Contacts of the helix formed by residues 129 - 154 (chain W) in PDB entry 4N3E
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 129 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93W ARG* 3.5 21.4 - - - +
95W ASN* 4.1 7.1 + - - +
127W THR 3.6 2.4 + - - -
128W VAL* 1.3 72.0 - - - +
130W GLU* 1.3 66.4 + - - +
131W GLU* 2.8 35.4 + - - +
132W GLU* 2.9 40.3 + - - +
133W VAL* 3.6 4.9 + - - +
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Residues in contact with GLU 130 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W TYR* 3.7 30.1 + - + +
128W VAL* 3.5 6.1 + - - +
129W ASN* 1.3 69.5 + - - +
131W GLU* 1.3 70.3 - - - +
133W VAL* 3.0 20.3 + - + +
134W LYS* 3.1 40.7 + - + +
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Residues in contact with GLU 131 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93W ARG* 3.4 22.4 + - - +
129W ASN* 2.8 29.9 + - - +
130W GLU* 1.3 77.2 - - - +
132W GLU* 1.3 57.4 + - - +
134W LYS* 3.1 20.2 + - - +
135W ILE* 3.3 26.8 + - + +
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Residues in contact with GLU 132 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W VAL 5.8 0.9 - - - +
92W LEU 4.8 4.5 - - - +
93W ARG* 2.7 42.8 + - - +
95W ASN* 3.3 8.8 + - - +
96W ILE* 2.6 43.5 - - + +
120W TYR* 3.4 24.4 + - + -
129W ASN* 2.9 40.9 + - - +
131W GLU* 1.3 71.5 - - - +
133W VAL* 1.3 63.4 + - + +
135W ILE* 4.1 12.1 - - + +
136W GLY* 3.5 9.7 + - - -
203W 2AN 4.3 7.3 - - + -
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Residues in contact with VAL 133 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4W TYR* 4.2 17.3 - - + -
6W ILE* 3.1 39.0 - - + -
120W TYR* 3.6 24.5 - - + -
128W VAL* 4.0 14.1 - - + -
129W ASN 3.8 12.8 - - - +
130W GLU* 3.0 15.4 + - + +
132W GLU* 1.3 77.8 - - - +
134W LYS* 1.3 66.9 + - + +
135W ILE 3.2 1.1 + - - -
136W GLY 3.4 0.5 + - - -
137W GLU* 2.9 31.9 + - + +
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Residues in contact with LYS 134 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130W GLU* 3.1 39.6 + - + +
131W GLU* 3.8 8.5 - - - +
133W VAL* 1.3 81.2 - - + +
135W ILE* 1.3 57.0 - - - +
137W GLU* 4.3 3.3 - - - +
138W LYS* 3.2 27.7 + - - +
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Residues in contact with ILE 135 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93W ARG* 3.8 26.7 - - - +
131W GLU* 3.3 28.4 + - + +
132W GLU* 4.2 10.5 - - + +
133W VAL 3.2 0.2 - - - -
134W LYS* 1.3 73.4 - - - +
136W GLY* 1.3 58.5 + - - +
137W GLU 3.1 4.3 - - - -
138W LYS* 3.5 5.0 + - - +
139W LYS* 2.9 50.8 + - + +
203W 2AN 3.5 21.3 - - + -
204W 2AN 5.9 0.9 - - - +
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Residues in contact with GLY 136 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101W TYR* 5.2 4.5 - - - -
120W TYR* 3.8 2.2 + - - -
132W GLU 3.5 4.0 + - - -
133W VAL 3.4 3.8 + - - -
135W ILE* 1.3 80.9 - - - +
137W GLU* 1.3 75.4 + - - +
139W LYS 4.1 1.8 - - - -
140W ALA* 3.7 19.1 - - - +
203W 2AN 3.3 38.4 + - - -
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Residues in contact with GLU 137 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6W ILE* 3.5 28.3 - - + -
8W LYS* 3.1 31.2 + - + +
101W TYR* 5.1 3.7 - - - -
118W VAL* 3.6 13.9 - - - +
120W TYR* 2.5 36.6 + - - -
133W VAL* 2.9 19.2 + - + +
134W LYS* 4.3 3.6 - - - +
135W ILE 3.1 0.4 - - - -
136W GLY* 1.3 84.0 - - - +
