Contacts of the helix formed by residues 123 - 145 (chain A) in PDB entry 2NUG
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A TYR* 3.5 2.4 + - - -
120A SER* 3.2 27.8 + - - +
121A GLY 3.3 1.3 - - - +
122A ARG* 1.3 74.9 - - - +
124A ALA* 1.3 58.6 + - - +
125A ASN* 3.7 2.3 - - - +
126A PHE* 2.9 34.0 + - + +
127A THR* 2.8 26.3 + - - -
125B ASN* 2.9 23.9 + - - +
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Residues in contact with ALA 124 (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 LEU* 5.1 3.8 - - + -
49A PHE* 5.2 2.9 - - + -
50A PHE* 4.2 3.0 - - + -
117A TYR* 3.5 21.4 - - + -
122A ARG 3.3 1.8 + - - -
123A ASP* 1.3 73.7 - - - +
125A ASN* 1.3 56.7 + - - +
127A THR* 3.4 2.4 + - - +
128A ARG* 2.9 31.9 + - - +
49B PHE* 4.2 16.8 - - + -
124B ALA* 3.7 23.6 - - + -
125B ASN* 2.7 18.8 + - - +
128B ARG* 4.5 2.2 - - - +
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Residues in contact with ASN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 3.3 5.1 + - - +
124A ALA* 1.3 75.3 - - - +
126A PHE* 1.3 63.5 + - - +
128A ARG* 3.7 16.7 + - - +
129A GLU* 3.1 29.6 + - + +
122B ARG 3.5 8.1 - - - +
123B ASP* 2.9 31.1 + - - +
124B ALA* 2.7 29.9 + - - +
125B ASN* 3.2 15.9 - - - +
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Residues in contact with PHE 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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12A GLY 5.5 1.6 - - - -
13A TYR* 3.6 39.3 - + + -
116A VAL* 4.1 13.5 - - + -
120A SER* 3.9 17.9 - - - -
123A ASP* 2.9 32.8 + - + +
125A ASN* 1.3 76.1 - - - +
127A THR* 1.3 61.9 + - - +
129A GLU* 3.3 6.6 + - + +
130A LEU* 2.9 46.5 + - + +
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Residues in contact with THR 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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46A LEU* 4.2 0.2 - - + -
50A PHE* 3.8 16.4 - - + -
113A TRP* 3.7 40.7 - - + +
116A VAL* 4.0 8.6 - - + +
117A TYR* 3.3 24.8 + - + +
120A SER* 3.7 5.4 + - - -
123A ASP 2.8 17.2 + - - -
124A ALA 4.0 3.1 - - - -
126A PHE* 1.3 84.0 - - - +
128A ARG* 1.3 58.1 + - - +
130A LEU* 3.3 4.5 + - - +
131A PHE* 2.9 28.4 + - - +
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Residues in contact with ARG 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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49A PHE* 4.8 5.6 - - + -
50A PHE* 3.5 30.6 - - + -
53A ASP* 3.8 8.5 - - - -
124A ALA 2.9 18.1 + - - +
125A ASN* 3.7 23.8 + - - +
127A THR* 1.3 76.2 - - - +
129A GLU* 1.3 90.6 + - - +
131A PHE* 3.3 3.6 + - - +
132A TYR* 2.9 59.4 + - + +
117B TYR* 2.8 36.1 + - - -
122B ARG* 2.9 32.2 + - - +
124B ALA* 4.6 2.4 - - - +
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Residues in contact with GLU 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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125A ASN* 3.1 20.3 + - + +
126A PHE* 3.8 6.1 - - + +
128A ARG* 1.3 109.2 + - - +
130A LEU* 1.3 59.5 + - - +
132A TYR* 3.3 21.4 + - - +
133A LYS* 2.8 28.6 + - - +
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Residues in contact with LEU 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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11A LEU* 3.5 25.8 - - + +
12A GLY* 4.1 12.1 - - - +
13A TYR* 3.8 25.1 - - + -
113A TRP* 3.9 20.0 - - + -
116A VAL* 4.1 15.5 - - + -
126A PHE* 2.9 32.0 + - + +
127A THR* 3.7 5.6 - - - +
128A ARG 3.3 0.2 - - - -
