Contacts of the helix formed by residues 114 - 139 (chain B) in PDB entry 2QE9
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 ARG 114 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3B TYR* 4.9 7.1 - - - -
56B ILE* 4.8 10.5 - - + -
93B HIS* 3.3 40.3 + - + +
94B SER 4.3 0.2 - - - -
95B ASP* 3.0 50.3 + - - +
97B ILE* 3.3 23.4 + - - +
98B LYS* 3.6 13.0 + - - +
100B GLU* 2.8 52.1 + - + +
102B VAL* 4.1 10.6 - - + +
113B THR* 1.3 71.7 - - - +
115B ASP* 1.3 59.1 + - - +
117B ILE* 3.3 6.3 + - - +
118B LEU* 3.0 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY* 5.3 1.0 - - - -
3A LYS* 3.4 33.3 - - - +
-3B TYR* 2.6 36.8 + - - +
98B LYS* 3.0 40.0 + - + +
99B ASP* 4.5 1.3 - - - +
113B THR* 3.2 6.5 - - - +
114B ARG* 1.3 76.1 - - - +
116B GLU* 1.3 61.6 + - - +
118B LEU* 3.9 1.5 - - - +
119B HIS* 2.7 51.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 6.1 2.7 - - + -
148A PHE* 3.5 25.0 - - + -
149A ILE* 3.6 16.4 - - + -
111B LEU 4.7 0.3 - - - +
112B TYR* 3.5 17.7 - - - +
113B THR* 3.0 45.0 + - - +
115B ASP* 1.3 78.0 - - + +
117B ILE* 1.3 58.3 + - - +
119B HIS 3.4 1.2 + - - -
120B HIS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 4.6 3.4 - - + -
52B TRP* 3.7 55.4 - - + -
56B ILE* 3.8 20.9 - - + -
102B VAL* 3.5 42.8 - - + -
112B TYR* 3.9 14.6 - - + -
113B THR 3.0 16.6 + - - +
114B ARG 3.7 3.8 - - - +
116B GLU* 1.3 73.3 - - - +
118B LEU* 1.3 62.2 + - - +
120B HIS* 3.2 6.3 + - - +
121B ILE* 2.9 32.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-3B TYR* 4.1 19.5 - - + +
-2B PHE* 5.8 6.7 - - + -
1B MSE 3.5 29.6 - - + -
5B PHE* 4.1 13.4 - - + -
56B ILE* 4.1 18.2 - - + -
90B LEU* 3.6 31.9 - - + -
93B HIS 5.3 2.7 - - - +
114B ARG* 3.0 36.2 + - + +
115B ASP 3.9 2.0 - - - +
116B GLU 3.3 0.2 - - - -
117B ILE* 1.3 74.9 - - - +
119B HIS* 1.3 62.3 + - - +
121B ILE* 3.5 8.3 + - + +
122B ILE* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A GLY* 2.7 34.0 + - - -
3A LYS* 3.7 16.7 - - + +
4A PHE* 3.3 45.5 - + + -
148A PHE* 3.5 31.9 - + + +
1B MSE 3.8 12.2 - - + +
115B ASP* 2.7 54.1 + - - -
116B GLU 3.6 1.1 - - - +
118B LEU* 1.3 76.5 - - - +
120B HIS* 1.3 58.4 + - - +
122B ILE* 3.4 2.3 + - - +
123B ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 3.6 17.7 - - - -
148A PHE* 3.7 10.7 - - + +
149A ILE* 3.4 32.0 + - + +
202A EDO 3.0 38.4 + - - -
48B VAL* 4.9 2.2 - - + +
52B TRP* 3.8 36.0 + + - -
116B GLU 2.9 18.7 + - - +
117B ILE* 3.5 5.2 - - - +
119B HIS* 1.3 76.7 - - - +
121B ILE* 1.3 54.3 + - - +
123B ALA 3.3 1.2 + - - -
124B HIS* 2.8 46.3 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.4 31.2 - - + -
8B ASN* 4.6 1.2 + - - +
48B VAL* 5.8 2.0 - - + -
49B GLU* 4.0 24.9 - - + +
52B TRP* 3.8 35.4 - - + -
53B ILE* 4.0 28.5 - - + -
117B ILE* 2.9 30.5 + - + +
118B LEU* 3.7 7.4 - - + +
120B HIS* 1.3 73.6 - - - +
122B ILE* 1.3 66.7 + - - +
124B HIS* 3.4 7.5 + - - +
125B GLU* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.8 19.7 - - + -
126A ILE* 5.6 0.2 - - + -
1B MSE 3.6 32.8 - - + +
4B PHE* 3.5 44.9 - - + -
5B PHE* 3.8 19.7 - - + -
8B ASN* 3.4 22.7 + - - +
