Contacts of the helix formed by residues 99 - 120 (chain A) in PDB entry 4A69
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 GLY 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.3 21.5 - - - -
97A PHE* 3.3 1.0 + - - -
98A PRO* 1.3 72.9 - - - +
100A LEU* 1.3 65.2 + - - +
101A PHE 3.3 2.7 - - - -
102A GLU* 3.3 10.8 + - - -
103A PHE* 2.9 21.3 + - - +
463C VAL* 5.7 1.3 - - - +
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Residues in contact with LEU 100 (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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70A LEU* 4.2 33.4 - - + +
73A VAL* 5.0 9.4 - - + +
90A VAL* 5.2 1.6 - - + -
95A PRO 3.6 24.2 - - - +
96A VAL* 4.0 19.5 - - + -
97A PHE* 3.3 38.2 + - + +
98A PRO 3.4 0.4 - - - -
99A GLY* 1.3 77.7 - - - +
101A PHE* 1.3 67.6 + - - +
103A PHE* 3.3 3.6 + - - +
104A CYS* 3.1 42.4 + - - -
146A TYR* 3.8 16.2 - - + -
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA 4.9 2.0 - - - -
54A SER* 4.9 1.6 - - - -
55A GLN 4.4 9.9 - - - -
58A MET* 3.7 36.1 - - + -
67A ILE* 3.9 10.8 - - + -
70A LEU* 3.9 23.5 + - + +
71A GLN* 3.6 52.5 - - + +
99A GLY 3.3 0.4 - - - -
100A LEU* 1.3 80.1 - - - +
102A GLU* 1.3 68.5 + - - +
104A CYS* 3.2 7.0 + - + +
105A SER* 2.9 32.8 + - - -
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Residues in contact with GLU 102 (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 ASP* 4.8 2.6 - - - +
16A PHE* 3.8 17.2 - - + -
52A GLN* 5.1 4.3 - - - +
99A GLY* 3.3 14.0 + - - +
101A PHE* 1.3 78.9 - - - +
103A PHE* 1.3 57.6 + - - +
105A SER* 3.4 6.9 + - - -
106A ARG* 2.6 77.4 + - + +
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Residues in contact with PHE 103 (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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13A VAL* 3.7 24.2 - - + -
16A PHE* 3.6 37.2 - + + -
18A TYR* 3.5 28.3 - + - -
24A MET* 5.6 4.3 - - + -
26A PRO* 3.9 20.6 - - + -
29A LEU* 4.6 9.0 - - + -
97A PHE* 4.0 17.9 - + + -
99A GLY 2.9 16.7 + - - +
100A LEU 3.6 4.7 - - - +
102A GLU* 1.3 75.3 - - - +
104A CYS* 1.3 61.6 + - - +
106A ARG* 3.2 4.4 + - - +
107A TYR* 2.9 59.5 + + + -
130A ALA 5.3 2.9 - - - -
133A LEU* 4.8 5.4 - - + -
146A TYR* 5.4 1.8 - + - -
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Residues in contact with CYS 104 (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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58A MET* 3.9 4.9 - - + -
70A LEU* 4.9 1.8 - - - -
100A LEU* 3.1 31.3 + - - -
101A PHE* 3.2 10.7 + - + +
103A PHE* 1.3 76.1 - - - +
105A SER* 1.3 62.6 + - - +
107A TYR* 3.6 16.2 + - + -
108A THR* 2.7 33.1 + - - -
146A TYR* 3.6 37.5 - - - -
147A VAL* 3.8 21.5 - - + -
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Residues in contact with SER 105 (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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52A GLN* 3.3 22.6 + - - +
53A ALA 2.9 33.6 + - - +
58A MET* 3.6 14.9 - - - +
101A PHE* 2.9 23.6 + - - -
102A GLU* 3.6 8.5 - - - -
104A CYS* 1.3 75.7 - - - +
106A ARG* 1.3 57.9 + - - +
109A GLY* 3.0 24.4 + - - -
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Residues in contact with ARG 106 (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 ASP* 3.2 39.6 + - - +
12A ASP* 3.6 24.9 + - - +
13A VAL* 3.9 28.0 - - + +
16A PHE* 4.2 6.7 - - - -
49A LYS* 4.7 6.7 - - - +
50A PRO* 5.3 2.3 + - - +
51A TYR 4.2 3.1 - - - +
52A GLN* 3.6 43.9 + - + +
102A GLU* 2.6 52.2 + - + +
103A PHE 3.2 4.7 + - - +
