Contacts of the helix formed by residues 102 - 125 (chain A) in PDB entry 3QJQ
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG 4.0 0.4 + - - -
101A PRO* 1.3 66.9 - - - +
103A MET* 1.3 61.0 + - - +
104A GLY* 3.6 10.7 + - - -
105A LEU* 3.8 30.7 + - + +
106A MET* 2.8 28.6 + - - +
161A TYR* 5.5 4.2 - - + -
162A ILE* 4.2 9.8 - - + +
165A ASP* 4.3 22.2 + - - +
169A ARG* 4.3 2.5 - - - +
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Residues in contact with MET 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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16A PRO* 3.7 29.4 - - + +
17A GLU* 3.9 22.7 - - - -
20A ALA* 3.8 11.7 - - + -
100A ARG* 3.8 22.0 - - - +
101A PRO* 2.9 17.2 + - - +
102A ASN* 1.3 69.5 + - - +
104A GLY* 1.3 70.2 + - - +
106A MET* 3.6 23.2 - - + +
107A TRP* 3.0 50.7 + - + +
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Residues in contact with GLY 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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102A ASN* 3.4 7.5 + - - -
103A MET* 1.3 72.2 - - - +
105A LEU* 1.3 54.5 + - - +
107A TRP* 2.6 32.7 + - - +
108A LEU* 2.9 12.0 + - - -
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Residues in contact with LEU 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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102A ASN* 3.7 23.7 + - + +
104A GLY* 1.3 71.8 - - - +
106A MET* 1.3 56.6 + - - +
108A LEU* 3.9 22.2 - - + -
109A SER* 2.9 16.5 + - - -
158A VAL* 3.4 17.5 - - + +
161A TYR* 3.8 34.8 - - + -
162A ILE* 2.9 29.2 - - + +
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Residues in contact with MET 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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17A GLU* 4.0 6.3 - - + +
20A ALA* 3.8 23.2 - - + +
21A THR* 3.4 29.4 - - - +
24A PHE* 4.0 17.4 - - + -
90A VAL* 4.3 21.8 - - + -
91A TYR* 6.0 0.2 - - - -
101A PRO* 3.7 28.5 - - + -
102A ASN 2.8 22.4 + - - +
103A MET* 3.6 25.8 - - + +
104A GLY 2.8 4.6 + - - -
105A LEU* 1.3 67.6 - - - +
107A TRP* 1.3 54.6 + - - +
109A SER* 2.0 26.8 + - - +
110A TRP* 3.5 3.1 + - - +
162A ILE* 3.4 9.8 - - + +
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Residues in contact with TRP 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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16A PRO* 4.9 4.2 + - - +
19A LYS* 3.7 32.2 - - + +
20A ALA* 3.6 32.7 - - + +
23A TYR* 3.9 32.8 - + - -
103A MET* 3.0 38.5 + - + +
104A GLY* 2.6 14.5 + - - +
106A MET* 1.3 71.4 - - - +
108A LEU* 1.3 67.2 + - - +
109A SER 3.3 0.2 - - - -
110A TRP* 3.0 41.4 + + + +
111A TRP* 3.1 31.1 + + + -
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Residues in contact with LEU 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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104A GLY 2.9 11.2 + - - +
105A LEU* 3.9 25.4 - - + +
106A MET 3.4 0.2 - - - -
107A TRP* 1.3 77.9 - - - +
109A SER* 1.3 65.6 + - - +
111A TRP* 3.2 7.1 + - + +
112A MET* 2.8 38.9 + - + +
158A VAL* 4.4 18.8 - - + -
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Residues in contact with SER 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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24A PHE* 3.8 12.5 - - - -
86A GLN* 4.8 2.5 - - - -
105A LEU 2.9 8.7 + - - -
106A MET* 2.0 40.0 + - - +
108A LEU* 1.3 74.3 - - - +
110A TRP* 1.3 66.3 + - - +
112A MET* 3.0 10.1 + - - +
113A ALA* 3.0 15.6 + - - +
155A SER* 3.2 22.4 + - - -
