Contacts of the helix formed by residues 120 - 143 (chain B) in PDB entry 2N5T
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 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B LEU* 3.3 6.7 + - + +
119B ASP* 1.3 81.2 - - - +
121B GLU* 1.3 82.1 + - - +
122B TYR* 2.9 24.2 + - - +
123B LEU* 3.2 43.1 - - + +
124B LYS* 3.1 24.0 + - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ASP* 1.3 80.5 + - - +
122B TYR* 1.3 96.7 + - + +
124B LYS* 3.5 8.8 + - - +
125B GLU* 3.2 28.5 + - + +
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Residues in contact with TYR 122 (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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120B ASP* 2.9 20.3 + - - +
121B GLU* 1.3 106.4 + - + +
123B LEU* 1.3 75.5 + - + +
125B GLU* 3.6 12.4 + - - +
126B ARG* 3.6 11.1 + - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.4 16.2 - - + +
118B LEU* 3.9 37.2 - - + -
120B ASP* 3.2 35.8 + - + +
121B GLU 3.4 0.2 - - - -
122B TYR* 1.3 82.4 - - + +
124B LYS* 1.3 66.7 + - - +
126B ARG* 3.3 8.2 + - - +
127B ALA* 3.1 19.6 + - - +
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Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 5.1 5.8 + - - +
116B GLU* 5.1 23.6 - - + +
118B LEU* 5.7 2.5 - - + +
120B ASP 3.1 19.3 + - - +
121B GLU* 3.7 9.2 - - - +
122B TYR 3.3 0.2 - - - -
123B LEU* 1.3 78.4 - - - +
125B GLU* 1.3 79.4 + - - +
127B ALA* 3.0 20.1 + - + +
128B ALA* 3.2 13.7 + - - +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU* 3.2 18.0 + - + +
122B TYR* 3.9 7.2 - - - +
123B LEU 3.3 0.4 - - - -
124B LYS* 1.3 90.3 - - - +
126B ARG* 1.3 60.6 + - - +
128B ALA* 2.7 36.1 + - - +
129B ASP* 3.2 8.1 + - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B HIS* 6.3 0.9 - - + -
79B LEU* 5.0 16.6 - - - +
111B GLN* 6.2 2.2 - - - -
115B LEU* 5.1 16.5 - - + +
122B TYR 3.6 8.5 + - - +
123B LEU* 3.3 10.4 + - - +
124B LYS 3.3 0.4 - - - -
125B GLU* 1.3 77.3 - - - +
127B ALA* 1.3 64.4 + - - +
129B ASP* 2.9 25.1 + - + +
130B VAL* 3.1 36.2 + - + +
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Residues in contact with ALA 127 (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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112B ALA* 4.2 11.2 - - + +
115B LEU* 3.5 32.2 - - + +
116B GLU* 4.6 5.6 - - + +
123B LEU 3.1 8.1 + - - +
124B LYS* 3.0 18.0 + - + +
126B ARG* 1.3 77.7 - - - +
128B ALA* 1.3 56.6 + - - +
130B VAL* 2.8 30.4 - - + +
131B ARG* 2.9 15.0 + - - +
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Residues in contact with ALA 128 (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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124B LYS* 3.2 12.5 + - - +
125B GLU* 2.7 27.8 + - - +
127B ALA* 1.3 79.0 - - - +
129B ASP* 1.3 62.8 + - - +
131B ARG* 3.3 10.6 + - - +
132B ASP* 3.0 22.9 + - - +
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Residues in contact with ASP 129 (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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72B ILE* 5.7 3.3 - - - +
76B HIS* 3.4 36.9 + - + +
125B GLU 3.2 9.0 + - - +
126B ARG* 2.9 17.4 + - + +
128B ALA* 1.3 81.9 - - - +
130B VAL* 1.3 63.3 + - + +
132B ASP* 3.3 15.9 + - - +
133B ILE* 3.4 10.4 + - - +
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Residues in contact with VAL 130 (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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76B HIS* 5.2 6.5 - - + -
