Contacts of the helix formed by residues 89 - 111 (chain O) in PDB entry 1JJ2
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 ASN 89 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7920 G 5.5 5.1 + - - -
85O GLY 3.6 10.8 + - - +
86O ALA 5.0 1.4 + - - -
88O GLN* 1.3 71.3 - - - +
90O SER* 1.3 60.2 + - - +
91O LYS* 3.1 13.9 + - - +
92O GLU* 2.8 53.0 + - + +
93O ASP* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8150 U 4.6 6.5 + - - -
81060 MG 4.1 14.4 - - - -
85O GLY* 4.7 4.7 + - - -
88O GLN* 3.2 8.1 + - - -
89O ASN* 1.3 72.4 + - - +
91O LYS* 1.3 63.7 + - - +
93O ASP* 3.4 8.4 + - - +
94O TRP* 3.1 22.5 + - - +
97O ARG* 4.6 3.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 91 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8150 U 5.8 0.2 - - - -
8160 G 2.6 44.6 + - - +
8170 G 2.9 30.7 + - - +
15390 U 4.0 28.0 - - - +
15400 G 5.4 0.9 - - - +
15970 A 3.3 21.1 + - - -
89O ASN* 3.1 10.1 + - - +
90O SER* 1.3 78.6 + - - +
92O GLU* 1.3 68.1 + - - +
94O TRP* 3.2 7.7 + - - +
95O GLU* 3.0 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 5.6 3.4 - - - +
16400 C 4.7 10.3 + - - -
17970 A 5.5 4.5 - - - +
89O ASN* 2.8 35.8 + - + +
91O LYS* 1.3 78.4 - - - +
93O ASP* 1.3 62.0 + - - +
95O GLU* 3.3 21.6 + - - +
96O SER* 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17930 C 4.5 10.4 + - - +
17940 G 5.7 0.5 - - - +
17990 G 5.1 1.9 + - - -
88O GLN* 3.6 37.6 + - + +
89O ASN 2.9 15.2 + - - +
90O SER* 3.6 9.9 - - - +
92O GLU* 1.3 78.5 - - - +
94O TRP* 1.3 56.3 + - - +
96O SER* 3.1 11.1 + - - -
97O ARG* 2.9 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8140 G 4.1 16.6 - - - -
8150 U 3.5 48.3 + - - +
8160 G 4.0 4.5 - - - +
15970 A 3.1 36.6 + - - -
15980 A 3.4 15.7 - - - -
90O SER 3.1 14.9 + - - +
91O LYS* 3.2 9.4 + - - +
93O ASP* 1.3 73.2 - - - +
95O GLU* 1.3 64.4 + - - +
97O ARG* 3.8 29.1 - - - +
98O ILE* 2.8 63.7 + - + +
101O GLN* 6.1 1.3 - - - -
126O ALA 3.9 16.6 - - - -
127O GLY 4.0 13.0 - - - -
129O GLY* 4.4 7.0 - - - -
131O PHE 6.1 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 3.6 28.5 + - - +
15970 A 3.3 47.5 - - - +
91O LYS* 3.0 30.5 + - + +
92O GLU* 3.5 24.0 - - - +
94O TRP* 1.3 76.3 - - + +
96O SER* 1.3 66.4 + - - +
98O ILE* 4.4 0.7 - - - -
99O ARG* 3.0 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 96 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 3.2 36.0 + - - +
17950 G 4.9 3.0 + - - -
17960 A 3.9 12.1 + - - -
92O GLU 3.1 12.6 + - - -
93O ASP* 3.2 15.9 - - - -
95O GLU* 1.3 79.0 - - - +
97O ARG* 1.3 63.5 + - - +
99O ARG* 3.8 4.6 - - - +
100O ALA* 3.0 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8150 U 4.7 5.1 + - - -
17930 C 3.7 24.4 + - - +
17940 G 4.1 16.7 + - - +
90O SER* 4.6 3.4 + - - +
93O ASP* 2.9 42.5 + - - +
94O TRP* 3.8 40.3 - - + +
96O SER* 1.3 77.2 - - - +
98O ILE* 1.3 58.8 + - - +
100O ALA* 3.2 3.6 + - - +
101O GLN* 2.9 40.5 + - - +
131O PHE 5.5 3.8 + - - -
132O ASP* 3.6 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15970 A 3.8 34.1 - - - +
94O TRP* 2.8 59.9 + - + +
95O GLU 3.9 0.7 - - - +
97O ARG* 1.3 73.1 - - - +
99O ARG* 1.3 61.5 + - - +
101O GLN* 4.4 7.2 - - + +
102O ARG* 3.0 67.2 + - + +
126O ALA* 4.3 11.4 - - + +
127O GLY 4.4 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15400 G 3.0 35.6 + - - -
15410 G 3.0 23.4 + - - -
15970 A 2.7 55.8 + - - +
95O GLU* 3.0 37.9 + - - +
96O SER* 3.8 3.8 - - - +
98O ILE* 1.3 74.9 - - - +
100O ALA* 1.3 59.7 + - - +
102O ARG* 3.2 6.3 + - - +
103O THR* 2.9 36.5 + - - +
106O ARG* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 3.7 8.1 - - - +
17950 G 3.4 38.8 + - - +
