Contacts of the helix formed by residues 120 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU* 3.3 6.1 + - + +
119A ASP* 1.3 80.0 - - - +
121A GLU* 1.3 83.0 + - - +
122A TYR* 2.9 25.1 + - - +
123A LEU* 3.2 42.8 - - + +
124A LYS* 3.1 23.8 + - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 1.3 81.2 + - - +
122A TYR* 1.3 95.7 + - + +
124A LYS* 3.5 8.5 + - - +
125A GLU* 3.2 29.0 + - + +
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 2.9 19.3 + - - +
121A GLU* 1.3 106.3 + - + +
123A LEU* 1.3 75.4 + - + +
125A GLU* 3.6 13.0 + - - +
126A ARG* 3.6 10.7 + - - +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 4.3 16.2 - - + +
118A LEU* 3.9 36.8 - - + -
120A ASP* 3.2 35.5 + - + +
121A GLU 3.4 0.2 - - - -
122A TYR* 1.3 82.7 - - + +
124A LYS* 1.3 66.7 + - - +
126A ARG* 3.3 8.8 + - - +
127A ALA* 3.1 19.6 + - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU 5.1 5.8 + - - +
116A GLU* 5.1 22.1 - - + +
118A LEU* 5.7 2.9 - - + +
120A ASP 3.1 18.8 + - - +
121A GLU* 3.7 9.0 - - - +
123A LEU* 1.3 78.2 - - - +
125A GLU* 1.3 79.8 + - - +
127A ALA* 3.0 20.2 + - + +
128A ALA* 3.2 14.8 + - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU* 3.2 16.2 + - + +
122A TYR* 3.9 7.2 - - - +
123A LEU 3.3 0.4 - - - -
124A LYS* 1.3 89.0 - - + +
126A ARG* 1.3 58.5 + - - +
128A ALA* 2.7 36.3 + - - +
129A ASP* 3.2 8.1 + - - -
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A HIS* 6.3 0.7 - - + -
79A LEU* 5.0 16.4 - - - +
111A GLN* 6.2 2.2 - - - -
115A LEU* 5.1 17.1 - - + +
122A TYR 3.6 7.8 + - - +
123A LEU* 3.3 11.1 + - - +
124A LYS 3.3 0.4 - - - -
125A GLU* 1.3 78.9 - - - +
127A ALA* 1.3 63.1 + - - +
129A ASP* 2.9 25.5 + - + +
130A VAL* 3.1 35.4 + - + +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 4.2 10.8 - - + +
115A LEU* 3.5 32.7 - - + +
116A GLU* 4.6 5.2 - - + +
123A LEU 3.1 7.4 + - - +
124A LYS* 3.0 18.6 + - + +
126A ARG* 1.3 77.5 - - - +
128A ALA* 1.3 56.0 + - - +
130A VAL* 2.8 31.9 - - + +
131A ARG* 2.9 15.2 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.2 12.5 + - - +
125A GLU* 2.7 27.6 + - - +
127A ALA* 1.3 78.9 - - - +
129A ASP* 1.3 63.5 + - - +
131A ARG* 3.3 10.1 + - - +
132A ASP* 3.0 22.7 + - - +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE* 5.7 3.7 - - - +
76A HIS* 3.4 37.6 + - + +
125A GLU 3.2 9.0 + - - +
126A ARG* 2.9 17.6 + - + +
128A ALA* 1.3 79.9 - - - +
130A VAL* 1.3 61.4 + - + +
132A ASP* 3.3 15.3 + - - +
133A ILE* 3.4 10.6 + - - +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A HIS* 5.2 7.0 - - + -
79A LEU* 6.4 2.0 - - + -
108A ILE* 5.1 5.1 - - - +
111A GLN* 4.9 15.0 - - + +
112A ALA* 3.5 25.8 - - + +
115A LEU* 5.9 2.2 - - + -
126A ARG* 3.1 43.3 + - + +
127A ALA* 2.8 20.9 - - - +
129A ASP* 1.3 76.2 - - + +
131A ARG* 1.3 65.0 + - - +
133A ILE* 2.8 34.6 - - + +
134A GLY 3.5 0.9 + - - -
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A HIS* 5.5 4.8 + - - -
108A ILE* 4.6 12.4 - - + +
109A GLU* 4.4 20.8 + - - +
112A ALA* 4.2 28.2 + - + +
113A SER* 4.7 8.3 + - - +
116A GLU* 5.5 6.7 - - - +
127A ALA* 2.9 15.3 + - - +
128A ALA* 3.6 10.1 - - - +
129A ASP 3.3 0.2 - - - -
130A VAL* 1.3 85.5 - - - +
132A ASP* 1.3 62.7 + - - +
134A GLY* 3.2 2.9 + - - -
135A LYS* 3.0 25.8 + - + +
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A HIS* 6.1 1.1 - - + +
128A ALA 3.0 13.1 + - - +
129A ASP* 3.4 13.5 - - - +
130A VAL 3.2 0.4 - - - -
131A ARG* 1.3 78.6 - - - +
133A ILE* 1.3 62.8 + - - +
135A LYS* 3.2 8.4 + - - -
136A ARG* 3.1 57.4 + - - +
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 6.3 1.3 - - + -