79B LEU* 6.4 2.5 - - + -
108B ILE* 5.1 5.8 - - - +
111B GLN* 4.9 13.9 - - + +
112B ALA* 3.5 26.0 - - + +
115B LEU* 5.9 2.5 - - + -
126B ARG* 3.1 43.9 + - + +
127B ALA* 2.8 21.3 - - - +
129B ASP* 1.3 76.2 - - + +
131B ARG* 1.3 65.1 + - - +
133B ILE* 2.8 34.6 - - + +
134B GLY* 3.5 0.9 + - - -
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Residues in contact with ARG 131 (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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105B HIS* 5.5 4.2 + - - -
108B ILE* 4.6 11.9 - - + +
109B GLU* 4.4 21.0 + - - +
112B ALA* 4.1 29.5 + - + +
113B SER* 4.7 7.9 + - - +
116B GLU* 5.4 6.7 - - - +
127B ALA* 2.9 15.7 + - - +
128B ALA* 3.6 9.4 - - - +
130B VAL* 1.3 86.2 - - - +
132B ASP* 1.3 62.1 + - - +
134B GLY* 3.2 3.0 + - - +
135B LYS* 3.0 25.4 + - + +
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Residues in contact with ASP 132 (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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76B HIS* 6.3 0.7 - - + -
128B ALA 3.0 13.6 + - - +
129B ASP* 3.4 13.7 - - - +
130B VAL 3.2 0.2 - - - -
131B ARG* 1.3 78.4 - - - +
133B ILE* 1.3 62.0 + - - +
135B LYS* 3.2 9.0 + - - +
136B ARG* 3.1 53.2 + - - +
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Residues in contact with ILE 133 (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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54B LEU* 6.3 2.0 - - + -
76B HIS* 3.8 45.7 - - + +
77B ILE* 4.8 6.1 - - + -
79B LEU* 6.4 0.9 - - + -
80B LEU* 4.5 20.0 - - + -
108B ILE* 4.5 11.4 - - + -
129B ASP 3.4 6.8 + - - +
130B VAL* 2.8 24.9 + - + +
132B ASP* 1.3 80.9 - - - +
134B GLY* 1.3 78.1 + - - +
136B ARG* 3.6 5.2 + - + +
137B LEU* 3.1 31.7 + - + +
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Residues in contact with GLY 134 (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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105B HIS* 5.8 0.7 - - - -
108B ILE* 3.7 31.0 - - - -
130B VAL 3.5 0.6 + - - -
131B ARG 3.2 3.6 + - - -
133B ILE* 1.3 86.2 - - - +
135B LYS* 1.3 66.6 + - - +
137B LEU* 3.2 20.4 + - - +
138B LEU* 3.2 22.1 - - - +
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Residues in contact with LYS 135 (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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24B ILE* 3.7 23.8 - - + +
105B HIS* 6.0 4.3 - - - -
108B ILE* 4.6 0.8 - - - +
131B ARG* 3.0 18.2 + - + +
132B ASP* 3.2 14.8 + - - +
134B GLY* 1.3 79.6 - - - +
136B ARG* 1.3 92.9 + - - +
138B LEU* 3.4 13.2 + - - +
139B ARG* 3.6 18.9 + - - +
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Residues in contact with ARG 136 (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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132B ASP* 3.1 35.1 + - - +
133B ILE* 4.1 4.7 - - + +
135B LYS* 1.3 119.6 - - - +
137B LEU* 1.3 64.4 + - + +
139B ARG* 2.9 43.8 + - + +
140B ASN* 2.7 37.0 + - - +
146B ILE* 4.9 6.8 - - - +
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Residues in contact with LEU 137 (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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43B PHE* 6.4 0.4 - - + -
47B ARG* 4.8 15.0 - - + +
50B ALA* 4.2 18.6 - - + -
80B LEU* 3.5 46.9 - - + -
