Contacts of the helix formed by residues 85 - 109 (chain E) in PDB entry 3I6A
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 85 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLY 3.6 1.2 - - - -
84E LYS* 1.3 99.1 - - - +
86E ILE* 1.3 60.9 + - + +
87E LYS* 3.3 10.8 + - - +
88E GLU* 2.8 40.3 + - - +
89E ARG* 2.9 41.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
85E ASP* 1.3 73.6 - - + +
87E LYS* 1.3 67.7 + - + +
89E ARG* 3.4 22.0 + - - +
90E ALA* 3.0 26.9 + - - +
74F TYR* 3.5 38.3 - - + +
77F SER* 3.4 17.3 - - - +
78F LYS* 3.3 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ASP* 3.3 8.5 + - - +
86E ILE* 1.3 83.8 - - + +
88E GLU* 1.3 65.1 + - + +
90E ALA* 3.2 16.0 + - - +
91E LEU* 3.2 19.2 + - + +
61F ASP* 2.9 36.5 + - - -
62F GLY* 4.5 5.5 - - - -
63F MET* 4.0 23.3 - - + +
74F TYR* 4.3 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLY* 3.3 9.0 - - - -
84E LYS* 2.7 53.4 + - - +
85E ASP* 2.8 26.0 + - - +
87E LYS* 1.3 70.2 - - + +
89E ARG* 1.3 57.6 + - - +
91E LEU* 3.2 10.4 + - + +
92E ILE* 2.9 33.3 + - - +
149E VAL* 3.9 18.8 - - + +
150E GLY* 3.7 25.4 - - - +
152E LYS* 5.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 3.0 52.0 + - + +
83E GLY 5.5 1.0 + - - -
84E LYS 5.0 1.6 - - - -
85E ASP* 2.9 31.5 + - - +
86E ILE* 3.7 23.8 - - + +
88E GLU* 1.3 75.5 - - - +
90E ALA* 1.3 58.5 + - - +
92E ILE* 3.8 7.5 - - - +
93E ASP* 2.8 37.9 + - - +
77F SER* 3.0 30.5 + - - -
89F ARG* 6.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ILE 3.0 14.6 + - - +
87E LYS 3.2 8.9 + - - +
89E ARG* 1.3 76.5 - - - +
91E LEU* 1.3 57.1 + - - +
93E ASP* 3.9 5.7 - - - +
94E MET* 3.0 30.3 + - - +
63F MET* 3.9 12.1 - - - -
65F LEU* 3.9 27.0 - - + +
70F ALA* 3.9 7.8 - - - +
74F TYR* 3.9 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E LYS 3.2 14.2 + - - +
88E GLU* 3.5 10.3 - - + +
90E ALA* 1.3 73.5 - - - +
92E ILE* 1.3 61.0 + - - +
94E MET* 3.5 22.0 + - + +
95E TYR* 2.9 56.5 + - + +
148E LEU 5.9 0.2 - - - +
149E VAL* 3.9 25.1 - - + -
63F MET* 5.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 3.5 41.7 - - + +
83E GLY* 3.5 10.5 - - - +
88E GLU 2.9 21.6 + - - +
89E ARG* 3.8 4.7 - - - +
91E LEU* 1.3 76.6 - - - +
93E ASP* 1.3 58.4 + - - +
95E TYR* 3.3 5.0 + - - +
96E ILE* 2.9 38.8 + - + +
149E VAL* 4.0 19.1 - - + -
154E SER* 4.1 20.4 - - - +
155E ARG* 3.7 33.4 - - + -
156E ALA* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 5.2 0.2 - - - +
82E TYR* 2.6 30.6 + - - -
89E ARG* 2.8 27.8 + - - +
90E ALA* 3.9 2.1 - - - +
92E ILE* 1.3 70.6 - - - +
94E MET* 1.3 63.4 + - - +
96E ILE* 3.9 12.3 - - - +
97E GLU* 3.0 33.7 + - + +
69F ARG 4.9 0.2 - - - -
