Contacts of the helix formed by residues 113 - 137 (chain A) in PDB entry 4CCZ
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 LEU 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 5.4 0.2 - - - +
56A PHE* 3.8 19.7 - - + -
69A ILE* 3.8 28.9 - - + -
72A ILE* 4.2 7.4 - - + -
110A LEU* 3.6 26.0 - - + +
111A GLU 3.0 1.6 + - - -
112A HIS* 1.3 99.2 - - + +
114A ALA* 1.3 65.0 + - - +
115A TYR 3.4 2.2 - - - -
116A ARG* 3.4 34.5 + - + +
117A MET* 3.1 29.9 + - + +
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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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100A SER 4.2 8.1 - - - +
101A THR* 4.0 8.3 - - - -
102A SER 3.9 23.8 - - - +
105A GLN* 5.5 0.2 - - - -
110A LEU 4.1 2.1 + - - +
111A GLU 3.5 9.7 + - - +
112A HIS 3.5 2.6 - - - -
113A LEU* 1.3 76.9 - - - +
115A TYR* 1.3 62.3 + - - +
117A MET* 3.2 11.3 + - - +
118A ASN* 2.7 34.3 + - - +
175A ALA 5.8 0.2 - - - +
178A GLU* 4.3 19.0 + - + +
179A GLN 5.4 1.1 - - - +
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A HIS 5.2 1.5 + - - +
113A LEU 3.4 0.4 - - - -
114A ALA* 1.3 79.3 - - - +
116A ARG* 1.3 64.5 + - + +
118A ASN* 3.4 4.8 + - - +
119A MET* 3.0 49.2 + - + +
178A GLU* 3.9 33.1 + - + +
181A LYS* 3.8 12.8 - - + -
182A GLY* 3.4 34.9 - - - -
185A ASP* 2.6 32.4 + - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 2.7 43.4 + - - -
72A ILE* 4.0 24.0 - - + +
113A LEU* 3.4 34.5 + - + +
114A ALA 3.3 0.4 - - - -
115A TYR* 1.3 84.3 - - + +
117A MET* 1.3 61.2 + - - +
119A MET* 3.3 7.4 + - + +
120A CYS* 2.9 43.8 + - - -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.5 46.8 - - + +
69A ILE* 3.7 30.5 - - + +
71A SER* 4.6 2.6 - - - -
72A ILE* 4.3 9.9 - - + -
100A SER* 3.6 13.5 - - - +
105A GLN* 3.6 36.1 - - - +
110A LEU* 4.8 1.3 - - - +
113A LEU* 3.1 35.6 + - + +
114A ALA* 3.2 7.8 + - - +
116A ARG* 1.3 76.7 - - - +
118A ASN* 1.3 51.3 - - - +
120A CYS* 3.7 1.8 - - - +
121A SER* 2.7 38.2 + - - -
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Residues in contact with ASN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 3.4 18.3 - - - +
100A SER* 3.0 25.0 + - - -
114A ALA 2.7 24.5 + - - -
115A TYR 3.7 5.8 - - - +
117A MET* 1.3 73.7 - - - +
119A MET* 1.3 60.6 + - - +
121A SER* 3.7 0.5 - - - -
122A ALA* 2.8 33.8 + - - +
179A GLN* 2.7 56.6 + - - +
182A GLY 4.3 2.2 - - - -
183A LEU* 3.5 15.4 - - + +
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Residues in contact with MET 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 TYR* 3.0 41.4 + - + +
116A ARG* 3.4 10.3 - - + +
118A ASN* 1.3 76.7 - - - +
120A CYS* 1.3 60.5 + - - +
122A ALA* 3.3 3.4 + - - +
123A GLY* 3.0 23.6 + - - -
182A GLY 3.7 9.1 + - - +
185A ASP* 3.8 18.4 - - + +
186A GLY* 3.7 27.7 - - - -
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Residues in contact with CYS 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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71A SER* 4.4 11.4 - - - +
72A ILE* 4.1 25.1 - - + -
116A ARG* 2.9 41.1 + - - +
117A MET 3.8 2.7 - - - +
119A MET* 1.3 77.3 - - - +
121A SER* 1.3 65.8 + - - +
123A GLY* 3.1 2.3 + - - +
124A VAL* 3.0 30.1 + - + +
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 5.5 1.3 - - - -
71A SER* 3.5 23.2 - - - -
78A ILE* 6.1 0.3 - - - +
82A HIS* 4.9 1.7 - - - -