158A VAL* 4.5 14.4 - - - +
159A SER* 4.9 7.0 - - - -
162A ILE* 5.0 1.6 - - - -
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Residues in contact with TRP 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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23A TYR* 3.5 39.2 + + + +
24A PHE* 3.4 51.6 - + + -
27A LEU* 4.1 20.1 - - + +
83A LEU* 5.5 0.4 - - + -
106A MET 4.3 0.9 - - - +
107A TRP* 3.0 34.3 + + + +
109A SER* 1.3 80.0 + - - +
111A TRP* 1.4 116.4 + + - +
113A ALA* 2.7 27.0 + - - +
114A PHE* 2.9 46.3 + + + -
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Residues in contact with TRP 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 TRP* 3.1 34.1 + + + -
108A LEU* 3.6 10.1 - - + +
110A TRP* 1.4 107.9 - + - +
112A MET* 1.3 55.8 + - - +
113A ALA 3.1 0.2 + - - -
114A PHE* 3.1 28.2 + + - -
115A ILE* 2.6 65.6 + - + +
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Residues in contact with MET 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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108A LEU* 2.8 36.2 + - + +
109A SER* 3.1 11.9 - - - +
111A TRP* 1.3 71.3 - - - +
113A ALA* 1.3 56.0 + - - +
115A ILE* 4.7 2.9 - - - +
116A GLY* 3.3 17.6 + - - +
151A VAL* 3.5 47.2 - - + +
154A LEU* 3.9 14.8 - - + -
155A SER* 3.4 41.3 - - - +
158A VAL* 4.2 17.3 - - - -
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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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24A PHE* 5.1 0.9 - - + -
27A LEU* 4.9 3.4 - - + -
82A GLN* 4.9 3.1 - - - +
83A LEU* 3.9 19.1 - - + -
86A GLN* 5.0 0.9 - - - +
109A SER 3.0 7.1 + - - +
110A TRP* 2.7 19.1 + - + +
112A MET* 1.3 71.3 - - - +
114A PHE* 1.3 58.2 + - - +
117A LEU* 2.8 33.0 + - - +
152A PHE* 3.4 30.8 - - + +
155A SER* 4.4 8.7 - - - +
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Residues in contact with PHE 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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27A LEU* 3.8 31.1 - - + +
110A TRP* 2.9 38.5 + + + +
111A TRP* 3.6 33.2 - + - +
113A ALA* 1.3 76.5 - - - +
115A ILE* 1.3 69.3 + - + +
117A LEU* 3.1 7.5 + - + +
118A VAL* 3.0 46.8 + - + +
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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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111A TRP* 2.6 60.6 + - + +
112A MET* 5.2 2.0 - - - +
114A PHE* 1.3 78.4 - - + +
116A GLY* 1.3 60.6 + - - +
118A VAL* 3.5 4.9 + - + +
119A VAL* 3.1 41.3 + - + +
151A VAL* 5.4 4.7 - - + -
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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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112A MET 3.3 17.7 + - - -
113A ALA 3.6 4.0 - - - -
114A PHE 3.1 0.6 - - - -
115A ILE* 1.3 78.1 - - - +
117A LEU* 1.3 56.0 + - - +
119A VAL* 3.4 1.7 + - - +
120A ALA* 3.0 29.6 + - - +
148A GLY* 3.7 22.4 - - - -
151A VAL* 4.3 9.1 - - - +
152A PHE* 4.0 9.4 - - - -
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Residues in contact with LEU 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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27A LEU* 4.6 25.4 - - + -
31A ALA* 5.3 6.7 - - + +
74A VAL* 6.0 1.3 - - + -
75A LEU* 4.2 17.0 - - + -
79A VAL* 3.6 42.2 - - + -
113A ALA 2.8 21.3 + - - +
114A PHE* 3.7 5.6 - - + +
116A GLY* 1.3 68.1 - - - +
118A VAL* 1.3 64.3 + - + +
120A ALA* 3.4 6.9 + - + -
121A ALA* 2.8 39.6 + - + +
152A PHE* 4.2 9.0 - - + -
