Contacts of the helix formed by residues 100 - 126 (chain A) in PDB entry 6XPD
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 VAL 100 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLU* 3.2 33.4 - - + +
89A VAL* 4.7 3.8 - - + -
91A GLY 4.4 5.6 - - - +
92A GLY* 3.9 26.5 - - - +
99A ALA* 1.3 80.5 - - + +
101A VAL* 1.3 57.5 + - - +
102A THR 3.1 3.6 - - - -
103A ASP* 2.9 7.9 + - - +
104A ALA* 2.5 36.3 + - + +
181A VAL* 3.6 30.1 - - + -
184A CYS* 6.2 1.8 - - - -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A VAL* 5.7 7.6 - - + -
97A SER 4.2 14.6 + - - +
98A LEU* 3.8 31.2 - - + -
99A ALA 4.6 0.2 - - - +
100A VAL* 1.3 80.2 - - - +
102A THR* 1.3 63.1 + - - +
104A ALA* 3.4 8.6 - - + -
105A ALA* 2.7 30.0 + - + +
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.5 10.4 + - - +
99A ALA 4.9 4.1 + - - -
100A VAL 3.1 1.0 - - - -
101A VAL* 1.3 86.2 - - - +
103A ASP* 1.3 62.6 + - - +
105A ALA* 3.3 19.5 - - + +
106A HIS* 4.0 3.1 + - - +
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 4.9 5.9 - - - +
99A ALA 5.3 0.6 + - - -
100A VAL* 2.9 10.4 + - - +
102A THR* 1.3 75.5 - - - +
104A ALA* 1.3 61.1 + - - +
105A ALA 2.9 11.2 + - - -
106A HIS* 3.2 19.0 + - - +
107A LEU* 3.7 16.9 + - - +
181A VAL* 4.3 24.3 - - + +
184A CYS* 4.6 6.4 - - - -
185A ALA* 3.2 33.5 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.8 15.5 - - + +
88A GLU* 4.3 17.5 - - + +
89A VAL* 4.6 17.0 - - + -
100A VAL* 2.5 22.7 + - + +
101A VAL* 3.4 11.2 - - + +
103A ASP* 1.3 75.6 + - - +
105A ALA* 1.3 64.1 + - - +
107A LEU* 3.7 13.8 + - - +
108A LEU* 3.6 12.6 + - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 2.7 12.2 + - + +
102A THR* 3.3 17.0 - - + +
103A ASP 2.9 1.8 + - - -
104A ALA* 1.3 75.3 - - - +
106A HIS* 1.3 56.6 + - - +
108A LEU* 2.8 33.6 + - - +
109A ILE* 3.3 13.3 + - + +
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Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR 4.0 3.2 + - - +
103A ASP* 3.2 13.9 + - - +
105A ALA* 1.3 78.7 - - - +
107A LEU* 1.3 57.9 + - + +
109A ILE* 2.9 34.5 + - + +
110A ASN* 2.9 21.9 + - - +
151A ILE* 6.0 3.8 - - + -
154A VAL* 3.9 27.1 - - + -
158A LEU* 3.9 14.4 - - + +
224A ASN* 3.1 32.1 + - + +
227A GLN* 3.6 32.2 - - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A CYS* 3.1 17.9 - - + +
84A PHE* 4.0 15.3 - - + +
85A MET* 3.8 37.5 - - + +
88A GLU* 5.5 7.9 - - + +
103A ASP* 3.7 15.1 + - - +
104A ALA* 3.7 15.0 + - - +
105A ALA 3.0 0.4 + - - -
106A HIS* 1.3 78.4 - - + +
108A LEU* 1.3 59.1 + - - +
110A ASN* 3.3 10.3 + - - +
111A LEU 2.9 24.6 + - - -
185A ALA* 6.5 1.6 - - - -
188A ALA* 5.2 10.5 - - + -
189A ASN* 4.4 8.1 - - - +
192A LEU* 4.0 27.4 - - + -
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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
----------------------------------------------------------
85A MET* 4.4 22.8 - - + +
104A ALA 3.6 6.7 + - - +
105A ALA* 2.8 14.3 + - - +
107A LEU* 1.3 77.8 - - - +
109A ILE* 1.3 52.1 + - + +
111A LEU* 3.8 24.5 - - + -
112A THR* 2.5 43.4 + - - +
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Residues in contact with ILE 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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105A ALA* 3.9 10.1 - - + +
106A HIS* 2.9 33.5 + - + +
108A LEU* 1.3 75.2 - - + +
110A ASN* 1.3 63.3 + - - +