129A GLU* 1.3 74.4 - - - +
131A PHE* 1.3 66.5 + - - +
133A LYS* 3.2 22.4 + - + +
134A LEU* 3.2 23.9 + - + +
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Residues in contact with PHE 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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47A VAL* 3.9 25.1 - - + -
50A PHE* 3.6 25.6 - + + -
51A ILE* 3.7 26.9 - - + -
83A LEU* 4.2 11.2 - - + -
109A PHE* 3.8 16.6 - + - -
113A TRP* 3.5 36.7 - + + -
127A THR 2.9 14.3 + - - +
128A ARG 3.4 7.9 - - - +
130A LEU* 1.3 78.0 - - - +
132A TYR* 1.3 70.6 + + - +
134A LEU 3.3 1.6 + - - -
135A PHE* 2.8 47.1 + + + -
139A ILE* 4.0 12.1 - - + -
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Residues in contact with TYR 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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50A PHE* 2.7 33.0 + - + -
51A ILE* 5.5 0.2 - - - -
53A ASP* 3.7 10.7 + - - +
54A LEU* 3.4 44.8 + - + -
57A GLN* 4.7 10.1 - - - -
128A ARG* 2.9 44.3 + - + +
129A GLU* 3.7 25.8 - - - +
130A LEU 3.2 0.2 - - - -
131A PHE* 1.3 92.4 - + - +
133A LYS* 1.3 66.9 + - - +
136A LYS* 2.8 47.8 + - + +
137A GLU 4.5 0.7 + - - -
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Residues in contact with LYS 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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11A LEU 5.9 0.4 - - - +
12A GLY* 6.3 2.9 - - - -
129A GLU 2.8 14.6 + - - +
130A LEU* 3.2 26.2 + - + +
132A TYR* 1.3 77.5 - - - +
134A LEU* 1.3 67.6 + - + +
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Residues in contact with LEU 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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10A LYS 3.6 18.2 - - - +
11A LEU* 3.8 33.4 - - + +
86A LYS* 2.9 40.5 + - + +
87A LEU* 4.4 4.9 - - + -
113A TRP* 3.8 30.3 - - + -
130A LEU* 3.2 7.5 + - + +
131A PHE 3.7 5.8 - - - +
132A TYR 3.1 0.4 - - - -
133A LYS* 1.3 90.2 - - + +
135A PHE* 1.3 77.9 + - + +
138A ASP* 3.3 1.0 - - - +
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Residues in contact with PHE 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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83A LEU* 3.3 51.8 - - + -
86A LYS* 3.9 17.5 - - + -
87A LEU* 4.2 15.5 - - + -
109A PHE* 3.7 24.0 - + - -
113A TRP* 3.7 24.0 - + - -
131A PHE* 2.8 45.6 + + + +
134A LEU* 1.3 89.9 - - + +
136A LYS* 1.3 64.3 + - - +
137A GLU 3.3 2.9 - - - -
138A ASP* 3.1 13.3 + - - +
139A ILE* 2.9 35.1 + - + +
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Residues in contact with LYS 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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54A LEU* 3.9 27.5 - - + +
57A GLN* 5.2 3.8 + - - +
58A TYR* 2.5 48.2 + - - -
132A TYR* 2.8 48.2 + - + +
134A LEU 4.0 0.2 - - - -
135A PHE* 1.3 71.3 - - - +
137A GLU* 1.3 75.4 + - + +
139A ILE* 3.3 2.8 + - - +
140A LEU* 3.0 35.3 + - + +
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Residues in contact with GLU 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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132A TYR 4.5 0.6 + - - -
134A LEU 5.6 0.2 + - - -
135A PHE 3.3 0.8 - - - -
136A LYS* 1.3 94.6 - - + +
138A ASP* 1.3 60.1 + - - +
140A LEU* 4.0 14.2 - - - +
141A SER* 2.9 33.9 + - - -
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Residues in contact with ASP 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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79A PHE* 4.7 2.5 - - + -
