Contacts of the helix formed by residues 120 - 143 (chain A) in PDB entry 1AX8
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 SER 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU 4.8 0.2 - - - -
119A TYR* 1.3 73.2 - - - +
121A THR* 1.3 62.5 + - - +
122A GLU* 3.2 20.2 + - - +
123A VAL* 2.8 44.4 + - - +
124A VAL* 3.1 9.6 + - - +
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Residues in contact with THR 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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68A MET* 4.1 10.4 - - - +
114A LEU* 3.5 24.8 - - + +
115A GLU* 3.0 42.2 - - - +
119A TYR 4.0 0.2 + - - -
120A SER* 1.3 73.6 - - - +
122A GLU* 1.3 75.2 + - - +
124A VAL* 3.9 0.5 - - - +
125A ALA* 2.8 33.1 + - - +
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Residues in contact with GLU 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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68A MET* 3.9 38.1 - - + +
120A SER* 3.2 21.3 - - - +
121A THR* 1.3 91.2 + - - +
123A VAL* 1.3 57.4 + - - +
125A ALA* 3.9 1.0 - - - +
126A LEU* 3.1 39.4 + - + +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 19.1 - - + -
119A TYR* 3.6 22.4 - - + -
120A SER* 2.8 46.6 + - - +
122A GLU* 1.3 77.8 - - - +
124A VAL* 1.3 56.5 + - + +
126A LEU* 3.6 4.0 + - + +
127A SER* 2.6 40.7 + - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.8 5.2 - - + -
42A ILE* 3.7 22.0 - - + -
113A VAL 3.7 22.2 - - - +
114A LEU* 3.6 22.2 - - - +
115A GLU 5.2 0.9 - - - +
116A ALA* 3.9 16.2 - - + -
119A TYR* 3.9 21.5 - - + -
120A SER 3.1 17.4 + - - +
121A THR 3.9 0.4 - - - +
123A VAL* 1.3 75.7 - - + +
125A ALA* 1.3 52.5 + - - +
127A SER* 3.2 6.6 + - - -
128A ARG* 2.8 42.4 + - - +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.0 7.5 - - + -
64A ILE* 3.9 28.7 - - + -
65A LEU* 5.1 3.6 - - + -
68A MET* 4.1 10.5 - - + -
114A LEU* 4.1 17.2 - - + +
121A THR 2.8 19.0 + - - +
122A GLU 3.9 3.6 - - - +
124A VAL* 1.3 76.9 - - - +
126A LEU* 1.3 59.2 + - + +
128A ARG* 3.8 3.9 - - - +
129A LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 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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21A ILE* 3.6 19.8 - - + +
24A ILE* 3.7 32.1 - - + -
65A LEU* 4.0 24.0 - - + -
68A MET* 5.4 1.1 - - - -
73A VAL* 4.1 18.6 - - + -
76A ILE* 3.8 22.4 - - + -
122A GLU* 3.1 23.5 + - + +
123A VAL* 4.2 3.8 - - - +
125A ALA* 1.3 76.9 - - + +
127A SER* 1.3 58.3 + - - +
128A ARG 3.4 0.2 - - - -
129A LEU* 3.7 15.9 - - + +
130A GLN* 3.1 26.7 + - - +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 5.4 0.7 - - - -
39A LEU* 3.5 27.3 - - - +
42A ILE* 3.6 25.5 - - - +
123A VAL* 2.6 29.0 + - - +
124A VAL* 3.5 7.0 - - - -
126A LEU* 1.3 75.8 - - - +
128A ARG* 1.3 65.0 + - - +
130A GLN* 3.5 10.9 + - - +
131A GLY* 3.2 16.1 + - - -
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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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42A ILE* 3.6 28.1 - - + +
43A PRO* 2.6 47.8 + - - +
44A GLY* 3.5 8.2 + - - -
45A LEU* 3.9 22.6 - - - +
61A TYR* 3.3 17.4 + - + +
112A GLY 5.3 0.2 + - - -
113A VAL* 2.8 46.0 + - - +
114A LEU* 4.4 7.9 - - - -
124A VAL* 2.8 23.7 + - - +
125A ALA* 3.8 4.5 - - - +
127A SER* 1.3 74.2 - - - +
129A LEU* 1.3 57.8 + - - +
131A GLY* 2.8 21.1 + - - -
132A SER* 2.8 12.1 + - - -