112A THR* 3.1 8.6 + - - -
113A SER* 2.9 27.5 + - - -
151A ILE* 6.1 1.1 - - + -
154A VAL* 4.3 33.0 - - + -
220A HIS* 4.2 16.8 - - + +
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Residues in contact with ASN 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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81A CYS* 4.5 3.1 - - - -
106A HIS* 2.9 12.2 + - - +
107A LEU* 3.7 15.2 - - - +
109A ILE* 1.3 78.0 - - - +
111A LEU* 1.3 61.7 + - - +
113A SER* 2.8 25.5 + - - -
114A PHE* 2.9 32.9 + - + -
189A ASN* 3.9 12.5 + - - -
192A LEU* 4.5 5.2 - - + +
220A HIS* 4.0 9.0 + - - -
221A ALA* 5.1 3.6 - - - +
224A ASN* 2.6 51.9 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.3 42.0 - - - +
81A CYS* 3.5 16.2 - - - -
82A PHE* 4.0 30.1 - - + -
85A MET* 5.5 4.5 - - + -
107A LEU 2.9 10.9 + - - +
108A LEU* 3.7 25.1 - - + +
110A ASN* 1.3 76.1 - - - +
112A THR* 1.3 64.3 + - - +
114A PHE* 3.2 8.5 + - - +
115A LEU* 2.9 33.6 + - + +
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Residues in contact with THR 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* 2.5 31.9 + - - +
109A ILE* 3.1 10.3 + - - -
111A LEU* 1.3 77.6 - - - +
113A SER* 1.3 59.1 + - - +
115A LEU* 3.3 5.2 + - - +
116A LEU* 2.9 36.7 + - + +
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Residues in contact with SER 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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109A ILE 2.9 6.8 + - - -
110A ASN 2.8 10.3 + - - -
112A THR* 1.3 76.9 - - - +
114A PHE* 1.3 62.4 + - - +
116A LEU* 3.3 7.9 + - - +
117A SER* 2.7 39.7 + - - -
147A SER* 4.8 10.6 + - - -
217A ALA* 5.3 0.7 - - - -
220A HIS* 2.9 50.4 - - - +
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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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74A LEU* 4.6 12.1 - - + +
77A ALA* 4.4 3.6 - - + -
78A SER* 4.1 31.4 - - - +
81A CYS* 4.2 3.8 - - + -
110A ASN* 2.9 41.0 + - + +
111A LEU* 3.6 10.3 - - - +
113A SER* 1.3 91.9 + - - +
115A LEU* 1.3 57.2 + - - +
117A SER* 3.2 6.6 + - - -
118A LEU* 2.9 28.5 + - - +
192A LEU* 3.8 25.4 - - + -
196A LEU* 3.6 28.9 - - + -
217A ALA* 3.8 26.2 - - + -
220A HIS* 4.6 1.8 - + - -
221A ALA* 4.3 11.4 - - + -
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Residues in contact with LEU 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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78A SER* 4.9 8.9 - - - +
111A LEU* 2.9 29.5 + - + +
112A THR* 3.9 5.2 - - - +
114A PHE* 1.3 77.1 - - - +
116A LEU* 1.3 57.3 + - - +
118A LEU* 3.3 15.5 + - + +
119A PHE* 2.9 32.8 + - + +
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Residues in contact with LEU 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 THR* 2.9 25.7 + - + +
113A SER* 3.5 8.3 - - - +
115A LEU* 1.3 75.0 - - - +
117A SER* 1.3 59.7 + - - +
119A PHE* 3.2 13.1 + - + +
120A SER* 2.9 36.8 + - - +
143A GLY* 3.8 15.7 - - - +
146A LEU* 4.7 21.8 - - + -
147A SER* 3.5 24.0 - - - +
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 9.9 - - - -
113A SER* 2.7 23.4 + - - -
114A PHE* 3.6 6.9 - - - -
116A LEU* 1.3 78.2 - - - +
118A LEU* 1.3 58.2 + - - +
120A SER* 3.1 8.0 + - - -
121A LEU* 2.9 20.3 + - - +
143A GLY 6.0 1.3 - - - -
144A ALA* 6.1 0.2 - - - -
147A SER* 4.3 9.5 + - - -
213A SER* 2.9 43.1 + - - -
