Contacts of the helix formed by residues 110 - 135 (chain A) in PDB entry 4Z1H
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 GLU 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLU* 4.0 26.1 - - + +
109A LYS* 1.3 78.3 - - - +
111A VAL* 1.3 60.6 + - - +
112A PHE* 3.3 4.2 + - - -
113A ILE* 3.9 7.1 + - - +
114A ARG 4.3 0.5 + - - -
264A PHE* 3.5 28.7 - - + -
269A ARG* 2.5 41.0 + - - +
273A VAL* 3.2 27.7 - - + +
276A LYS* 3.7 14.5 + - - +
277A TYR* 3.2 33.0 + - + +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.7 28.0 - - + -
108A GLU* 3.3 28.0 - - + +
109A LYS 3.1 0.2 + - - -
110A GLU* 1.3 78.5 - - - +
112A PHE* 1.3 61.1 + - - +
113A ILE 3.3 1.8 - - - -
114A ARG* 3.2 48.1 - - - +
115A GLU* 2.9 30.7 + - - +
210A MET* 4.4 3.6 - - + -
277A TYR* 4.1 22.0 - - + +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS 3.2 22.1 + - - +
110A GLU 4.1 1.6 - - - -
111A VAL* 1.3 77.9 - - - +
113A ILE* 1.3 92.9 + - + +
115A GLU* 3.4 1.0 + - - +
116A LEU* 2.9 35.3 + - + +
154A ILE* 4.0 22.4 - - + -
207A SER* 3.5 39.7 - - - +
208A ALA* 4.2 2.5 - - - +
210A MET* 5.1 0.6 - - + +
211A VAL* 3.8 33.2 - - + -
255A ILE* 4.1 17.3 - - + -
264A PHE* 3.7 45.8 - + + -
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Residues in contact with ILE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU 4.0 5.6 - - - +
112A PHE* 1.3 102.5 - - + +
114A ARG* 1.3 57.0 + - - +
116A LEU* 3.8 5.1 - - - +
117A ILE* 2.9 54.8 + - + +
145A LEU* 3.9 17.0 - - + -
154A ILE* 4.1 9.2 - - + -
156A ILE* 4.9 0.6 - - + +
264A PHE* 3.9 26.0 - - + -
270A VAL* 4.1 20.2 - - + -
273A VAL* 3.9 24.0 - - + -
274A VAL* 4.1 9.9 - - + +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.5 24.2 - - - -
110A GLU 4.3 1.2 + - - +
111A VAL* 3.2 44.8 + - - +
113A ILE* 1.3 81.4 - - - +
115A GLU* 1.3 81.4 + - - +
117A ILE* 3.3 3.1 + - - +
118A SER* 2.9 29.8 + - - -
273A VAL* 5.3 0.8 - - - +
277A TYR* 3.8 25.7 - - + -
278A SER* 4.4 10.5 - - - -
370A VAL* 3.3 27.0 - - + +
371A LEU 3.4 28.6 + - - -
372A ILE* 4.1 21.2 + - - +
397A PRO 5.4 3.8 + - - -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.9 29.4 + - + +
111A VAL 2.9 23.5 + - - +
114A ARG* 1.3 100.2 + - - +
116A LEU* 1.3 61.1 + - - +
118A SER* 3.1 13.4 + - - -
119A ASN* 2.9 33.1 + - - +
201A PHE 6.0 0.2 + - - -
204A GLY* 3.9 27.4 - - - +
207A SER* 4.0 7.9 - - - +
370A VAL* 5.4 2.6 - - - +
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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
----------------------------------------------------------
112A PHE* 2.9 35.4 + - + +
113A ILE* 3.8 4.5 - - - +
115A GLU* 1.3 75.7 - - - +
117A ILE* 1.3 63.2 + - - +
119A ASN* 3.1 10.4 + - + +
120A ALA* 2.9 22.7 + - - +
156A ILE* 3.7 32.0 - - + +
204A GLY 4.9 0.9 - - - +
205A PHE* 4.0 34.5 - - + +
207A SER* 5.1 1.6 - - - +
208A ALA* 4.9 3.4 - - + -
253A ILE* 4.0 23.1 - - + -
255A ILE* 3.6 31.4 - - + -
601A 4KP 5.4 1.0 + - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 2.9 38.9 + - + +