138W LYS* 1.3 65.0 + - - +
139W LYS 3.3 0.2 - - - -
140W ALA* 4.0 1.1 - - - +
141W TYR* 3.1 24.8 + - - +
202W 2AN 5.3 1.6 - - - -
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Residues in contact with LYS 138 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134W LYS 3.2 19.5 + - - +
135W ILE* 3.7 5.4 - - - +
137W GLU* 1.3 78.5 - - - +
139W LYS* 1.3 88.5 + - + +
141W TYR* 3.2 5.5 + - - +
142W GLU* 3.0 44.3 + - + +
204W 2AN 3.7 20.4 + - - -
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Residues in contact with LYS 139 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W GLN* 5.0 0.7 + - - -
135W ILE* 2.9 40.0 + - + +
138W LYS* 1.3 100.5 - - + +
140W ALA* 1.3 61.2 + - - +
142W GLU* 3.8 10.0 - - - +
143W PHE* 3.2 22.3 + - - +
203W 2AN 3.7 59.1 - - + +
204W 2AN 2.3 56.9 + - - -
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Residues in contact with ALA 140 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27W ARG* 3.5 12.8 + - - +
101W TYR* 5.6 2.0 - - + -
136W GLY 3.7 15.9 + - - +
137W GLU* 3.6 3.9 + - - +
138W LYS 3.3 0.4 - - - -
139W LYS* 1.3 79.4 - - - +
141W TYR* 1.3 57.7 + - - +
143W PHE* 3.7 5.2 + - - +
144W TYR* 3.2 26.0 + - - +
202W 2AN 3.6 23.6 + - + -
203W 2AN 3.5 28.9 - - - +
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Residues in contact with TYR 141 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W LYS* 5.7 4.7 - - + +
10W GLU* 4.0 24.7 + - + -
137W GLU 3.1 20.2 + - - +
138W LYS* 3.6 5.6 - - - +
140W ALA* 1.3 74.3 - - - +
142W GLU* 1.3 67.9 + - - +
143W PHE 3.3 0.2 - - - -
144W TYR* 3.3 35.0 + + - +
145W LYS* 3.1 50.0 + - + +
202W 2AN 4.0 17.2 + - - +
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Residues in contact with GLU 142 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W GLN* 3.9 17.0 + - - -
138W LYS* 3.0 39.5 + - + +
139W LYS* 3.8 9.9 - - - +
141W TYR* 1.3 80.3 - - - +
143W PHE* 1.3 63.4 + - - +
145W LYS* 3.0 17.7 + - - +
146W GLN* 3.1 26.1 + - + +
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Residues in contact with PHE 143 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22W ALA 4.6 2.2 - - - -
23W LEU* 3.7 21.8 - - + -
27W ARG* 4.0 31.9 - - + -
30W VAL* 3.7 14.4 - - + -
31W LEU* 3.7 51.6 - - + -
34W ALA* 4.0 12.8 - - + -
35W GLN* 4.3 6.9 - - - +
139W LYS 3.2 16.7 + - - +
140W ALA 3.9 3.8 - - - +
141W TYR 3.3 0.2 - - - -
142W GLU* 1.3 77.9 - - - +
144W TYR* 1.3 58.1 + - - +
146W GLN* 3.2 14.3 + - - +
147W VAL* 3.0 56.3 + - + +
203W 2AN 3.8 9.0 - + + -
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Residues in contact with TYR 144 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W GLU* 3.8 5.4 + - + -
11W GLU 3.6 10.9 + - - -
12W SER* 4.2 2.7 - - - -
19W LEU* 4.5 5.4 - - + -
23W LEU* 4.0 30.7 - - + -
140W ALA 3.2 10.7 + - - +
141W TYR* 3.5 31.4 - + - +
142W GLU 3.1 0.6 - - - -
143W PHE* 1.3 77.5 - - - +
145W LYS* 1.3 79.8 + - + +
147W VAL* 3.5 1.6 + - - +
148W GLU* 2.8 53.2 + - + +
202W 2AN 3.0 66.8 - + + +
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Residues in contact with LYS 145 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W GLU* 5.7 0.6 + - - -
141W TYR* 3.1 38.8 + - + +
142W GLU* 3.3 10.8 - - - +
144W TYR* 1.3 103.4 + - + +
146W GLN* 1.3 58.9 + - + +
148W GLU* 3.0 30.3 + - - +
149W GLU* 3.1 25.5 + - - +