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Residues in contact with LEU 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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21A ILE* 4.0 10.3 - - + -
58A LEU* 4.7 3.8 - - + -
61A TYR* 3.4 39.4 + - + -
65A LEU* 4.3 6.3 - - + -
76A ILE* 3.9 27.4 - - + -
80A LEU* 4.1 21.8 - - + -
125A ALA 3.0 17.4 + - - +
126A LEU* 3.7 19.7 - - + +
127A SER 3.3 0.2 - - - -
128A ARG* 1.3 78.3 - - - +
130A GLN* 1.3 57.5 + - - +
132A SER* 3.3 1.3 + - - -
133A LEU* 2.9 44.1 + - + +
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Residues in contact with GLN 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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18A VAL* 3.0 41.0 + - + +
21A ILE* 3.7 25.5 - - + +
22A ASN* 2.8 30.9 + - - +
126A LEU 3.1 18.1 + - - +
127A SER* 3.7 8.6 - - - +
128A ARG 3.2 0.2 - - - -
129A LEU* 1.3 73.6 - - - +
131A GLY* 1.3 65.9 + - - +
133A LEU* 3.3 5.6 + - - +
134A GLN* 2.9 37.0 + - - +
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Residues in contact with GLY 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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42A ILE 4.5 11.4 - - - -
44A GLY* 4.9 4.0 - - - -
47A PRO* 5.2 0.2 - - - -
127A SER 3.2 10.3 + - - -
128A ARG 2.8 10.0 + - - -
130A GLN* 1.3 76.7 - - - +
132A SER* 1.3 60.6 + - - -
134A GLN* 3.2 12.1 + - - +
135A ASP* 3.0 23.6 + - - +
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Residues in contact with SER 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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44A GLY* 3.3 12.5 - - - -
47A PRO* 3.3 28.8 - - - +
61A TYR* 2.7 39.3 + - - -
128A ARG 2.8 2.8 + - - -
129A LEU* 3.5 8.7 - - - -
131A GLY* 1.3 75.3 - - - +
133A LEU* 1.3 57.3 + - - +
135A ASP* 3.0 4.7 - - - +
136A MET* 2.9 41.9 + - - +
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Residues in contact with LEU 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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14A ILE* 3.5 22.6 - - + +
17A ILE* 3.6 37.9 - - + -
18A VAL* 3.8 17.0 - - + -
21A ILE* 4.1 8.5 - - + -
58A LEU* 4.5 4.3 - - + -
80A LEU* 5.1 1.3 - - + -
83A LEU* 3.6 30.5 - - + -
129A LEU* 2.9 41.1 + - + +
130A GLN* 3.6 4.9 - - - +
132A SER* 1.3 75.5 - - - +
134A GLN* 1.3 59.3 + - - +
136A MET* 3.4 11.5 + - - +
137A LEU 3.0 22.3 + - - -
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Residues in contact with GLN 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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18A VAL* 3.6 31.2 - - + +
22A ASN* 5.7 0.6 + - - +
40A ASP 5.5 2.4 - - - +
130A GLN* 2.9 37.6 + - - +
131A GLY* 3.8 8.4 - - - +
133A LEU* 1.3 75.5 - - - +
135A ASP* 1.3 61.1 + - - +
137A LEU* 3.4 23.2 - - + +
138A TRP* 3.2 16.2 - - - +
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Residues in contact with ASP 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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47A PRO* 3.5 31.5 - - + +
48A ILE 5.9 0.9 - - - +
131A GLY 3.0 12.9 + - - +
132A SER* 3.0 13.7 + - - +
134A GLN* 1.3 76.0 - - - +
136A MET* 1.3 65.3 + - + +
138A TRP* 3.1 37.8 + - - +
139A GLN* 3.2 29.2 + - - +
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Residues in contact with MET 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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14A ILE* 4.2 11.0 - - + -