95A THR* 3.9 6.7 - - - +
96A ASN 4.2 11.3 + - - +
97A THR* 3.2 30.5 - - - -
117A MET 2.7 22.8 + - - -
118A ASN 3.7 0.7 - - - -
120A CYS* 1.3 73.1 - - - +
122A ALA* 1.3 61.0 + - - +
124A VAL* 4.3 2.7 - - - +
125A ALA* 3.4 22.9 + - - +
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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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95A THR* 3.8 12.3 - - + +
118A ASN 2.8 18.2 + - - +
119A MET 3.7 4.7 - - - +
121A SER* 1.3 76.7 - - - +
123A GLY* 1.3 58.7 + - - +
125A ALA* 3.7 1.4 + - - +
126A ARG* 3.0 28.9 + - - +
183A LEU* 4.1 4.0 - - - +
186A GLY* 3.7 28.3 - - - +
187A GLY 5.8 0.2 - - - -
188A VAL* 3.9 20.9 - - + +
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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 MET 3.0 14.6 + - - -
120A CYS* 3.1 3.7 + - - -
122A ALA* 1.3 76.0 - - - +
124A VAL* 1.3 59.0 + - - +
126A ARG* 3.1 5.7 + - - +
127A LYS* 2.9 31.1 + - - +
186A GLY* 4.8 3.6 - - - -
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Residues in contact with VAL 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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71A SER* 4.0 21.8 - - - +
75A PRO* 3.9 15.9 - - + +
78A ILE* 4.1 16.2 - - + -
79A TYR* 3.7 45.2 - - + +
82A HIS* 4.1 1.5 + - - +
120A CYS* 3.0 21.3 + - + +
121A SER* 4.4 4.0 - - - +
123A GLY* 1.3 75.4 - - - +
125A ALA* 1.3 60.6 + - - +
127A LYS* 3.7 4.2 + - - -
128A ALA* 3.5 16.8 + - - +
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Residues in contact with ALA 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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82A HIS* 3.5 31.4 + - + +
93A ILE* 5.1 9.3 - - + +
94A GLU 4.8 1.3 - - - +
95A THR* 4.3 14.8 - - + -
121A SER 3.4 17.4 + - - +
122A ALA 4.0 3.6 - - - +
123A GLY 3.2 0.2 - - - -
124A VAL* 1.3 78.7 - - - +
126A ARG* 1.3 59.1 + - - +
128A ALA* 3.4 3.3 + - - +
129A ALA* 3.0 27.6 + - - +
142A VAL* 5.0 10.4 - - + +
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Residues in contact with ARG 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 3.0 20.4 + - - +
123A GLY* 3.1 6.9 + - - +
125A ALA* 1.3 73.8 - - - +
127A LYS* 1.3 63.9 + - - +
129A ALA* 3.6 6.5 + - - +
130A GLU* 3.3 40.0 + - - +
142A VAL* 5.1 7.8 - - + +
186A GLY 4.6 8.3 - - - +
187A GLY 5.1 7.6 - - - +
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Residues in contact with LYS 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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79A TYR* 3.8 16.1 + - + -
123A GLY 2.9 16.3 + - - +
124A VAL* 3.9 8.3 - - - +
125A ALA 3.3 0.2 - - - -
126A ARG* 1.3 76.9 - - - +
128A ALA* 1.3 60.5 + - - +
130A GLU* 3.7 6.6 + - - +
131A GLU* 3.4 20.4 + - - +
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Residues in contact with ALA 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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79A TYR* 3.6 23.5 - - + +
82A HIS* 3.7 21.3 - - + -
83A LYS* 4.5 3.4 - - + +
86A LEU* 3.3 23.7 - - + +
124A VAL 3.5 9.8 + - - +
125A ALA 3.4 6.4 + - - +
126A ARG 3.3 0.2 - - - -
127A LYS* 1.3 77.4 - - - +
129A ALA* 1.3 65.7 + - - +
131A GLU* 3.2 12.6 + - - +
132A VAL* 3.2 10.2 + - - +
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Residues in contact with ALA 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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86A LEU* 3.6 12.9 - - + +