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Residues in contact with GLN 146 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W ALA* 3.5 28.3 + - + +
35W GLN* 2.5 37.3 + - - +
37W HIS* 6.0 0.6 - - - -
142W GLU* 3.1 25.9 + - + +
143W PHE* 3.6 11.8 + - - +
145W LYS* 1.3 76.3 - - + +
147W VAL* 1.3 63.3 + - + +
149W GLU* 3.8 7.5 - - - +
150W TYR* 3.0 28.1 + - - +
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Residues in contact with VAL 147 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19W LEU* 5.2 1.3 - - + -
22W ALA* 3.8 29.6 - - + -
23W LEU* 4.3 9.9 - - + -
30W VAL* 4.0 15.3 - - + -
34W ALA* 4.3 8.5 - - + -
143W PHE* 3.0 44.7 + - + +
144W TYR 4.1 3.4 - - - +
146W GLN* 1.3 79.7 - - - +
148W GLU* 1.3 59.4 + - - +
150W TYR* 4.2 6.7 - - + -
151W LEU* 2.8 49.9 + - + +
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Residues in contact with GLU 148 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11W GLU 4.5 0.3 - - - +
12W SER* 2.5 30.6 + - - +
13W PRO* 3.5 17.2 - - + +
14W ILE* 3.9 15.1 - - + +
19W LEU* 5.2 3.5 - - + +
144W TYR* 2.8 44.1 + - + +
145W LYS* 3.0 31.9 + - - +
147W VAL* 1.3 77.7 - - - +
149W GLU* 1.3 60.7 + - - +
151W LEU* 5.0 0.9 - - - -
152W ALA* 3.1 25.4 + - + +
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Residues in contact with GLU 149 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145W LYS 3.1 17.2 + - - +
146W GLN* 3.8 7.7 - - - +
147W VAL 3.2 0.2 - - - -
148W GLU* 1.3 75.7 - - - +
150W TYR* 1.3 73.8 + - - +
152W ALA* 3.5 4.5 + - - +
153W ALA* 3.0 30.7 + - - +
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Residues in contact with TYR 150 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146W GLN 3.0 18.6 + - - +
147W VAL* 3.8 8.3 - - + +
149W GLU* 1.3 86.3 + - - +
151W LEU* 1.3 69.7 - - + +
153W ALA* 3.0 3.4 + - - -
154W ASN* 2.9 66.6 + - + +
157W VAL* 4.3 27.5 - - + +
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Residues in contact with LEU 151 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14W ILE* 3.7 31.2 - - + -
18W ARG* 2.9 57.6 + - + +
19W LEU* 4.2 7.9 - - + -
22W ALA* 4.2 1.8 - - + -
147W VAL* 2.8 41.9 + - + +
150W TYR* 1.3 87.2 - - + +
152W ALA* 1.3 61.0 + - - +
154W ASN 3.0 15.3 - - - +
155W PRO* 3.9 0.7 - - - +
157W VAL* 4.1 10.8 - - + +
158W PHE* 3.9 25.1 - - + -
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Residues in contact with ALA 152 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13W PRO* 6.1 4.7 - - + -
14W ILE* 3.4 17.1 - - + +
18W ARG* 4.7 1.3 - - - +
148W GLU* 3.1 21.0 + - + +
149W GLU* 3.8 5.4 - - - +
151W LEU* 1.3 75.9 - - - +
153W ALA* 1.3 56.9 + - - +
154W ASN 4.9 0.7 - - - -
155W PRO* 5.0 5.5 - - - +
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Residues in contact with ALA 153 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149W GLU* 3.0 28.0 + - - +
150W TYR* 3.0 7.3 + - - +
152W ALA* 1.3 76.7 - - - +
154W ASN* 1.3 71.1 + - - +
155W PRO* 3.9 7.0 - - - +
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Residues in contact with ASN 154 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W ARG* 2.6 29.8 + - - -
150W TYR* 2.9 54.7 + - + +
151W LEU* 3.0 4.0 - - - +
153W ALA* 1.3 89.0 + - - +
155W PRO* 1.4 58.4 - - - +
156W GLU* 3.2 16.0 + - - +
157W VAL* 3.4 18.1 + - + +
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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