47A PRO* 4.9 5.6 - - + -
48A ILE 5.4 3.1 - - - +
54A MET* 3.8 44.0 - - + +
57A THR* 4.6 7.4 - - + -
58A LEU* 3.3 42.8 - - + -
83A LEU* 4.7 5.4 - - - -
87A LEU* 5.3 2.7 - - - -
132A SER* 2.9 32.8 + - - +
133A LEU* 3.7 16.4 - - + +
135A ASP* 1.3 73.4 - - + +
137A LEU* 1.3 68.1 + - - +
139A GLN* 3.0 7.0 + - - +
140A LEU* 2.9 36.4 + - + +
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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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11A LYS* 3.2 76.8 + - + +
14A ILE* 3.9 22.8 - - + +
15A LYS* 4.5 16.8 - - + -
18A VAL* 6.1 1.6 - - + -
133A LEU 3.0 11.7 + - - +
134A GLN* 3.4 22.0 - - + +
135A ASP 3.2 0.2 - - - -
136A MET* 1.3 77.4 - - - +
138A TRP* 1.3 60.4 + - + +
140A LEU* 4.1 4.9 + - - +
141A ASP* 3.6 4.5 + - - +
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Residues in contact with TRP 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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134A GLN 3.2 16.4 - - - +
135A ASP* 3.1 32.8 + - - +
136A MET 3.2 0.2 - - - -
137A LEU* 1.3 79.3 - - + +
139A GLN* 1.3 91.5 + - + +
140A LEU 3.3 0.7 - - - -
141A ASP* 3.2 21.4 + - - +
142A LEU* 3.7 31.3 + - + +
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Residues in contact with GLN 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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47A PRO 4.9 0.8 + - - -
48A ILE 2.9 28.8 + - - +
49A LEU* 3.1 22.1 - - - +
54A MET* 4.0 12.9 - - + +
135A ASP* 3.2 34.2 + - - +
136A MET 3.0 2.3 + - - +
138A TRP* 1.3 110.8 - - + +
140A LEU* 1.3 60.0 + - - +
142A LEU* 2.8 31.6 + - + +
144A PRO* 3.4 13.0 - - + +
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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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7A GLN* 3.6 19.7 + - + +
10A THR* 3.8 19.7 - - + -
11A LYS* 5.3 5.6 - - - +
14A ILE* 3.6 28.5 - - + -
51A LEU* 4.3 9.4 - - + -
54A MET* 3.6 29.4 - - + -
87A LEU* 4.4 10.1 - - + -
90A LEU* 5.0 8.1 - - + -
136A MET* 2.9 28.3 + - + +
137A LEU* 4.2 6.5 - - + +
139A GLN* 1.3 76.8 - - - +
141A ASP* 1.3 59.6 + - - +
142A LEU 3.1 0.7 - - - -
143A SER* 3.1 16.5 + - - -
144A PRO* 3.6 15.9 - - + +
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Residues in contact with ASP 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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7A GLN* 5.4 1.6 - - - +
11A LYS* 2.7 41.4 + - - -
137A LEU 3.6 3.8 - - - +
138A TRP* 3.2 13.6 + - - +
139A GLN 3.1 0.6 - - - -
140A LEU* 1.3 77.5 - - - +
142A LEU* 1.3 62.5 + - + +
143A SER* 3.1 7.4 + - - -
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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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138A TRP* 3.7 37.9 - - + +
139A GLN* 2.8 16.8 + - + +
141A ASP* 1.3 81.0 - - + +
143A SER* 1.3 72.1 + - - +
144A PRO* 3.4 2.9 - - + +
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Residues in contact with SER 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLN* 3.7 18.5 + - - +
94A LYS* 5.6 4.2 - - - +
140A LEU 3.1 8.4 + - - -
141A ASP 3.1 4.1 + - - -
142A LEU* 1.3 83.6 - - - +
144A PRO* 1.3 73.5 - - - +
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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