118B LEU 3.0 19.7 + - - +
119B HIS 3.7 3.6 - - - +
121B ILE* 1.3 82.8 - - - +
123B ALA* 1.3 63.5 + - - +
126B ILE* 3.4 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.9 2.9 - - + -
7A TYR* 3.8 34.8 - - + +
126A ILE* 3.7 21.2 - - + +
148A PHE* 4.8 2.7 - - + -
202A EDO 3.8 9.2 - - - +
119B HIS 3.0 17.5 + - - +
120B HIS* 3.8 3.4 - - - +
122B ILE* 1.3 76.6 - - - +
124B HIS* 1.3 57.4 + - - +
126B ILE* 3.4 0.9 + - - -
127B HIS* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A EDO 3.3 21.0 - - - -
44B HIS* 3.3 15.5 - + - -
45B ILE* 4.4 10.4 + - - +
48B VAL* 3.5 35.4 - - + +
120B HIS* 2.8 28.8 + - - +
121B ILE* 3.5 8.7 - - - +
122B ILE 3.3 0.4 - - - -
123B ALA* 1.3 72.9 - - - +
125B GLU* 1.3 64.6 + - - +
127B HIS* 3.5 1.4 + - - +
128B HIS* 3.1 36.2 + + - -
200B NI 2.1 44.1 - - + +
201B CIT 3.1 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN* 3.5 39.9 + - - +
12B ARG* 2.9 55.5 + - - +
45B ILE* 3.3 30.8 - - + +
49B GLU* 4.3 5.9 - - - +
121B ILE* 3.3 8.7 + - + +
123B ALA 3.4 0.2 - - - -
124B HIS* 1.3 78.2 + - - +
126B ILE* 1.3 59.8 + - - +
128B HIS* 3.3 1.6 + - - +
129B ILE* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 3.7 31.6 - - + +
126A ILE* 3.7 19.1 - - + -
127A HIS* 3.6 32.4 + - + +
4B PHE* 4.6 7.2 - - + -
7B TYR* 4.0 16.2 - - + +
8B ASN* 3.2 23.1 - - - +
122B ILE* 3.4 28.7 + - + +
123B ALA 3.4 2.9 + - - +
125B GLU* 1.3 75.9 - - - +
127B HIS* 1.3 57.4 + - - +
129B ILE* 3.8 6.5 - - + +
130B GLY* 2.9 26.7 + - - -
146B ALA* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 5.4 0.2 - - - +
126A ILE* 3.7 16.6 + - + +
129A ILE* 5.0 4.2 - - + +
130A GLY* 3.5 20.6 + - - -
133A SER* 3.7 28.7 - - - -
144A VAL 5.7 2.2 - - - -
146A ALA* 3.5 25.7 - - + +
202A EDO 4.3 5.2 - - - -
123B ALA 2.9 18.9 + - - +
124B HIS* 3.5 3.8 - - - +
125B GLU 3.2 0.2 - - - -
126B ILE* 1.3 75.6 - - - +
128B HIS* 1.3 74.9 + + - +
130B GLY 3.2 9.0 + - - -
131B GLN* 3.3 24.1 + - - +
201B CIT 3.6 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY* 4.7 2.9 - - - -
35B VAL* 4.3 9.1 + - + -
41B THR* 3.8 22.1 - - + +
44B HIS* 3.2 13.2 + + - -
45B ILE* 3.8 15.3 - - + -
124B HIS* 3.1 32.3 + + - +
127B HIS* 1.3 83.6 - + - +
129B ILE* 1.3 66.5 + - - +
131B GLN* 2.8 41.8 + - - +
132B LEU* 3.2 14.2 + - - +
200B NI 2.1 44.3 - - + +
201B CIT 2.8 14.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A HIS* 5.1 6.2 + - + +
11B VAL* 4.0 16.6 - - + -
12B ARG* 5.0 4.0 - - - -
15B TRP* 3.3 36.9 - - + +
42B LEU* 4.3 7.2 - - + -
45B ILE* 3.8 15.7 - - + -
125B GLU* 2.9 40.8 + - + +
126B ILE* 3.8 6.3 - - + +
128B HIS* 1.3 76.3 - - - +
130B GLY* 1.3 61.9 + - - +
132B LEU* 3.1 36.1 + - + +
133B SER* 3.3 10.9 + - - -
146B ALA* 5.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A HIS* 3.6 34.5 + - - -
130A GLY 4.0 6.7 - - - -
131A GLN* 3.4 10.0 - - - +
126B ILE 2.9 13.9 + - - -
127B HIS 3.2 5.9 + - - -
129B ILE* 1.3 76.9 - - - +
131B GLN* 1.3 59.4 + - - +
133B SER* 2.6 23.0 + - - -
134B VAL 3.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 3.3 17.3 - - - +
133A SER* 2.9 19.5 + - - +
134A VAL* 3.5 20.7 - - + +