105A SER* 1.3 79.4 - - - +
107A TYR* 1.3 62.7 + - - +
109A GLY* 4.1 0.7 - - - -
110A ALA* 3.6 18.2 + - - +
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Residues in contact with TYR 107 (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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13A VAL* 4.2 4.4 - - + +
103A PHE* 2.9 48.4 + + + +
104A CYS* 3.6 21.3 - - - -
106A ARG* 1.3 73.6 - - - +
108A THR* 1.3 76.2 + - - +
110A ALA* 3.6 1.3 + - - -
111A SER* 3.5 6.4 + - - -
128A ASN* 3.2 24.1 + - - -
130A ALA* 3.3 35.9 - - + +
133A LEU* 3.6 35.7 - - + +
146A TYR* 3.7 4.4 + + - -
147A VAL* 2.6 46.2 + - + +
149A ASP* 3.5 17.9 - - - -
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Residues in contact with THR 108 (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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53A ALA* 3.8 18.6 - - + -
57A ASP* 5.8 0.2 - - + -
58A MET* 4.5 3.8 - - + -
104A CYS 2.7 22.5 + - - -
107A TYR* 1.3 82.8 - - - +
109A GLY* 1.3 67.5 + - - +
111A SER* 3.0 5.5 + - - -
112A LEU* 3.0 21.3 + - + +
147A VAL* 3.4 19.5 - - + +
149A ASP* 3.7 15.5 - - + +
152A ILE* 3.7 37.5 - - + -
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Residues in contact with GLY 109 (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 TYR* 3.1 33.7 - - - -
53A ALA* 3.6 19.6 - - - +
105A SER 3.0 11.6 + - - -
107A TYR 3.4 0.2 - - - -
108A THR* 1.3 75.6 - - - +
110A ALA* 1.3 56.3 + - - +
112A LEU* 3.4 2.4 + - - +
113A GLN* 2.9 30.8 + - - +
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Residues in contact with ALA 110 (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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8A PHE* 4.0 16.4 - - + -
50A PRO* 3.9 28.5 - - + -
51A TYR 3.6 1.2 + - - -
106A ARG 3.6 10.4 + - - +
107A TYR* 3.9 3.1 - - - +
108A THR 3.2 0.6 - - - -
109A GLY* 1.3 72.6 - - - +
111A SER* 1.3 66.4 + - - +
113A GLN* 3.9 3.5 - - - +
114A GLY* 3.0 21.0 + - - -
128A ASN* 3.2 31.9 - - + +
130A ALA* 5.6 0.4 - - + -
291A LEU* 5.5 0.2 - - - +
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Residues in contact with SER 111 (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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107A TYR 3.5 1.4 + - - -
108A THR 3.0 9.3 + - - -
110A ALA* 1.3 80.2 - - - +
112A LEU* 1.3 56.0 + - - +
114A GLY* 3.4 2.3 + - - -
115A ALA* 3.1 27.4 + - - +
128A ASN* 2.8 22.0 + - - +
149A ASP* 2.6 44.1 + - - -
153A GLY* 4.7 4.1 - - - -
291A LEU* 4.2 9.8 - - - +
293A LEU* 3.5 18.1 - - - +
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Residues in contact with LEU 112 (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 TYR* 4.1 9.0 - - + -
53A ALA* 5.0 3.1 - - + -
57A ASP* 3.9 37.2 - - + +
60A ARG* 3.8 18.2 - - - +
108A THR 3.0 12.0 + - - +
109A GLY* 3.6 7.9 - - - +
111A SER* 1.3 73.9 - - - +
113A GLN* 1.3 60.9 + - - +
115A ALA* 3.2 6.1 + - - +
116A THR* 2.9 29.3 + - - -
152A ILE* 4.0 24.2 - - + +
153A GLY* 4.9 2.2 - - - -
156A GLU* 3.7 31.9 - - + +
505A GOL 4.0 15.7 - - - +
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Residues in contact with GLN 113 (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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8A PHE* 3.5 18.9 - - + -
48A PHE* 4.2 15.2 - - - +
49A LYS 4.8 2.2 + - - -
50A PRO* 3.3 10.7 - - - +
51A TYR* 2.9 32.4 + - + +
109A GLY 2.9 16.7 + - - +
110A ALA 3.9 2.0 - - - +
112A LEU* 1.3 74.3 - - - +
114A GLY* 1.3 56.7 + - - +