83A LEU* 4.4 14.5 - - + +
86A LYS* 2.5 39.6 + - - -
134A LEU 3.3 8.3 - - - +
135A PHE* 3.1 13.9 + - - +
137A GLU* 1.3 79.5 - - - +
139A ILE* 1.3 59.8 + - - +
141A SER* 2.8 19.3 + - - -
142A ALA* 3.0 18.4 + - - +
147A ARG* 4.7 0.3 + - - -
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Residues in contact with ILE 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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51A ILE* 3.3 32.1 - - + -
54A LEU* 4.0 24.2 - - + -
55A LEU* 5.3 2.2 - - + -
74A LEU* 4.0 27.9 - - + +
79A PHE* 3.9 25.4 - - + -
83A LEU* 4.7 0.7 - - + -
131A PHE* 4.0 16.4 - - + -
135A PHE* 2.9 27.1 + - + +
136A LYS* 3.6 4.5 - - - +
138A ASP* 1.3 72.6 - - - +
140A LEU* 1.3 68.1 + - + +
142A ALA* 3.2 3.6 + - - +
143A ILE* 3.1 29.0 + - + +
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Residues in contact with LEU 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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54A LEU* 4.6 12.1 - - + +
55A LEU* 6.2 1.8 - - + -
58A TYR* 4.3 38.6 - - + -
136A LYS* 3.0 46.8 + - + +
137A GLU* 4.0 15.7 - - - +
139A ILE* 1.3 76.6 - - + +
141A SER* 1.3 58.1 + - - +
143A ILE* 3.3 18.3 + - + +
144A LYS* 3.0 42.3 + - + +
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Residues in contact with SER 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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137A GLU 2.9 16.5 + - - -
138A ASP* 2.8 25.5 + - - -
140A LEU* 1.3 74.4 - - - +
142A ALA* 1.3 59.3 + - - +
144A LYS* 4.4 6.5 - - - +
145A GLU* 2.8 53.8 + - - +
147A ARG* 3.4 11.1 + - - -
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Residues in contact with ALA 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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73A TYR* 6.0 0.4 - - + -
74A LEU* 5.0 2.5 - - + -
79A PHE* 4.2 23.3 - - + -
138A ASP 3.0 18.7 + - - +
139A ILE 3.2 5.4 + - - +
141A SER* 1.3 77.5 + - - +
143A ILE* 1.3 61.4 + - - +
146A GLY 3.4 0.7 + - - -
147A ARG* 2.8 56.6 + - + +
148A VAL* 3.6 10.7 + - + -
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Residues in contact with ILE 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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55A LEU* 3.9 28.5 - - + -
66A PHE* 6.2 1.3 - - + -
70A LEU* 4.5 25.1 - - + -
74A LEU* 4.0 12.8 - - + -
139A ILE* 3.1 19.6 + - + +
140A LEU* 3.4 19.7 - - + +
141A SER 3.1 0.6 - - - -
142A ALA* 1.3 76.7 - - - +
144A LYS* 1.3 68.8 + - + +
146A GLY* 3.2 13.3 + - - -
148A VAL* 3.9 19.9 - - + +
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Residues in contact with LYS 144 (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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140A LEU* 3.0 29.4 + - + +
141A SER* 4.1 5.4 - - - +
143A ILE* 1.3 81.3 - - + +
145A GLU* 1.3 62.0 + - + +
146A GLY 3.2 2.8 + - - -
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Residues in contact with GLU 145 (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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141A SER* 2.8 37.0 + - - +
144A LYS* 1.3 76.8 - - + +
146A GLY* 1.3 62.2 + - - +
147A ARG* 2.6 43.3 + - - +
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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
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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