76A HIS* 3.8 45.5 - - + +
77A ILE* 4.8 6.1 - - + -
79A LEU* 6.4 0.7 - - + -
80A LEU* 4.5 20.4 - - + -
108A ILE* 4.5 11.7 - - + -
129A ASP 3.4 7.1 + - - +
130A VAL* 2.8 23.8 + - + +
132A ASP* 1.3 81.0 - - - +
134A GLY* 1.3 78.2 + - - +
136A ARG* 4.1 4.9 - - + +
137A LEU* 3.1 31.9 + - + +
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A HIS* 5.9 0.4 - - - -
108A ILE* 3.7 30.7 - - - -
130A VAL 3.5 0.6 + - - -
131A ARG 3.2 3.4 + - - -
133A ILE* 1.3 86.8 - - - +
135A LYS* 1.3 66.7 + - - +
137A LEU* 3.2 21.1 + - - +
138A LEU* 3.2 21.4 - - - +
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 5.6 6.7 + - - -
24A ILE* 3.6 14.7 - - + +
105A HIS* 6.0 4.5 - - - -
108A ILE* 4.6 1.6 - - - +
131A ARG* 3.0 19.6 + - + +
132A ASP* 3.5 13.0 - - - +
134A GLY* 1.3 78.4 - - - +
136A ARG* 1.3 93.0 + - - +
138A LEU* 3.4 14.4 + - - +
139A ARG* 3.6 24.6 + - - +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ASP* 3.1 36.3 + - - +
133A ILE* 4.1 5.4 - - + +
135A LYS* 1.3 120.4 - - - +
137A LEU* 1.3 63.2 + - - +
139A ARG* 2.9 36.9 + - - +
140A ASN* 2.7 38.0 + - - +
146A ILE* 3.5 16.3 - - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 6.3 0.2 - - - -
47A ARG* 4.8 14.6 - - - +
50A ALA* 4.2 19.3 - - + -
80A LEU* 3.5 46.2 - - + -
104A ALA* 6.1 5.2 - - + -
108A ILE* 4.6 11.2 - - + -
133A ILE* 3.1 24.6 + - + +
134A GLY* 3.2 17.7 + - - +
136A ARG* 1.3 79.3 - - - +
138A LEU* 1.3 68.4 + - + +
140A ASN* 3.1 7.2 + - + +
141A ILE* 3.0 33.9 + - + +
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 3.3 30.5 - - + -
26A ILE* 3.4 16.2 - - + -
101A ASP* 3.0 54.7 - - + +
104A ALA* 4.9 7.0 - - + -
105A HIS* 4.4 24.9 - - + +
108A ILE* 5.8 0.4 - - + -
134A GLY* 3.2 16.5 + - - +
135A LYS* 3.6 4.0 - - - +
136A ARG 3.1 0.6 - - - -
137A LEU* 1.3 83.2 - - + +
139A ARG* 1.3 62.2 + - - +
141A ILE* 3.4 4.2 + - + +
142A LEU* 3.2 29.5 + - - +
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP 6.0 0.2 + - - -
24A ILE* 3.5 26.5 - - + -
135A LYS* 4.1 14.1 - - - +
136A ARG* 2.9 46.4 + - - +
138A LEU* 1.3 77.9 - - - +
140A ASN* 1.3 53.0 + - - +
142A LEU 3.3 0.2 + - - -
143A GLY* 2.5 34.1 + - - -
144A LEU* 2.9 34.7 + - + -
145A LYS 3.9 14.9 + - - -
146A ILE* 2.8 44.5 - - + +
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY* 4.2 17.3 - - - +
49A LYS* 5.2 8.4 - - + +
50A ALA* 3.7 35.1 - - + +
53A GLN* 3.6 23.0 + - - -
136A ARG* 2.7 33.2 + - - +
137A LEU* 3.4 11.5 - - + +
139A ARG* 1.3 77.6 - - - +
141A ILE* 1.3 63.4 + - + +
143A GLY* 3.4 10.5 + - - -
146A ILE* 4.0 15.8 - - - +
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.7 18.8 - - + +
43A PHE* 4.8 16.2 - - + +
46A GLY* 4.3 20.1 - - - -
47A ARG* 5.0 1.1 - - - +
100A ALA* 4.5 19.5 - - + +
101A ASP* 4.5 26.5 - - + +
104A ALA* 4.9 8.3 - - + -
137A LEU* 3.0 28.3 + - + +
138A LEU* 3.9 7.2 - - + +
140A ASN* 1.3 78.0 - - + +
142A LEU* 1.3 72.6 + - + +
143A GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU 5.2 0.4 - - - +
24A ILE* 4.0 23.6 - - + -
25A VAL* 4.0 17.3 - - + +
101A ASP* 3.9 27.1 - - + +
138A LEU 3.2 16.9 + - - +
139A ARG 3.8 2.5 - - - +
141A ILE* 1.3 87.6 - - + +
143A GLY* 1.3 60.3 + - - +
144A LEU* 3.8 29.3 - - + +
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ARG 2.5 15.4 + - - -
140A ASN* 3.4 8.3 + - - -
141A ILE 3.2 3.0 - - - -
142A LEU* 1.3 75.6 - - - +
144A LEU* 1.3 66.0 + - - +
145A LYS* 3.6 19.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
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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