33B GLY 4.8 0.2 - - - -
34B GLY* 3.3 34.8 - - - +
35B VAL 4.5 0.7 + - - -
41B THR* 4.7 4.3 + - - +
127B HIS* 3.3 27.2 + - - +
128B HIS* 2.8 34.0 + - - +
130B GLY* 1.3 74.7 - - - +
132B LEU* 1.3 63.3 + - - +
134B VAL* 3.1 15.6 + - - +
135B TRP* 3.4 22.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.8 32.3 - - + -
18B TRP* 5.3 0.9 - - + -
38B ILE* 4.1 19.5 - - + +
41B THR* 3.7 27.1 - - + -
42B LEU* 4.1 20.2 - - + -
128B HIS 3.2 11.2 + - - +
129B ILE* 3.1 34.1 + - + +
131B GLN* 1.3 76.6 - - - +
133B SER* 1.3 56.2 + - - +
135B TRP* 3.3 28.3 + - + +
136B ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 4.3 2.4 - - - -
34A GLY 5.0 0.5 + - - -
127A HIS* 3.8 14.4 - - - -
131A GLN* 2.9 26.2 + - - +
15B TRP* 3.8 14.3 - - - -
129B ILE 3.3 6.5 + - - -
130B GLY 2.6 20.3 + - - -
131B GLN 3.2 0.2 - - - -
132B LEU* 1.3 78.7 - - - +
134B VAL* 1.3 58.7 + - - +
136B ALA* 3.6 2.6 - - - +
137B ARG* 3.5 23.7 + - - +
143B PRO* 4.0 20.1 - - - +
144B VAL 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU 3.5 17.4 - - - +
33A GLY* 4.2 11.4 - - - -
131A GLN* 3.6 48.0 - - + +
134A VAL* 3.6 26.7 - - + -
135A TRP* 3.7 12.3 - - + +
130B GLY 4.0 2.7 - - - +
131B GLN 3.1 8.3 + - - +
133B SER* 1.3 75.4 + - - +
135B TRP* 1.3 66.7 + - - +
137B ARG* 3.1 6.4 + - - +
138B GLU* 3.0 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 3.7 15.7 - - + +
18B TRP* 5.3 0.2 - - - -
31B ARG* 3.6 30.4 - - + +
32B LEU 3.2 19.5 + - - -
33B GLY* 3.2 33.0 - - - -
35B VAL 4.9 1.3 - - - -
36B GLU* 3.7 20.0 - - - -
37B ASN 3.7 11.0 - - - -
38B ILE* 3.9 17.3 - - + -
41B THR* 3.4 26.2 - - + -
131B GLN* 3.4 13.6 + - + -
132B LEU* 3.3 34.2 + - + +
134B VAL* 1.3 76.6 - - - +
136B ALA* 1.3 57.3 + - - +
138B GLU* 3.3 24.2 + - - +
139B LEU* 3.0 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.0 3.1 - - + -
18B TRP* 3.5 32.3 - - + -
132B LEU 2.9 17.4 + - - +
133B SER 3.6 8.1 - - - +
134B VAL 3.2 0.2 - - - -
135B TRP* 1.3 75.9 - - - +
137B ARG* 1.3 59.2 + - - +
139B LEU* 3.2 10.0 + - - +
141B LEU* 2.9 33.5 + - - +
143B PRO* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.8 20.8 - - + +
33A GLY* 3.5 39.9 - - - +
34A GLY 4.9 0.9 - - - +
133B SER 3.5 6.7 + - - +
134B VAL 3.1 3.1 + - - +
136B ALA* 1.3 76.4 - - - +
138B GLU* 1.3 61.2 + - - +
140B LYS* 3.1 22.0 + - - +
141B LEU 3.6 9.8 + - - +
142B SER* 3.5 28.3 + - - +
143B PRO* 3.5 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.8 29.7 + - + +
135A TRP* 5.0 0.2 + - - -
138A GLU* 2.6 37.5 - - - +
31B ARG* 5.2 8.7 + - - +
134B VAL* 3.0 27.9 + - + +
135B TRP* 3.5 25.6 - - - +
137B ARG* 1.3 76.0 - - - +
139B LEU* 1.3 57.9 + - + +
140B LYS* 3.2 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 4.3 7.6 - - + -
22B LEU* 4.1 21.8 - - + -
26B GLU* 4.9 12.3 - - + +
29B LYS* 6.2 0.2 - - + -
31B ARG* 3.5 39.0 - - - +
38B ILE* 3.8 22.0 - - + -
135B TRP 3.0 19.8 + - - +
136B ALA 3.2 5.8 + - - +
138B GLU* 1.3 76.7 - - - +
140B LYS* 1.3 69.6 + - - +
141B LEU* 3.3 18.8 + - + +
----------------------------------------------------------
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