Contacts of the helix formed by residues 107 - 129 (chain A) in PDB entry 4QA7
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 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A MET* 4.1 7.5 - - - +
83A SER* 2.9 21.7 + - - -
106A GLU* 1.3 76.1 - - - +
108A ILE* 1.3 58.5 + - - +
109A PHE 3.1 2.9 - - - -
110A ASP* 3.2 19.3 + - - +
111A TYR* 3.0 25.9 + - - +
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Residues in contact with ILE 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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30A SER 6.0 1.3 - - - +
31A LEU* 4.9 4.9 - - + -
79A LEU* 3.9 23.8 - - + +
82A VAL* 4.9 4.7 - - + -
83A SER* 3.0 11.9 + - - -
98A LEU* 6.2 0.2 - - + -
103A PRO 4.5 0.4 - - - +
104A ALA* 5.1 1.3 - - - -
105A THR* 3.4 38.4 - - - +
106A GLU 3.2 1.8 - - - -
107A GLY* 1.3 78.4 - - - +
109A PHE* 1.3 59.8 + - - +
111A TYR* 3.4 25.2 - - + +
112A ALA* 3.0 26.3 + - - +
154A TYR* 3.5 49.4 - - + +
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Residues in contact with PHE 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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64A MET* 3.5 27.1 - - + -
67A MET* 3.6 31.2 - - + -
76A LEU* 3.7 22.9 - - + -
79A LEU* 3.9 13.7 - - + +
80A GLN* 3.5 39.0 - - + +
83A SER* 3.0 22.8 + - - +
108A ILE* 1.3 78.3 - - - +
110A ASP* 1.3 71.5 + - - +
112A ALA* 3.4 4.8 + - + +
113A ALA* 2.9 31.3 + - + +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 4.1 11.5 - - - +
61A VAL* 5.5 0.9 - - - +
83A SER* 4.3 3.3 + - - -
107A GLY* 3.2 21.3 + - - +
109A PHE* 1.3 82.9 - - - +
111A TYR* 1.3 60.3 + - - +
113A ALA* 3.8 6.8 - - - +
114A ALA* 2.9 32.1 + - - +
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Residues in contact with TYR 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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27A MET* 3.3 45.4 - - + -
28A CYS* 4.0 7.9 + - - +
30A SER* 3.8 5.8 - - - -
31A LEU* 3.2 54.4 - - + +
34A ILE* 5.2 0.2 - - - +
107A GLY 3.0 13.6 + - - +
108A ILE* 3.4 29.8 - - + +
109A PHE 3.2 0.2 - - - -
110A ASP* 1.3 75.8 - - - +
112A ALA* 1.3 68.1 + - - +
114A ALA* 3.3 3.8 + - - +
115A ILE* 3.1 54.7 + - + +
141A TRP* 4.1 8.5 - + - -
152A PHE 5.1 1.3 + - - -
154A TYR* 4.1 13.9 - + + -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A MET* 5.4 0.7 - - - -
79A LEU* 4.5 9.4 - - + -
108A ILE 3.0 14.9 + - - +
109A PHE* 3.8 4.7 - - + +
111A TYR* 1.3 85.4 - - - +
113A ALA* 1.3 58.3 + - - +
115A ILE* 3.3 3.7 + - - +
116A GLY* 2.8 30.0 + - - -
154A TYR* 4.4 13.5 - - + -
155A LEU* 3.7 37.0 - - + +
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Residues in contact with ALA 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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61A VAL* 4.5 6.7 - - + -
62A ALA* 2.9 34.7 + - - +
67A MET* 4.0 21.9 - - + -
109A PHE* 2.9 23.7 + - + +
110A ASP* 3.8 7.2 - - - +
112A ALA* 1.3 75.1 - - - +
114A ALA* 1.3 57.8 + - - +
117A GLY 2.9 22.5 + - - -
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Residues in contact with ALA 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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24A TYR* 3.7 18.0 - - + -
27A MET* 3.9 19.5 - - + -
59A PRO* 5.0 0.5 - - - +
60A LYS 4.2 2.8 - - - +
61A VAL* 4.2 19.7 - - + +
110A ASP 2.9 18.4 + - - +
111A TYR 3.5 4.9 - - - +
113A ALA* 1.3 74.7 - - - +
115A ILE* 1.3 61.0 - - + +
117A GLY* 3.4 1.2 + - - -
