Contacts of the helix formed by residues 111 - 133 (chain A) in PDB entry 4ZDR
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 GLN 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 4.5 0.3 - - - -
110A SER* 1.3 84.0 + - - +
112A ALA* 1.3 88.2 + - + +
113A GLU* 3.2 19.1 - - + +
114A SER* 3.0 23.8 + - - +
115A LYS* 3.4 5.1 + - - +
159A GLU* 6.0 2.2 + - - -
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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
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110A SER 4.0 0.8 + - - -
111A GLN* 1.3 84.0 + - + +
113A GLU* 1.3 59.3 + - - +
115A LYS* 3.1 10.7 + - - +
116A VAL* 2.8 35.9 + - + +
155A ILE* 3.8 22.9 - - + -
159A GLU* 4.2 24.2 - - + +
160A MET* 5.1 1.1 - - + -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.6 23.4 + - - +
41A ARG* 3.8 12.3 + - - +
111A GLN* 3.2 15.4 - - + +
112A ALA* 1.3 78.0 - - - +
114A SER* 1.3 60.2 + - - +
116A VAL* 3.6 3.1 + - - +
117A PHE* 3.0 24.4 + - - +
160A MET* 4.0 22.7 - - + +
164A HIS* 3.2 27.1 + - - +
166A ILE* 3.7 19.2 - - + +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 4.4 9.3 + - - -
38A ASN* 4.9 4.0 + - - -
41A ARG* 4.5 12.0 + - - +
109A ALA* 4.3 14.1 - - - -
110A SER 4.7 2.7 - - - -
111A GLN* 3.0 15.2 + - - +
113A GLU* 1.3 79.2 + - - +
115A LYS* 1.3 66.4 + - - +
117A PHE* 3.0 10.3 + - - +
118A TYR* 2.9 39.9 + - - -
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Residues in contact with LYS 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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106A ILE* 5.7 6.0 - - + +
109A ALA* 3.8 20.0 - - + +
111A GLN 3.4 3.4 + - - +
112A ALA* 3.1 15.5 + - - +
114A SER* 1.3 76.1 - - - +
116A VAL* 1.3 59.0 + - - +
118A TYR* 3.1 5.0 + - - +
119A LEU* 2.8 39.5 + - + +
155A ILE* 4.6 15.7 - - + -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 2.8 24.3 + - - +
113A GLU 3.6 5.6 - - - +
115A LYS* 1.3 72.2 - - - +
117A PHE* 1.3 63.7 + - - +
119A LEU* 3.9 6.7 - - - +
120A LYS* 3.0 23.2 + - - +
152A ALA* 3.9 10.4 - - + +
155A ILE* 3.7 30.7 - - + -
156A SER* 3.8 27.4 - - - +
160A MET* 3.9 12.8 - - - -
166A ILE* 3.7 18.6 - - + +
170A LEU* 4.3 13.0 - - + -
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Residues in contact with PHE 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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41A ARG* 3.3 56.5 - - + +
42A ASN* 4.0 6.7 - - - -
45A SER* 4.1 4.3 - - - -
113A GLU 3.0 14.3 + - - +
114A SER* 3.0 14.5 + - - +
116A VAL* 1.3 79.2 - - - +
118A TYR* 1.3 66.1 + + + +
120A LYS* 3.3 7.1 + - - +
121A MET* 3.1 47.5 + - + +
166A ILE* 3.7 23.1 - - + +
243A PRO* 3.8 22.7 - - + -
244A TYR* 3.7 24.5 - + - -
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Residues in contact with TYR 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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35A GLU* 5.9 4.5 - - + +
36A LEU* 4.1 18.0 + - - +
41A ARG* 3.2 41.3 - - + +
44A LEU* 5.0 3.6 - - + -
101A LEU* 3.8 15.1 - - + +
105A LEU* 3.7 54.5 - - + +
106A ILE* 3.7 23.0 - - + +
109A ALA* 4.7 4.0 - - + -
114A SER* 2.9 40.5 + - - +
115A LYS 4.1 2.2 - - - +
117A PHE* 1.3 81.6 - + - +
119A LEU* 1.3 60.4 + - - +
121A MET* 3.2 12.6 + - + +
122A LYS* 2.9 27.9 + - - +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE* 3.8 29.6 - - + -
115A LYS* 2.8 24.4 + - + +
116A VAL 3.9 0.2 - - - +
118A TYR* 1.3 74.3 - - - +
120A LYS* 1.3 64.1 + - - +
122A LYS* 3.1 17.3 + - + +