114A ARG 3.6 4.7 - - - +
116A LEU* 1.3 74.7 - - - +
118A SER* 1.3 58.3 + - - +
120A ALA* 3.3 4.2 + - - +
121A SER* 2.9 27.0 + - - -
143A ILE* 4.0 3.9 - - + +
145A LEU* 4.3 5.4 - - + -
156A ILE* 3.9 19.3 - - + -
274A VAL* 4.3 10.5 - - + -
278A SER* 3.6 27.6 - - - +
281A VAL* 4.0 18.4 - - + -
285A LEU* 3.6 35.2 - - + -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 2.9 18.0 + - - +
115A GLU* 3.1 19.7 + - - -
117A ILE* 1.3 77.3 - - - +
119A ASN* 1.3 64.4 + - - +
121A SER* 3.1 9.6 + - - -
122A ASP* 3.0 29.3 + - - -
368A ARG* 5.6 4.2 + - - -
370A VAL* 3.9 25.3 - - - +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLU 2.9 18.9 + - - +
116A LEU* 3.5 10.7 - - + +
118A SER* 1.3 77.7 - - - +
120A ALA* 1.3 58.4 + - - +
122A ASP* 3.3 9.3 + - - +
123A ALA* 2.9 29.6 + - - +
201A PHE* 4.1 18.5 + - - -
202A GLY* 3.9 4.1 + - - -
204A GLY* 4.3 2.7 + - - -
205A PHE* 3.6 29.3 - - - +
253A ILE* 6.5 0.4 - - + -
601A 4KP 3.6 43.2 + - + +
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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
----------------------------------------------------------
116A LEU 2.9 13.3 + - - +
117A ILE* 3.5 9.0 - - - +
119A ASN* 1.3 76.9 - - - +
121A SER* 1.3 57.8 + - - +
123A ALA* 3.4 2.1 + - - +
124A LEU* 2.9 34.1 + - - +
143A ILE* 3.9 23.8 - - + -
156A ILE* 4.5 4.9 - - + -
158A ASP* 3.6 35.8 - - + +
601A 4KP 4.2 2.1 + - - +
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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
----------------------------------------------------------
117A ILE 2.9 13.5 + - - -
118A SER* 3.1 13.0 + - - -
120A ALA* 1.3 77.8 - - - +
122A ASP* 1.3 62.2 + - - +
124A LEU 3.4 1.0 + - - -
125A GLU* 2.9 25.7 + - - +
143A ILE* 4.0 3.6 - - - +
281A VAL* 4.2 20.7 - - - +
282A SER* 4.4 7.8 + - - -
283A PHE* 3.4 24.8 - - - -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.0 21.4 + - - +
119A ASN* 3.9 8.2 - - - +
121A SER* 1.3 76.6 + - - +
123A ALA* 1.3 61.2 + - - +
125A GLU* 3.2 9.1 + - - +
126A LYS* 2.9 30.0 + - - +
201A PHE* 5.7 5.4 - - - +
368A ARG* 2.7 39.3 + - - -
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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 ASN 2.9 18.2 + - - +
120A ALA 3.5 4.7 - - - +
122A ASP* 1.3 75.9 - - - +
124A LEU* 1.3 57.6 + - - +
126A LYS* 3.2 1.8 + - - -
127A LEU 3.0 24.6 + - - -
158A ASP* 3.9 9.2 - - - +
161A ILE* 3.2 32.7 + - - +
601A 4KP 3.5 28.9 - - + +
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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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120A ALA 2.9 17.2 + - - +
123A ALA* 1.3 75.8 - - - +
125A GLU* 1.3 58.0 + - - +
127A LEU* 3.4 2.4 + - - +
128A ARG* 2.9 30.5 + - - +
141A MET* 3.5 22.5 - - + +
142A GLU 3.8 10.8 - - - +
143A ILE* 3.5 32.3 - - + -
158A ASP* 4.5 2.5 - - + -
159A THR* 3.5 19.1 - - - +
160A GLY* 3.4 30.5 - - - +
283A PHE* 3.5 37.1 - - + -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 2.9 18.1 + - - +