96O SER 3.0 12.5 + - - +
97O ARG 3.5 8.7 - - - +
99O ARG* 1.3 78.2 - - - +
101O GLN* 1.3 61.3 - - - +
103O THR* 3.4 5.5 + - - -
104O LYS* 3.0 24.1 + - - +
134O VAL* 3.8 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 101 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17940 G 5.3 0.2 - - - +
94O TRP* 6.1 1.8 - - - -
97O ARG* 2.9 28.7 + - - +
98O ILE* 3.9 8.7 - - - +
100O ALA* 1.3 77.7 - - - +
102O ARG* 1.3 60.3 + - - +
104O LYS* 3.4 4.2 + - - +
105O LEU* 3.1 30.0 + - - +
126O ALA* 3.6 29.2 - - + +
131O PHE* 2.8 44.2 + - - +
132O ASP 3.8 2.2 + - - -
133O SER* 3.5 32.7 - - - +
134O VAL* 4.3 9.4 - - + +
137O LEU* 4.0 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15960 U 3.2 40.6 + - - -
15970 A 3.2 24.7 + - - -
15980 A 2.8 44.0 + - - -
98O ILE* 3.0 46.8 + - + +
99O ARG* 3.2 4.9 + - - +
101O GLN* 1.3 73.9 - - - +
103O THR* 1.3 61.5 + - - +
105O LEU* 3.5 8.7 + - + +
106O ARG* 2.9 44.0 + - - +
119O TYR* 5.0 2.8 + - - -
123O TYR* 3.6 35.1 + - + -
126O ALA* 5.6 2.2 - - + -
127O GLY* 4.2 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99O ARG* 2.9 19.7 + - - +
100O ALA* 3.8 6.5 - - - -
102O ARG* 1.3 74.1 - - - +
104O LYS* 1.3 66.4 + - - +
106O ARG* 3.0 30.0 + - - +
107O GLU* 2.9 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100O ALA 3.0 13.7 + - - +
101O GLN* 3.5 12.3 - - - +
103O THR* 1.3 76.6 - - - +
105O LEU* 1.3 64.1 + - - +
107O GLU* 3.0 30.7 + - + +
108O LEU* 3.1 38.6 + - + +
134O VAL* 4.0 19.7 - - + -
137O LEU* 4.3 13.5 - - + -
138O GLU* 3.4 38.2 + - + -
141O ILE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101O GLN 3.1 18.2 + - - +
102O ARG* 3.8 4.0 - - - +
104O LYS* 1.3 78.6 - - - +
106O ARG* 1.3 62.5 + - - +
108O LEU* 3.4 7.4 + - + +
109O ARG 3.1 17.8 + - - -
114O LEU* 4.3 8.5 - - + +
119O TYR* 3.5 25.4 - - + +
122O LEU* 3.7 31.4 - - + +
123O TYR* 3.4 46.0 - - + +
126O ALA* 4.6 7.9 - - + -
137O LEU* 3.4 25.8 - - + -
141O ILE* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15950 G 5.2 5.8 + - - -
15960 U 3.6 25.4 + - - -
99O ARG 5.1 0.2 + - - -
102O ARG* 2.9 35.0 + - - +
103O THR* 3.1 46.9 + - - +
105O LEU* 1.3 79.0 - - - +
107O GLU* 1.3 60.0 + - + +
109O ARG* 3.5 17.1 + - - +
110O ASP* 2.8 38.3 + - - +
119O TYR* 4.0 14.2 + - + +
123O TYR* 5.7 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103O THR* 2.9 31.9 + - + +
104O LYS* 3.0 22.6 + - + +
106O ARG* 1.3 76.4 - - + +
108O LEU* 1.3 61.6 + - + +
109O ARG 3.1 1.8 - - - -
110O ASP* 3.4 5.9 + - - +
111O GLU* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O LYS* 3.1 44.0 + - + +
105O LEU* 3.9 4.7 - - - +
107O GLU* 1.3 77.0 - - + +
109O ARG* 1.3 59.8 + - - +
111O GLU* 3.7 26.5 - - - +
112O GLY 3.3 1.2 + - - -
113O THR* 3.0 39.2 + - + -
114O LEU* 3.1 29.9 + - + -
138O GLU* 5.8 1.1 - - + -
141O ILE* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15940 C 2.8 37.6 + - - -
15950 G 3.2 26.5 + - - -
16070 A 5.6 3.2 + - - -
105O LEU 3.1 15.8 + - - +
106O ARG* 3.8 15.7 + - - +
107O GLU 3.1 1.0 - - - -
108O LEU* 1.3 76.5 - - - +
110O ASP* 1.3 80.9 + - - +
112O GLY* 3.1 12.8 + - - -
114O LEU* 3.8 21.0 - - + +
116O SER* 4.5 11.2 - - - +
119O TYR* 3.0 46.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106O ARG* 2.8 27.8 - - - +
107O GLU* 3.4 5.6 + - - +
109O ARG* 1.3 89.6 + - - +
111O GLU* 1.3 62.9 + - - +
112O GLY* 3.0 7.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107O GLU* 2.9 22.3 + - - +
108O LEU* 3.7 25.0 - - - +
110O ASP* 1.3 76.4 - - - +
112O GLY* 1.3 56.9 + - - +
113O THR* 2.7 24.8 + - - +
----------------------------------------------------------
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