123A GLY* 2.9 19.8 + - - -
148A ALA* 3.7 14.6 - - - +
151A GLU* 3.8 33.4 - - + +
152A ALA* 3.6 38.6 - - + +
155A ILE* 4.2 13.0 - - + -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 4.1 12.9 - - - +
116A VAL* 3.0 19.2 + - + +
117A PHE* 3.5 6.5 - - - +
119A LEU* 1.3 75.7 - - - +
121A MET* 1.3 66.3 + - + +
123A GLY 3.2 2.3 + - - -
124A ASP* 2.9 48.0 + - - +
149A TYR* 3.6 8.9 - - + -
152A ALA* 4.1 1.5 - - - +
166A ILE* 5.4 4.0 - - + +
169A GLY 3.9 10.1 - - - -
170A LEU* 3.6 42.6 - - + +
173A ASN* 3.3 24.4 - - - +
243A PRO 4.6 2.7 + - - +
244A TYR* 2.6 33.9 + - - +
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Residues in contact with MET 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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41A ARG 5.1 0.4 - - - +
44A LEU* 4.9 10.8 - - + -
45A SER* 3.6 28.3 - - - +
97A VAL* 4.8 5.8 - - + -
101A LEU* 3.7 24.7 - - + -
117A PHE* 3.1 44.5 + - + +
118A TYR* 3.3 19.1 - - + +
119A LEU 3.2 0.2 - - - -
120A LYS* 1.3 80.2 - - + +
122A LYS* 1.3 62.8 + - - +
124A ASP* 3.1 22.4 + - - +
125A TYR* 3.1 40.7 + - + -
243A PRO 5.2 0.9 - - - +
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Residues in contact with LYS 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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98A LEU* 4.0 9.6 - - + +
101A LEU* 3.7 15.7 - - + +
102A GLU* 3.3 25.0 + - - +
106A ILE* 4.0 17.6 - - + +
118A TYR 2.9 13.3 + - - +
119A LEU* 3.2 17.8 - - + +
121A MET* 1.3 73.3 - - - +
123A GLY* 1.3 60.4 + - - +
125A TYR 3.3 0.9 + - - -
126A TYR* 2.9 63.7 + - + +
144A GLN 5.4 1.3 - - - -
148A ALA* 4.0 15.9 - - + +
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Residues in contact with GLY 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 LEU 2.9 11.6 + - - -
120A LYS 3.2 4.0 + - - -
122A LYS* 1.3 76.4 - - - +
124A ASP* 1.3 56.4 + - - +
126A TYR 3.8 0.2 - - - -
127A ARG* 2.8 31.2 + - - +
145A SER* 3.2 29.2 + - - -
148A ALA* 3.6 6.6 - - - +
149A TYR* 3.4 14.4 - - - -
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Residues in contact with ASP 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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49A LYS* 5.3 2.6 - - - -
120A LYS* 2.9 42.5 + - - +
121A MET* 3.1 14.0 + - - +
123A GLY* 1.3 75.7 - - - +
125A TYR* 1.3 65.8 + - + +
127A ARG* 3.0 10.5 + - - +
128A TYR* 2.9 47.2 + - + +
149A TYR* 2.5 30.7 + - - -
173A ASN* 2.8 23.4 + - - +
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Residues in contact with TYR 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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45A SER* 4.2 4.3 + - - -
48A TYR* 3.0 38.4 + + + +
49A LYS* 3.3 11.9 + - + +
52A VAL* 3.6 27.8 - - + -
93A ILE* 5.5 0.7 - - + -
94A CYS* 3.5 25.8 - - - +
97A VAL* 3.9 27.6 - - + -
98A LEU* 4.3 19.3 - - + -
101A LEU* 5.0 0.2 - - + -
121A MET* 3.1 45.6 + - + +
124A ASP* 1.3 82.8 - - + +
126A TYR* 1.3 64.7 + - - +
127A ARG 3.2 0.2 - - - -
128A TYR* 3.4 17.9 + + - -
129A LEU* 3.3 27.9 + - - +
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Residues in contact with TYR 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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98A LEU* 3.6 30.1 - - + +
102A GLU* 6.1 0.7 - - - +
122A LYS* 2.9 55.6 + - + +
125A TYR* 1.3 76.6 - - - +
127A ARG* 1.3 62.9 + - - +
129A LEU* 3.2 12.8 + - + +
130A ALA* 3.0 18.7 + - - +
141A ILE* 3.3 22.4 - - + +
144A GLN* 3.1 52.6 + - + -