70F ALA* 3.5 23.0 - - + +
73F ASN* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ALA 3.0 13.7 + - - +
91E LEU* 3.7 25.4 - - + +
92E ILE 3.4 0.2 - - - -
93E ASP* 1.3 76.9 - - - +
95E TYR* 1.3 70.7 + - + +
98E GLY 3.3 7.3 + - - -
51F MET* 3.8 20.4 - - - +
52F PHE* 3.3 21.0 - - + -
64F LYS 4.0 10.8 - - - +
65F LEU* 3.8 22.2 - - + -
66F VAL* 3.5 54.3 - - + +
67F GLN* 3.8 4.5 - - - +
70F ALA* 3.4 8.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 2.9 47.2 + - + +
92E ILE* 3.7 4.0 - - - +
94E MET* 1.3 88.2 - - + +
96E ILE* 1.3 62.1 + - + +
98E GLY* 3.2 2.9 + - - -
99E ILE* 3.1 30.6 + - + +
136E PHE* 3.4 19.4 - + + -
139E VAL* 3.4 35.6 - - + +
148E LEU* 3.9 17.3 + - + -
149E VAL* 3.2 31.2 - - + -
156E ALA* 4.7 7.4 - - + -
51F MET* 3.5 35.0 - - + -
52F PHE* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASN* 5.2 0.7 - - - +
92E ILE* 2.9 26.7 + - + +
93E ASP* 3.6 18.8 - - - +
95E TYR* 1.3 75.9 - - - +
97E GLU* 1.3 67.0 + - + +
99E ILE* 3.2 14.0 + - + +
100E ALA* 2.7 33.7 + - - +
155E ARG* 3.4 41.5 - - - +
156E ALA* 3.7 31.2 - - + -
159E HIS* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 2.8 48.1 + - - +
93E ASP* 3.0 29.8 + - + +
96E ILE* 1.3 83.5 - - + +
98E GLY* 1.3 60.3 + - - +
100E ALA* 3.5 4.4 - - - +
101E ASP* 2.8 36.6 + - - +
67F GLN* 3.2 32.5 - - + +
69F ARG* 3.6 32.7 + - + +
70F ALA 4.6 1.1 - - - +
5106F GSH 5.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E MET 3.3 5.9 + - - -
95E TYR 3.2 8.5 + - - -
97E GLU* 1.3 80.1 - - - +
99E ILE* 1.3 59.9 + - - +
101E ASP* 3.3 2.4 + - - +
102E LEU* 3.1 18.9 + - - +
132E TYR* 3.5 22.1 - - - -
136E PHE* 4.6 0.7 - - - -
52F PHE* 3.6 23.8 - - - -
67F GLN* 3.5 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 3.1 18.6 + - + +
96E ILE* 3.2 15.9 + - + +
98E GLY* 1.3 74.2 - - - +
100E ALA* 1.3 54.5 + - - +
102E LEU* 3.3 4.3 + - - +
103E GLY* 2.7 33.1 + - - -
136E PHE* 3.5 24.2 - - + -
148E LEU* 5.5 0.9 - - + -
156E ALA 4.0 7.4 - - - +
159E HIS* 3.7 30.1 - - + +
160E LEU* 3.8 31.9 - - + +
163E LEU* 3.7 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 3.7 28.8 + - - +
96E ILE 2.7 20.1 + - - +
97E GLU* 3.5 11.7 - - - +
99E ILE* 1.3 69.8 - - - +
101E ASP* 1.3 65.9 + - - +
103E GLY* 3.9 1.7 - - - +
104E GLU* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 5.2 3.3 + - - -
97E GLU* 2.8 21.7 + - - +
98E GLY 3.3 7.4 + - - +
100E ALA* 1.3 75.5 - - - +
102E LEU* 1.3 65.0 + - - +
104E GLU* 3.3 12.1 + - - +
105E MET* 3.5 16.8 + - - +
132E TYR* 3.7 14.5 + - - +
54F GLN* 3.9 8.9 + - - +
67F GLN* 3.1 14.6 + - - +
5106F GSH 2.8 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E GLY 3.1 12.8 + - - +
