159E HIS* 3.9 13.9 - - + +
165E VAL* 4.9 4.9 - - + -
168E ILE* 4.0 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E HIS* 3.1 20.7 + + - -
38E HIS* 3.6 27.1 - + + +
41E TYR* 3.3 28.3 - + - -
80E GLY 2.6 25.9 + - - +
81E HIS 3.2 2.8 + - - +
83E LEU* 1.3 75.0 - - - +
85E ALA* 1.3 64.0 + - - +
87E TYR* 3.3 8.2 + + - +
88E TRP* 2.9 43.1 + + - +
135E TRP* 3.5 20.4 - + - -
155E HIS* 3.8 7.0 - + - -
170E ASP* 3.4 3.3 + - - -
174E HIS* 3.8 0.8 + - - -
326E FE 2.1 31.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PRO* 4.6 8.3 - - + -
38E HIS* 3.7 13.2 - - + -
81E HIS* 3.0 23.3 + - + +
82E LYS* 3.5 13.0 - - - +
84E HIS* 1.3 78.9 - - - +
86E ILE* 1.3 60.8 + - + +
88E TRP* 3.8 5.7 + - - +
89E ASN* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ALA* 6.0 0.4 - - + -
162C GLU* 3.6 26.2 - - - +
82E LYS* 3.2 19.6 + - + +
83E LEU* 3.8 14.1 - - + +
84E HIS 3.2 0.2 - - - -
85E ALA* 1.3 76.0 - - + +
87E TYR* 1.3 61.5 + - - +
89E ASN* 3.2 3.8 + - - +
90E ASN* 2.8 29.8 + - + +
165E VAL* 4.0 29.8 - - + -
168E ILE* 4.0 18.2 - - + -
203E ARG* 3.7 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ILE* 4.1 10.0 - - - +
30E ILE* 5.9 1.1 - - + +
33E HIS* 3.7 21.6 + + - -
83E LEU 3.0 19.0 + - - +
84E HIS* 3.3 10.7 + + - +
86E ILE* 1.3 76.9 - - - +
88E TRP* 1.3 99.6 + + - +
90E ASN* 3.2 10.9 + - - +
91E MET* 3.5 40.0 + - + +
135E TRP* 3.9 9.4 - + + -
168E ILE* 3.9 27.5 - - + +
169E VAL* 4.5 1.3 - - - -
170E ASP* 3.6 32.2 - - + +
175E ALA* 4.6 2.4 + - - +
187E TYR* 3.1 21.1 + - - -
191E TRP* 4.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PRO* 5.4 2.5 - - + -
13E GLN 5.7 1.8 - - - -
14E LEU* 3.7 21.5 - - + -
15E PRO* 3.8 20.6 - - + -
16E TYR* 2.7 40.1 + + - +
30E ILE* 4.2 22.0 - - + -
33E HIS* 3.6 36.1 - + + -
34E TYR* 3.9 30.1 - + + -
38E HIS* 2.9 31.4 + + - -
84E HIS* 2.9 32.9 + + - +
85E ALA* 4.1 6.3 - - - +
86E ILE 3.3 0.2 - - - -
87E TYR* 1.3 98.7 - + - +
89E ASN* 1.3 62.7 + - - +
91E MET* 3.4 7.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PRO* 3.3 25.0 - - - +
85E ALA* 3.0 21.6 + - - +
86E ILE* 3.2 6.9 + - - +
88E TRP* 1.3 73.4 - - - +
90E ASN* 1.3 56.3 + - - +
91E MET 3.1 10.2 + - - +
196E ASN* 3.4 10.2 + - - -
199E ASP* 3.1 35.8 - - - +
203E ARG* 4.1 9.9 - - - +
----------------------------------------------------------
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