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Residues in contact with VAL 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 PHE* 3.0 49.0 + - + +
115A ILE* 4.0 5.4 - - + +
117A LEU* 1.3 80.1 - - + +
119A VAL* 1.3 65.9 + - + +
121A ALA* 3.3 4.8 + - - +
122A LEU* 3.0 36.2 + - + +
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Residues in contact with VAL 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* 3.1 31.8 + - + +
116A GLY* 3.8 3.8 - - - +
118A VAL* 1.3 78.1 - - + +
120A ALA* 1.3 50.9 + - - +
122A LEU* 3.2 12.4 + - + +
123A PRO* 2.7 34.3 - - - +
143A TRP* 5.4 1.1 - - + -
144A ALA* 3.3 34.3 - - + +
147A LEU* 4.6 13.7 - - + -
148A GLY* 4.1 10.1 - - - +
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Residues in contact with ALA 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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74A VAL* 6.0 4.0 - - + -
116A GLY 3.0 17.6 + - - +
117A LEU* 3.8 9.0 - - + +
119A VAL* 1.3 76.8 - - - +
121A ALA* 1.3 61.7 + - - +
123A PRO* 3.2 10.4 - - - +
124A LEU* 3.4 22.6 + - + +
144A ALA 3.7 10.5 + - - -
145A PHE* 4.3 15.7 - - + +
148A GLY* 3.9 11.4 - - - -
149A ALA* 4.1 10.3 - - + +
152A PHE* 6.3 0.7 - - + -
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Residues in contact with ALA 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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71A LEU* 6.1 0.9 - - + -
75A LEU* 6.0 4.0 - - + -
117A LEU* 2.8 30.2 + - + +
118A VAL* 3.8 5.4 - - - +
120A ALA* 1.3 71.1 - - - +
122A LEU* 1.3 59.7 + - - +
124A LEU* 2.9 11.4 + - + -
125A LEU* 2.7 52.7 + - + +
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Residues in contact with LEU 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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118A VAL* 3.0 28.4 + - + +
119A VAL* 3.4 12.1 - - + +
121A ALA* 1.3 75.0 - - - +
123A PRO* 1.4 67.2 - - + +
125A LEU* 4.4 5.2 - - + +
126A ALA* 3.4 19.9 + - - +
144A ALA* 5.8 0.4 - - + -
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Residues in contact with PRO 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 VAL 2.7 28.9 - - - +
120A ALA 3.2 10.5 - - - +
122A LEU* 1.4 80.5 - - + +
124A LEU* 1.3 64.1 + - - +
126A ALA* 2.8 13.9 + - + -
128A GLU* 3.1 26.7 + - + -
129A ALA* 4.3 9.0 - - + -
142A HIS* 3.7 29.6 - - + -
144A ALA* 3.7 23.1 - - + -
145A PHE 3.8 11.2 - - - +
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Residues in contact with LEU 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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67A GLN* 2.6 32.7 + - - +
70A THR* 3.4 30.5 - - + -
71A LEU* 3.8 27.5 - - + +
74A VAL* 3.7 32.5 - - + -
75A LEU* 5.6 2.9 - - + -
120A ALA* 3.4 17.9 + - + +
121A ALA* 2.9 12.9 + - + +
123A PRO* 1.3 79.4 - - - +
125A LEU* 1.3 52.6 + - - +
126A ALA 3.1 0.5 + - - -
127A ASN* 3.4 3.1 + - - -
128A GLU 4.5 0.2 + - - -
129A ALA* 3.6 25.9 + - + +
130A THR* 5.1 1.6 + - - -
145A PHE* 4.0 12.8 - - + -
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Residues in contact with LEU 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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34A VAL* 6.0 5.8 - - + -
61A PHE* 4.0 44.7 - - + +
67A GLN* 3.5 10.8 + - - +
71A LEU* 3.9 31.0 - - + -
121A ALA* 2.7 36.5 + - + +
122A LEU* 4.4 4.9 - - + +
124A LEU* 1.3 72.2 - - - +
126A ALA* 1.3 57.3 + - - +
127A ASN 3.4 1.7 + - - -
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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