Contacts of the helix formed by residues 131 - 154 (chain B) 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 GLU 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN* 4.1 3.1 - - - +
130B GLU* 1.3 88.0 - - + +
132B GLU* 1.3 57.1 + - - +
133B VAL* 2.9 11.6 - - - +
134B LYS* 3.9 22.0 - - + +
135B ILE* 2.9 38.1 + - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL 3.4 14.7 - - - +
92B LEU* 4.0 5.6 - - - +
93B ARG* 4.5 12.3 + - - +
95B ASN* 5.1 0.2 - - - +
96B ILE* 3.2 35.2 - - + +
99B VAL* 5.6 0.7 - - - -
120B TYR* 3.2 42.7 + - + +
129B ASN* 2.7 27.2 + - - +
130B GLU 3.1 4.6 - - - -
131B GLU* 1.3 76.3 - - - +
133B VAL* 1.3 64.6 + - - +
135B ILE* 4.5 7.2 - - + -
136B GLY 3.4 5.9 + - - -
201B 2AN 3.3 25.3 - - + -
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 6.2 0.2 - - - -
2A ALA* 4.5 13.0 - - + +
4B TYR* 4.0 42.2 - - + +
6B ILE* 3.9 27.6 - - + +
120B TYR* 4.7 17.6 + - + -
128B VAL* 5.2 2.5 - - + -
129B ASN 5.2 0.9 - - - +
130B GLU* 5.1 5.2 - - + -
131B GLU 2.9 9.1 - - - +
132B GLU* 1.3 79.7 - - - +
134B LYS* 1.3 71.9 + - + +
135B ILE 3.3 0.2 + - - -
137B GLU* 2.9 27.7 + - + +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLU* 6.0 2.5 - - + -
131B GLU* 3.9 18.6 - - + +
133B VAL* 1.3 82.2 - - + +
135B ILE* 1.3 66.9 + - - +
137B GLU* 3.7 9.7 - - - +
138B LYS* 2.8 44.8 + - + +
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ARG* 5.1 15.7 - - - +
131B GLU* 2.9 29.2 + - + +
132B GLU* 4.5 5.8 - - + -
133B VAL 3.3 0.8 - - - -
134B LYS* 1.3 80.5 - - + +
136B GLY* 1.3 61.7 + - - +
138B LYS* 3.2 11.0 + - - +
139B LYS* 3.0 47.1 + - + +
201B 2AN 4.9 9.2 - - + -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.6 22.0 - - - -
132B GLU 3.4 5.8 + - - -
133B VAL 3.4 2.4 + - - -
135B ILE* 1.3 75.4 - - - +
137B GLU* 1.3 66.7 - - - +
139B LYS 3.4 0.5 + - - -
140B ALA* 3.3 23.4 + - - +
201B 2AN 3.8 26.6 + - - -
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.0 32.0 - - + +
8B LYS* 4.4 21.0 + - + +
120B TYR* 4.7 1.2 + - - -
133B VAL* 2.9 20.5 + - + +
134B LYS* 3.7 8.6 - - - +
136B GLY* 1.3 76.2 - - - +
138B LYS* 1.3 61.8 - - + +
140B ALA* 3.7 3.1 + - - +
141B TYR* 3.1 33.0 + - + +
202B 2AN 4.8 1.4 + - - -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 2.8 39.4 + - + +
135B ILE* 3.2 10.1 + - - +
137B GLU* 1.3 82.8 - - + +
139B LYS* 1.3 62.5 + - + +
141B TYR* 3.9 4.7 - - + +
142B GLU* 3.1 32.2 + - + +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 4.8 3.2 + - - +
38B VAL* 6.1 3.2 - - - +
63B HIS* 5.5 7.5 + - - -
135B ILE* 3.0 33.0 + - + +
136B GLY* 3.9 5.2 - - - +
137B GLU 3.2 0.4 - - - -
138B LYS* 1.3 75.7 - - + +
140B ALA* 1.3 67.0 - - - +
142B GLU* 3.9 16.4 + - - +
143B PHE* 3.3 24.4 + - - +
201B 2AN 3.9 59.3 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 3.8 12.7 + - - +
101B TYR* 5.8 5.2 - - + -
136B GLY 3.3 10.3 + - - +
137B GLU* 4.1 2.9 - - - +
139B LYS* 1.3 78.8 - - - +
141B TYR* 1.3 61.3 + - - +
143B PHE* 3.5 4.7 + - - +
144B TYR* 3.2 23.7 + - - +
201B 2AN 3.6 29.3 + - - +
202B 2AN 3.9 23.3 + - + -
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS* 5.5 4.5 - - + -
10B GLU* 3.8 29.3 + - + -
137B GLU* 3.1 24.9 + - + +
138B LYS* 4.0 6.3 - - + +
139B LYS 3.1 0.6 - - - -
140B ALA* 1.3 75.2 - - - +
142B GLU* 1.3 67.5 + - - +
143B PHE 3.3 0.3 + - - -
144B TYR* 3.3 21.4 + + - +
145B LYS* 3.0 54.7 + - + +
202B 2AN 3.4 23.3 + - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 4.8 11.6 + - - +
138B LYS* 3.1 22.9 + - + +
139B LYS* 3.9 18.6 + - - +
141B TYR* 1.3 77.4 - - - +
143B PHE* 1.3 56.9 + - - +
145B LYS* 3.1 9.9 + - - +
146B GLN* 3.0 38.9 + - + +
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Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA 4.6 0.2 - - - -
23B LEU* 3.6 19.7 - - + -
27B ARG* 3.7 37.0 - - + -