99E ILE 3.6 6.7 - - - +
101E ASP* 1.3 75.4 - - - +
103E GLY* 1.3 63.6 + - - +
105E MET* 3.1 26.5 + - - +
106E ILE* 3.4 12.3 + - + +
124E ILE* 3.8 29.6 - - + +
127E LYS* 5.1 0.4 - - + -
128E ILE* 3.5 28.0 - - + -
132E TYR* 4.1 34.7 + - + -
133E PHE* 5.0 3.6 - - + -
163E LEU* 3.7 32.1 - - + -
167E VAL* 4.7 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ILE* 2.7 20.3 + - - -
100E ALA* 3.9 3.4 - - - -
102E LEU* 1.3 73.2 - - - +
104E GLU* 1.3 56.0 + - - +
106E ILE* 3.2 8.2 + - - +
107E ILE* 3.0 36.9 + - - +
163E LEU* 4.4 13.2 - - - +
166E TYR* 6.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 2.7 47.3 + - - -
100E ALA 3.0 19.3 + - - +
101E ASP* 3.6 7.4 - - - +
102E LEU 3.2 0.2 - - - -
103E GLY* 1.3 74.0 - - - +
105E MET* 1.3 65.7 + - - +
107E ILE* 4.5 7.6 - - - +
108E MET* 3.1 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ASP* 3.7 15.9 - - - +
102E LEU* 3.1 21.5 + - - +
104E GLU* 1.3 77.7 - - + +
106E ILE* 1.3 58.0 + - - +
108E MET* 4.9 1.1 - - - -
109E LEU* 3.2 26.2 + - - +
120E LYS* 3.6 20.4 + - + +
123E LEU* 4.4 6.1 - - + -
124E ILE* 3.3 48.2 - - + +
127E LYS* 3.5 41.1 - - + -
132E TYR* 5.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 3.4 12.3 + - + +
103E GLY* 3.2 9.6 + - - +
104E GLU 3.2 0.8 - - - -
105E MET* 1.3 75.0 - - - +
107E ILE* 1.3 68.4 + - + +
108E MET 3.2 1.8 - - - -
109E LEU* 3.2 8.6 + - + +
110E PRO* 3.2 20.8 - - - +
124E ILE* 4.5 12.8 - - + -
128E ILE* 5.3 0.4 - - + -
163E LEU* 4.1 26.2 - - + -
166E TYR* 4.2 32.3 - - + -
167E VAL* 4.8 8.5 - - + -
170E LEU* 4.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY* 3.4 42.4 - - - +
15E ARG* 4.3 35.0 - - + +
103E GLY 3.0 22.3 + - - +
104E GLU* 4.3 8.1 - - - +
105E MET 3.6 0.2 - - - -
106E ILE* 1.3 80.0 - - + +
108E MET* 1.3 61.5 + - - +
110E PRO* 3.6 9.7 - - - +
111E PHE* 3.7 19.0 - - + -
166E TYR* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 3.9 21.8 - - - -
104E GLU* 3.1 31.2 + - + +
105E MET* 4.1 1.1 - - - +
106E ILE 3.2 0.4 - - - -
107E ILE* 1.3 83.6 - - + +
109E LEU* 1.3 65.8 + - - +
110E PRO 3.4 1.1 - - - -
111E PHE* 2.9 32.6 + - + +
112E CYS* 3.5 9.8 - - - -
120E LYS* 3.5 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E MET 3.2 11.4 + - - +
106E ILE* 3.2 11.0 + - + +
108E MET* 1.3 75.9 - - - +
110E PRO* 1.4 69.0 - - + +
111E PHE 3.2 0.9 + - - -
112E CYS* 3.3 11.0 + - - +
117E LYS* 3.3 44.9 - - + +
120E LYS* 3.3 35.7 - - + +
121E LEU* 4.3 21.3 - - + +
124E ILE* 3.9 19.1 - - + -
170E LEU* 4.5 9.2 - - + -
----------------------------------------------------------
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