118A ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 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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24A TYR* 4.0 7.2 - - + +
27A MET* 5.9 0.2 - - + -
28A CYS* 3.8 23.6 - - + -
111A TYR* 3.1 56.1 + - + +
112A ALA* 3.9 4.5 - - - +
114A ALA* 1.3 73.5 - - + +
116A GLY* 1.3 65.3 + - - +
118A ALA* 3.3 10.4 + - - +
119A THR* 3.3 15.4 + - - -
136A ASN* 4.1 0.5 + - - -
138A SER 3.5 12.3 - - - +
139A GLY* 4.3 1.8 - - - -
141A TRP* 3.3 37.5 - - + +
155A LEU* 5.4 3.1 - - + +
157A ASP* 3.8 13.2 - - + +
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Residues in contact with GLY 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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62A ALA* 4.0 6.7 - - - -
112A ALA 2.8 20.4 + - - -
113A ALA 4.0 0.7 - - - -
115A ILE* 1.3 74.1 - - - +
117A GLY* 1.3 60.6 + - - +
119A THR* 3.5 3.8 + - - -
120A ILE* 3.2 28.3 + - - +
155A LEU* 3.6 21.2 - - - +
157A ASP* 3.9 8.1 - - - -
160A LEU* 4.3 5.0 - - - +
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Residues in contact with GLY 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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60A LYS* 3.2 20.5 - - - +
61A VAL 4.1 0.2 - - - -
62A ALA* 3.5 20.7 - - - +
66A GLU* 5.6 0.2 - - - -
113A ALA 2.9 12.0 + - - -
116A GLY* 1.3 73.3 - - - +
118A ALA* 1.3 55.5 + - - +
120A ILE* 3.6 6.1 - - - +
121A THR* 2.7 37.9 + - - -
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Residues in contact with ALA 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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19A ILE* 3.8 11.8 - - + +
24A TYR* 3.3 38.1 - - + +
59A PRO* 3.7 20.0 - - + -
60A LYS 3.6 0.4 + - - -
114A ALA 3.0 12.2 + - - +
115A ILE 3.6 3.1 - - - +
116A GLY 3.3 0.4 - - - -
117A GLY* 1.3 77.6 - - - +
119A THR* 1.3 57.5 + - - +
121A THR* 3.5 3.8 + - - -
122A ALA* 3.1 25.5 + - - +
136A ASN* 3.7 6.4 + - - +
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Residues in contact with THR 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 ILE 3.3 2.5 + - - -
116A GLY 4.0 2.0 - - - -
117A GLY 3.3 0.2 - - - -
118A ALA* 1.3 75.7 - - - +
120A ILE* 1.3 61.2 + - - +
122A ALA* 3.3 5.4 + - - +
123A ALA* 2.9 27.2 + - - +
136A ASN* 3.0 16.6 + - - +
157A ASP* 2.8 59.6 + - - +
158A ALA* 4.7 0.2 - - - -
161A GLY* 4.0 11.7 - - - -
299A LEU* 3.8 9.8 - - + +
301A LEU* 3.9 18.8 - - + +
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Residues in contact with ILE 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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62A ALA* 4.2 13.0 - - + -
66A GLU* 4.0 36.1 - - + +
116A GLY 3.2 15.7 + - - +
117A GLY* 3.6 7.6 - - - +
119A THR* 1.3 77.8 - - - +
121A THR* 1.3 52.1 + - - +
123A ALA* 3.1 8.7 + - - +
124A GLN* 2.8 32.7 + - + +
160A LEU* 4.1 33.9 - - + +
161A GLY* 4.9 1.6 - - - -
164A ARG* 3.5 38.7 - - + +
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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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19A ILE* 3.9 7.9 - - + -
57A VAL* 3.8 28.9 - - + -
58A LYS 4.1 8.3 - - - +
59A PRO* 4.4 0.9 - - + -
60A LYS* 3.2 25.3 + - + +
117A GLY 2.7 23.3 + - - -
118A ALA* 3.6 8.5 - - - -
120A ILE* 1.3 78.1 - - - +
122A ALA* 1.3 60.9 + - - +
124A GLN* 3.1 9.7 + - + +
125A CYS* 3.0 25.6 + - - -
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Residues in contact with ALA 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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19A ILE* 3.9 18.6 - - + +