30B VAL* 3.9 10.5 - - + -
31B LEU* 3.9 51.4 - - + -
34B ALA* 3.9 14.4 - - + -
35B GLN* 4.1 10.5 - - - +
139B LYS 3.3 16.0 + - - +
140B ALA 3.7 2.0 - - - +
141B TYR 3.2 0.6 - - - -
142B GLU* 1.3 76.3 - - - +
144B TYR* 1.3 57.6 + - + +
146B GLN* 3.6 10.4 + - - +
147B VAL* 2.8 64.5 + - + +
201B 2AN 4.4 4.5 - + + -
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 3.8 14.9 + - + +
11B GLU 3.6 13.2 + - - -
12B SER* 4.2 2.0 - - - -
19B LEU* 4.4 5.8 - - + -
23B LEU* 4.0 30.1 - - + -
27B ARG* 6.2 0.2 - - - +
140B ALA 3.2 7.7 + - - +
141B TYR* 3.4 22.2 - + - +
143B PHE* 1.3 79.9 - - - +
145B LYS* 1.3 79.1 + - + +
147B VAL* 4.0 0.7 - - - +
148B GLU* 2.9 52.0 + - + +
202B 2AN 2.9 66.3 - + + +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 5.3 2.2 + - - -
141B TYR* 3.0 46.5 + - + +
142B GLU* 3.1 9.4 + - - +
144B TYR* 1.3 104.2 + - + +
146B GLN* 1.3 60.4 + - - +
148B GLU* 3.3 24.8 + - - +
149B GLU* 3.2 25.1 + - - +
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ALA* 3.5 29.8 + - + +
35B GLN* 2.7 38.8 + - - +
37B HIS* 5.5 4.0 - - - -
142B GLU* 3.0 25.1 + - + +
143B PHE* 3.6 11.1 - - - +
145B LYS* 1.3 76.2 - - - +
147B VAL* 1.3 61.1 + - - +
149B GLU* 3.7 8.3 + - - +
150B TYR* 3.3 20.8 + - - +
205B 2AN 4.6 4.8 - - + -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 5.2 2.9 - - + -
22B ALA* 3.8 21.3 - - + -
23B LEU* 4.0 10.8 - - + -
30B VAL* 3.8 11.9 - - + -
34B ALA* 4.7 3.4 - - + -
143B PHE* 2.8 55.6 + - + +
144B TYR 4.0 3.6 - - - +
146B GLN* 1.3 71.5 - - - +
148B GLU* 1.3 60.0 + - - +
150B TYR* 3.8 5.1 - - - +
151B LEU* 2.8 45.1 + - + +
205B 2AN 4.2 11.2 - - + -
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B SER* 2.8 22.2 + - - -
13B PRO* 3.5 20.3 - - + +
14B ILE* 3.9 20.5 - - + +
19B LEU* 5.4 2.0 - - + +
144B TYR* 2.9 42.0 + - + +
145B LYS* 3.3 31.4 + - - +
146B GLN 3.4 0.2 - - - -
147B VAL* 1.3 77.0 - - - +
149B GLU* 1.3 60.1 + - - +
151B LEU* 3.7 2.3 - - - +
152B ALA* 2.8 32.2 + - + +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS 3.2 16.2 + - - +
146B GLN* 3.8 8.9 - - - +
148B GLU* 1.3 81.7 - - - +
150B TYR* 1.3 69.6 + - - +
152B ALA* 3.4 5.3 + - - +
153B ALA* 3.0 34.6 + - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLN 3.3 15.3 + - - +
147B VAL 3.8 3.6 - - - +
148B GLU 3.3 0.4 - - - -
149B GLU* 1.3 85.0 + - - +
151B LEU* 1.3 63.7 + - + +
153B ALA* 3.2 1.7 + - - -
154B ASN* 2.9 68.5 + - + +
157B VAL* 4.1 11.2 - - + +
205B 2AN 2.5 94.5 + + + -
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.7 30.7 - - + -
18B ARG* 2.9 70.5 + - + +
19B LEU* 4.2 4.3 - - + +
22B ALA* 4.0 9.0 - - + -
147B VAL* 2.8 30.3 + - + +
148B GLU 3.8 2.9 - - - +
150B TYR* 1.3 75.0 - - + +
152B ALA* 1.3 60.1 + - - +
154B ASN 3.2 8.3 - - - +
155B PRO* 3.8 0.5 - - - +
157B VAL* 4.0 25.1 - - + +
158B PHE* 4.2 8.5 - - + -
205B 2AN 4.4 11.7 - - + -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PRO* 5.5 6.7 - - + -
14B ILE* 3.7 15.4 - - + +
18B ARG* 5.0 0.4 - - - +
148B GLU* 2.8 21.4 + - + +
149B GLU* 3.8 4.9 - - - +
151B LEU* 1.3 78.5 - - - +
153B ALA* 1.3 58.9 + - - +
154B ASN 3.6 0.2 + - - -
155B PRO* 4.0 12.0 - - - +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLU* 3.0 28.7 + - - +
150B TYR* 4.6 0.9 - - - -
152B ALA* 1.3 74.6 - - - +
154B ASN* 1.3 72.0 + - - +
155B PRO* 3.5 8.0 - - - +
156B GLU* 4.9 0.7 - - - +
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ARG* 2.7 26.7 + - - -
150B TYR* 2.9 59.7 + - + +
151B LEU 3.2 4.1 - - - +
153B ALA* 1.3 90.8 - - - +
155B PRO* 1.3 54.4 - - - +
156B GLU* 2.9 19.7 + - - +
157B VAL* 3.3 22.3 + - + +
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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) + - + + + + + -
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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