145A SER* 3.7 20.6 - - - +
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Residues in contact with ARG 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 GLY 2.8 15.1 + - - +
124A ASP* 3.0 15.0 + - - +
126A TYR* 1.3 77.8 - - - +
128A TYR* 1.3 67.2 + - + +
130A ALA* 3.2 8.7 + - - +
131A GLU* 2.9 37.0 + - + +
145A SER* 3.7 10.9 + - - +
149A TYR* 3.0 16.7 + - - -
173A ASN* 3.6 25.6 + - - +
176A VAL* 3.6 22.8 - - - +
177A PHE* 3.8 25.1 - - + +
180A GLU* 4.1 6.7 + - - -
181A ILE* 3.9 21.1 - - + +
303A SO4 3.0 40.8 + - - -
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Residues in contact with TYR 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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49A LYS* 5.8 3.8 - - - +
52A VAL* 3.9 19.9 - - + +
56A ARG* 3.4 46.6 + - + +
90A LEU* 5.2 6.7 - - + +
94A CYS* 3.8 13.7 - - - -
124A ASP* 2.9 39.8 + - + +
125A TYR* 3.5 37.5 - + - -
126A TYR 3.2 0.6 - - - -
127A ARG* 1.3 91.8 + - + +
129A LEU* 1.3 67.7 + - - +
131A GLU* 3.2 23.1 + - - +
132A VAL* 3.6 9.8 + - - +
173A ASN* 4.8 0.2 + - - -
303A SO4 3.2 19.4 + - - -
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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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90A LEU 5.1 0.2 - - - -
91A ARG* 3.8 35.1 + - + +
94A CYS* 3.5 23.1 - - + -
95A ASN* 3.8 14.6 - - - +
98A LEU* 3.6 31.2 - - + -
125A TYR 3.3 11.2 + - - +
126A TYR* 3.2 17.7 + - + +
128A TYR* 1.3 77.8 - - - +
130A ALA* 1.3 53.5 + - - +
132A VAL* 3.0 11.6 + - + +
133A ALA* 2.8 36.2 + - + +
141A ILE* 3.8 15.5 - - + -
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Residues in contact with ALA 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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126A TYR 3.0 13.2 + - - +
127A ARG* 3.2 13.9 - - - +
129A LEU* 1.3 76.9 - - - +
131A GLU* 1.3 57.4 + - - +
132A VAL 2.8 6.8 + - - -
133A ALA* 3.1 17.9 + - - +
138A LYS* 4.8 5.2 - - - +
141A ILE* 3.5 12.4 - - + +
142A VAL* 3.6 35.0 - - + +
181A ILE* 4.9 10.1 - - + -
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Residues in contact with GLU 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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56A ARG* 2.5 47.6 + - - +
59A TRP* 3.8 25.3 - - + -
60A ARG* 5.4 0.7 + - - -
127A ARG* 2.9 33.2 + - + +
128A TYR* 3.2 17.4 + - - +
130A ALA* 1.3 71.9 - - - +
132A VAL* 1.3 58.8 + - + +
133A ALA 5.4 0.2 - - - -
180A GLU* 4.9 4.7 - - - +
181A ILE* 4.2 19.5 - - + +
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Residues in contact with VAL 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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59A TRP* 3.0 44.2 - - + +
87A GLU* 3.4 22.5 - - + +
90A LEU* 4.0 20.0 - - + -
91A ARG* 2.8 45.8 + - + +
128A TYR 3.9 10.1 - - - +
129A LEU* 3.0 17.8 + - - +
130A ALA 2.9 0.2 - - - -
131A GLU* 1.3 77.4 - - + +
133A ALA* 1.3 64.5 + - - +
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Residues in contact with ALA 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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91A ARG* 4.1 7.0 - - - +
129A LEU* 2.8 15.1 + - + +
130A ALA* 3.1 16.9 + - - +
131A GLU 5.4 0.2 - - - -
132A VAL* 1.3 83.3 - - - +
134A ALA* 1.3 62.1 + - - +
137A ASP* 4.7 2.7 - - + -
138A LYS* 3.9 26.8 - - - +
141A ILE* 4.3 11.0 - - + -
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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