116A THR* 3.4 2.4 + - + -
117A GLN* 2.9 55.4 + - + +
505A GOL 3.6 25.0 - - - +
413C ASN 4.8 7.7 + - - -
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Residues in contact with GLY 114 (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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8A PHE* 3.6 24.3 - - - -
110A ALA 3.0 12.6 + - - -
111A SER 3.7 3.8 - - - -
112A LEU 3.3 0.2 - - - -
113A GLN* 1.3 75.1 - - - +
115A ALA* 1.3 56.9 + - - +
117A GLN* 3.4 2.9 + - - +
118A LEU* 3.0 34.0 + - - +
126A ALA* 3.8 11.9 - - - +
291A LEU* 4.2 8.3 - - - -
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Residues in contact with ALA 115 (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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111A SER 3.1 13.0 + - - +
112A LEU 3.4 8.7 - - - +
114A GLY* 1.3 74.8 - - - +
116A THR* 1.3 53.1 + - - +
118A LEU* 3.4 4.2 + - - -
119A ASN* 2.9 39.3 + - - +
153A GLY* 3.5 28.9 - - - +
156A GLU* 3.9 11.7 - - + -
157A LEU* 3.6 19.8 - - + +
291A LEU* 4.4 6.3 - - + +
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Residues in contact with THR 116 (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 LEU* 2.9 17.1 + - - +
113A GLN* 3.4 7.2 - - + +
115A ALA* 1.3 76.9 - - - +
117A GLN* 1.3 64.2 + - + +
119A ASN* 3.4 2.9 + - - +
120A ASN* 2.9 45.9 + - - +
156A GLU* 3.7 8.6 + - - +
505A GOL 3.1 36.9 + - - +
506A GOL 3.5 22.8 - - - -
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Residues in contact with GLN 117 (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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6A ALA* 3.2 28.4 - - - +
8A PHE* 3.9 11.4 - - - -
48A PHE* 3.4 32.5 - - - -
113A GLN* 2.9 43.0 + - + +
114A GLY* 3.8 4.5 - - - +
116A THR* 1.3 76.4 - - + +
118A LEU* 1.3 64.4 + - - +
120A ASN* 4.8 0.2 - - - +
121A LYS 3.1 2.9 + - - -
122A ILE* 2.8 61.0 + - + +
123A CYS* 3.6 10.0 + - - -
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Residues in contact with LEU 118 (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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114A GLY 3.0 21.4 + - - +
115A ALA* 3.7 4.0 - - - +
117A GLN* 1.3 73.8 - - - +
119A ASN* 1.3 65.5 + - - +
121A LYS* 3.1 17.3 + - - +
123A CYS* 3.9 15.5 - - - +
124A ASP 3.6 32.3 - - - +
125A ILE 4.0 1.8 - - - +
126A ALA* 4.3 6.3 - - + +
157A LEU* 4.3 10.8 - - + -
161A HIS* 4.8 5.9 + - - +
251A CYS* 4.4 14.8 - - - -
289A PRO* 4.2 12.6 - - + +
290A LEU 3.8 13.5 - - - +
291A LEU* 3.6 39.0 - - + +
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Residues in contact with ASN 119 (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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115A ALA 2.9 18.4 + - - +
116A THR 3.5 5.6 - - - +
118A LEU* 1.3 78.0 - - - +
120A ASN* 1.3 57.9 + - - +
121A LYS* 3.3 9.7 + - - +
156A GLU* 2.8 26.1 + - - +
157A LEU* 3.6 8.3 + - - +
159A LYS* 4.6 1.2 - - - +
160A TYR* 3.5 37.4 - - + +
161A HIS* 3.2 30.6 + - - -
506A GOL 2.6 32.0 + - - +
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Residues in contact with ASN 120 (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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116A THR* 2.9 32.5 + - - +
117A GLN* 3.5 0.6 + - - +
118A LEU 3.2 0.2 - - - -
119A ASN* 1.3 73.2 - - - +
121A LYS* 1.3 69.5 + - - +
122A ILE* 3.2 24.0 + - + +
160A TYR* 4.6 4.4 + - - -
506A GOL 2.6 26.4 + - - -
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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