216A ALA* 5.1 3.4 - - - +
217A ALA* 4.3 9.5 + - - +
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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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71A LYS* 4.4 18.6 - - + +
74A LEU* 3.8 17.6 - - + +
75A CYS* 3.7 40.2 - - + +
78A SER* 5.6 3.1 - - - -
114A PHE 2.9 17.4 + - - +
115A LEU* 3.6 16.2 - - + +
117A SER* 1.3 76.5 - - - +
119A PHE* 1.3 64.3 - - - +
121A LEU* 3.1 7.5 + - + +
122A TRP* 2.9 25.1 + - + +
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Residues in contact with PHE 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 LEU* 2.9 20.3 + - + +
116A LEU* 3.2 15.7 + - + +
118A LEU* 1.3 80.2 - - - +
120A SER* 1.3 60.0 + - - +
122A TRP* 3.2 28.0 + + - +
123A LEU* 2.9 57.0 + - + +
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 2.9 18.2 + - - +
117A SER* 3.1 11.2 + - - -
119A PHE* 1.3 81.0 - - - +
121A LEU* 1.3 57.1 + - - +
123A LEU* 3.3 8.7 + - - +
124A SER* 2.9 27.7 + - - -
139A ALA* 3.9 18.4 - - - -
140A GLU* 4.1 15.4 + - - +
143A GLY* 3.5 22.7 - - - -
144A ALA 5.3 0.2 - - - -
213A SER* 4.6 3.6 - - - -
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Residues in contact with LEU 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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67A TYR* 3.5 35.8 - - + +
70A ALA* 3.7 30.1 - - + -
71A LYS* 4.0 19.5 - - + +
74A LEU* 4.2 14.4 - - + -
117A SER 2.9 8.2 + - - +
118A LEU* 3.1 11.9 + - + +
120A SER* 1.3 76.8 - - - +
122A TRP* 1.3 64.0 + - - +
124A SER* 3.0 14.6 + - - -
125A SER 3.0 10.0 + - - -
140A GLU* 3.2 28.5 - - - +
211A ASN* 5.7 5.4 - - - +
213A SER* 4.0 16.5 + - - -
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Residues in contact with TRP 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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67A TYR* 4.0 14.3 + - - +
71A LYS* 5.2 7.4 - - - +
118A LEU* 2.9 18.8 + - + +
119A PHE* 3.2 30.9 + + - +
121A LEU* 1.3 76.9 - - - +
123A LEU* 1.3 82.4 + - + +
125A SER* 2.8 33.9 + - - -
126A LYS* 3.8 24.0 + - + +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 2.9 54.8 + - + +
120A SER* 3.5 9.4 - - - +
122A TRP* 1.3 86.9 - - + +
124A SER* 1.3 65.2 + - - +
125A SER 3.0 1.8 - - - -
126A LYS* 2.8 40.4 + - + +
136A TRP* 3.3 44.1 - - + +
139A ALA* 3.9 15.9 - - + -
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Residues in contact with SER 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 5.1 3.5 - - - -
120A SER 2.9 7.8 + - - -
121A LEU* 3.0 9.5 + - - +
123A LEU* 1.3 75.3 - - - +
125A SER* 1.3 61.8 + - - +
126A LYS 3.3 6.8 + - - +
136A TRP 3.4 18.1 + - - +
137A HIS* 4.1 28.0 + - - -
139A ALA* 4.4 0.2 - - - +
140A GLU* 2.9 44.4 + - - -
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.4 36.1 - - - -
121A LEU 3.0 4.9 + - - -
122A TRP* 2.8 28.1 + - - -
123A LEU 3.0 1.0 + - - -
124A SER* 1.3 77.9 - - - +
126A LYS* 1.3 65.7 + - - +
127A PRO* 3.6 1.7 - - - +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TRP* 3.9 31.6 - - + +
123A LEU* 2.8 39.5 + - + +
124A SER 3.6 6.6 - - - +
125A SER* 1.3 84.2 - - - +
127A PRO* 1.3 76.8 - - + +
128A PRO* 4.6 0.9 - - - +
135A GLY* 5.0 0.2 - - - -
136A TRP* 3.5 36.7 + - + +
137A HIS* 5.6 1.9 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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