118A ALA 3.1 11.9 + - - +
119A THR* 3.5 9.9 - - - +
120A ILE 3.3 0.2 - - - -
121A THR* 1.3 78.8 - - - +
123A ALA* 1.3 62.2 + - - +
125A CYS* 3.3 4.1 + - - +
126A LEU* 3.2 27.6 + - - +
134A ALA* 3.5 25.9 - - + +
136A ASN* 4.9 3.1 - - + -
299A LEU* 3.9 16.8 - - + -
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Residues in contact with ALA 123 (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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119A THR 2.9 13.2 + - - +
120A ILE 3.4 9.0 - - - +
122A ALA* 1.3 76.2 - - - +
124A GLN* 1.3 61.8 + - - +
126A LEU* 3.3 5.0 + - - +
127A ILE* 3.1 28.4 + - - +
161A GLY* 3.6 25.1 - - - +
164A ARG* 3.7 15.0 - - + -
165A LEU* 3.5 12.8 - - + +
299A LEU* 3.8 11.6 - - + +
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Residues in contact with GLN 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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120A ILE 2.8 13.8 + - - +
121A THR* 3.1 13.9 + - + +
123A ALA* 1.3 78.3 - - - +
125A CYS* 1.3 57.2 + - - +
127A ILE* 3.4 14.8 + - - +
128A ASP* 3.1 67.7 + - - +
164A ARG* 2.6 40.4 + - - +
167A ARG* 5.0 2.1 + - - -
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Residues in contact with CYS 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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17A VAL* 4.1 18.2 - - + -
57A VAL* 4.3 15.9 - - - -
121A THR* 3.0 22.2 + - - -
122A ALA* 3.5 9.6 - - - +
123A ALA 3.2 0.2 - - - -
124A GLN* 1.3 75.9 - - - +
126A LEU* 1.3 65.2 + - - +
128A ASP 3.5 0.7 + - - -
129A GLY 3.1 17.0 + - - -
130A MET* 3.3 52.0 + - + +
131A CYS* 3.9 12.6 + - - -
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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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122A ALA 3.2 22.5 + - - +
123A ALA* 3.3 9.2 + - - +
125A CYS* 1.3 79.4 - - - +
127A ILE* 1.3 64.1 + - - +
129A GLY* 3.2 12.5 + - - -
131A CYS* 3.5 35.8 - - - +
132A LYS 3.7 18.8 - - - +
133A VAL 4.1 0.7 - - - +
134A ALA* 3.7 14.6 - - + +
165A LEU* 3.8 14.1 - - + -
168A LYS* 5.2 0.5 + - - -
169A PHE* 4.2 12.0 - - + -
297A ALA* 3.9 23.8 - - + +
298A THR 4.0 5.6 - - - +
299A LEU* 3.9 26.0 - - + +
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Residues in contact with ILE 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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123A ALA 3.1 16.2 + - - +
124A GLN* 3.6 18.2 - - - +
125A CYS 3.3 0.4 - - - -
126A LEU* 1.3 77.0 - - - +
128A ASP* 1.3 70.0 + - - +
129A GLY* 3.2 1.7 + - - -
164A ARG* 3.2 45.3 - - + +
165A LEU* 4.4 8.3 - - + -
167A ARG* 4.5 10.5 - - + -
168A LYS* 3.4 52.6 + - + -
169A PHE* 4.5 1.3 - - + -
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN* 3.1 45.4 + - - +
125A CYS 3.5 3.8 + - - +
126A LEU 3.4 0.2 - - - -
127A ILE* 1.3 79.1 - - - +
129A GLY* 1.3 61.1 + - - +
130A MET* 3.5 18.9 + - + +
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Residues in contact with GLY 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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13A SER* 3.7 19.4 + - - -
125A CYS 3.1 5.0 + - - -
126A LEU 3.2 10.5 + - - -
127A ILE 3.1 5.3 - - - -
128A ASP* 1.3 81.0 - - - +
130A MET* 1.3 59.1 + - - +
131A CYS 3.1 11.7 + - - -
168A LYS* 6.2 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
------------------------------------------------------------
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