104B ALA* 6.1 5.2 - - + -
108B ILE* 4.6 10.8 - - + -
133B ILE* 3.1 25.0 + - + +
134B GLY* 3.2 19.2 + - - +
136B ARG* 1.3 79.5 - - - +
138B LEU* 1.3 67.9 + - + +
140B ASN* 3.1 6.8 + - + +
141B ILE* 3.0 32.8 + - + +
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Residues in contact with LEU 138 (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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24B ILE* 3.6 33.4 - - + -
26B ILE* 4.6 5.2 - - + -
101B ASP* 3.0 54.3 - - + +
104B ALA* 4.9 6.5 - - + -
105B HIS* 4.5 26.5 - - + +
108B ILE* 5.8 0.4 - - + -
134B GLY* 3.2 16.3 + - - +
135B LYS* 3.6 9.4 - - - +
136B ARG 3.1 0.4 - - - -
137B LEU* 1.3 83.9 - - + +
139B ARG* 1.3 61.7 + - - +
141B ILE* 3.4 5.1 + - + +
142B LEU* 3.2 29.6 + - + +
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Residues in contact with ARG 139 (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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21B GLU* 4.5 25.5 - - - +
22B ASP 4.2 16.6 - - - +
24B ILE* 3.8 23.6 - - + -
135B LYS* 4.0 14.6 - - - +
136B ARG* 2.9 57.8 + - - +
138B LEU* 1.3 77.3 - - - +
140B ASN* 1.3 54.8 + - - +
142B LEU* 3.3 4.6 + - - -
143B GLY 2.5 33.1 + - - -
144B LEU* 3.2 24.5 + - + +
145B LYS 4.2 18.4 + - - -
146B ILE* 3.7 24.2 - - + +
147B ILE 4.6 4.9 - - - +
148B ASP 5.6 1.4 - - - +
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Residues in contact with ASN 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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46B GLY* 4.2 18.6 - - - +
49B LYS* 5.2 8.9 - - + +
50B ALA* 3.7 34.7 - - + +
53B GLN* 3.5 23.6 + - - -
136B ARG* 2.7 33.0 + - - +
137B LEU* 3.4 10.5 - - + +
139B ARG* 1.3 79.5 - - - +
141B ILE* 1.3 64.1 + - + +
143B GLY* 3.4 9.8 + - - +
144B LEU 5.5 0.7 - - - -
146B ILE* 4.3 15.1 - - - +
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Residues in contact with ILE 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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42B ARG* 4.7 18.6 - - + +
43B PHE* 4.8 15.7 - - + +
46B GLY* 4.3 21.9 - - - -
47B ARG* 5.0 0.9 - - - +
100B ALA* 4.5 19.7 - - + +
101B ASP* 4.5 26.0 - - - +
104B ALA* 4.9 9.0 - - + -
137B LEU* 3.0 28.3 + - + +
138B LEU* 3.9 6.1 - - + +
140B ASN* 1.3 78.4 - - + +
142B LEU* 1.3 74.0 + - + +
143B GLY* 4.4 0.3 - - - -
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Residues in contact with LEU 142 (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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23B GLU 4.3 11.2 - - - +
24B ILE* 4.3 5.2 - - + -
25B VAL* 3.6 38.1 - - + +
101B ASP* 3.9 27.4 - - + +
138B LEU* 3.2 20.3 + - + +
139B ARG 3.8 2.9 - - - +
141B ILE* 1.3 87.4 - - + +
143B GLY* 1.3 60.4 + - - +
144B LEU* 3.4 19.5 + - + +
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Residues in contact with GLY 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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139B ARG 2.5 16.4 + - - -
140B ASN* 3.4 9.8 + - - -
141B ILE 3.2 2.2 - - - -
142B LEU* 1.3 77.6 - - - +
144B LEU* 1.3 66.4 + - - +
145B LYS* 3.4 4.2 + - - +
146B ILE* 6.1 0.2 - - - -
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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
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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