93A ILE* 5.8 1.8 - - + -
125A ALA 3.0 17.5 + - - +
126A ARG* 3.8 10.1 - - - +
127A LYS 3.5 0.2 - - - -
128A ALA* 1.3 78.3 - - - +
130A GLU* 1.3 55.2 + - + +
132A VAL* 3.6 1.0 + - - +
133A THR* 2.7 36.6 + - - -
140A ARG* 3.5 28.4 - - + +
141A PHE 4.9 8.3 - - - +
142A VAL* 5.3 2.9 - - + +
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Residues in contact with GLU 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 ARG* 3.3 27.4 + - - +
127A LYS* 4.2 6.2 - - - +
128A ALA 3.2 0.8 - - - -
129A ALA* 1.3 77.0 - - + +
131A GLU* 1.3 60.6 + - - +
133A THR* 3.5 9.2 - - - +
134A LEU* 2.9 28.4 + - - +
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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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79A TYR* 3.9 16.8 - - - +
127A LYS 3.4 11.9 + - - +
128A ALA 3.2 9.2 + - - +
130A GLU* 1.3 75.5 - - - +
132A VAL* 1.3 59.5 + - - +
134A LEU* 3.2 6.3 + - - +
135A GLN* 2.9 31.8 + - - +
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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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83A LYS* 6.3 0.2 - - - -
86A LEU* 3.7 33.7 - - + +
87A LEU* 5.1 2.2 - - + +
128A ALA 3.2 7.4 + - - +
129A ALA 3.9 7.2 - - - +
131A GLU* 1.3 75.5 - - - +
133A THR* 1.3 59.3 + - - +
135A GLN* 4.5 3.4 - - - +
136A THR* 2.8 41.1 + - - +
138A ILE 4.6 1.3 - - - -
140A ARG* 4.3 13.2 - - + +
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Residues in contact with THR 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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129A ALA 2.7 24.2 + - - -
130A GLU* 3.5 10.6 - - - -
131A GLU 3.2 0.4 - - - -
132A VAL* 1.3 78.0 - - - +
134A LEU* 1.3 57.3 + - - +
137A GLY* 3.0 29.1 + - - +
138A ILE 3.5 9.0 - - - +
139A LYS* 3.8 24.7 - - + +
140A ARG* 3.1 21.3 + - - +
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Residues in contact with LEU 134 (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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130A GLU 2.9 17.8 + - - +
131A GLU* 3.2 6.5 + - - +
133A THR* 1.3 79.5 - - - +
135A GLN* 1.3 62.5 + - - +
137A GLY* 4.1 4.0 + - - -
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Residues in contact with GLN 135 (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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131A GLU 2.9 20.6 + - - +
132A VAL* 4.4 3.6 - - - +
134A LEU* 1.3 77.1 - - - +
136A THR* 1.3 61.4 + - - +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL* 2.8 26.2 + - - -
135A GLN* 1.3 76.7 - - - +
137A GLY* 1.3 55.5 + - - +
138A ILE* 3.4 3.6 + - - -
140A ARG* 3.5 28.9 - - - -
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Residues in contact with GLY 137 (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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133A THR* 3.0 21.8 + - - +
134A LEU 4.1 3.8 + - - -
135A GLN 3.5 0.8 - - - -
136A THR* 1.3 77.6 - - - +
138A ILE* 1.3 60.9 + - - +
139A LYS 3.9 1.0 + - - -
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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
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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