122A ASP* 3.5 11.9 - - - +
123A ALA 3.2 0.2 - - - -
124A LEU* 1.3 77.5 - - - +
126A LYS* 1.3 57.1 + - - +
128A ARG* 3.4 11.8 + - - +
129A HIS* 2.9 37.4 + - + +
282A SER* 5.0 5.9 + - - -
283A PHE* 3.5 20.6 - - + -
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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 ASP 2.9 15.7 + - - +
123A ALA* 3.2 3.6 + - - +
125A GLU* 1.3 75.2 - - - +
127A LEU* 1.3 64.8 + - - +
129A HIS* 3.7 30.9 - - + +
130A LYS* 2.9 36.7 + - - +
161A ILE* 4.0 24.4 - - + +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA 3.0 5.9 + - - -
124A LEU 3.6 6.3 - - - +
126A LYS* 1.3 77.4 - - - +
128A ARG* 1.3 57.7 + - - +
130A LYS* 3.6 6.0 - - + +
131A LEU* 2.9 50.8 + - + +
139A PRO* 4.1 22.4 - - + -
141A MET* 4.4 10.3 - - + -
159A THR 3.2 27.1 - - - +
160A GLY* 3.8 5.6 - - - +
161A ILE* 3.4 24.5 - - + +
222A ALA* 3.7 29.8 - - + -
249A THR* 5.5 3.1 - - + -
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Residues in contact with ARG 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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124A LEU 2.9 17.9 + - - +
125A GLU* 3.7 14.7 + - - +
127A LEU* 1.3 73.6 - - - +
129A HIS* 1.3 66.1 + - - +
131A LEU* 3.2 4.8 + - - +
132A VAL* 2.9 49.1 + - + +
138A LEU* 4.0 18.2 - - + +
141A MET* 3.5 34.9 - - + +
283A PHE* 4.2 14.6 - - - -
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 2.9 29.2 + - + +
126A LYS* 3.7 28.9 - - + +
128A ARG* 1.3 73.8 - - - +
130A LYS* 1.3 54.9 + - - +
132A VAL* 3.9 4.4 - - - +
133A SER* 2.6 53.2 + - - -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 2.9 29.9 + - - +
127A LEU* 3.6 10.3 - - + +
129A HIS* 1.3 77.3 - - - +
131A LEU* 1.3 60.9 + - + +
133A SER* 3.2 6.5 + - - -
134A ASP* 2.9 48.2 + - - +
161A ILE* 4.3 19.6 - - + +
222A ALA* 4.2 8.7 + - - +
223A ALA* 3.9 31.5 - - - +
224A PRO* 4.8 5.5 - - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 2.9 45.0 + - + +
128A ARG* 4.9 0.7 - - - -
130A LYS* 1.3 82.1 - - + +
132A VAL* 1.3 59.6 + - - +
134A ASP* 3.5 6.4 + - - +
135A GLY 2.8 6.2 + - - -
136A GLN* 2.8 47.0 + - + +
137A ALA 4.0 9.9 - - - +
138A LEU* 3.8 16.2 - - + -
139A PRO* 3.5 33.9 - - + -
141A MET* 5.5 0.2 - - - -
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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
----------------------------------------------------------
128A ARG* 2.9 44.0 + - - +
129A HIS* 4.1 4.0 - - - +
131A LEU* 1.3 73.3 - - - +
133A SER* 1.3 65.8 + - - +
135A GLY* 3.1 14.0 + - - +
136A GLN 4.7 2.2 - - - +
138A LEU* 3.7 25.8 - - + -
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A HIS* 2.6 45.3 + - - -
130A LYS* 3.2 7.6 + - - -
132A VAL* 1.3 78.7 - - - +
134A ASP* 1.3 65.4 + - - +
135A GLY 3.5 0.3 + - - -
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Residues in contact with ASP 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 2.9 38.3 + - - +
131A LEU* 3.9 8.6 - - - +
133A SER* 1.3 81.1 - - - +
135A GLY* 1.3 61.2 + - - +
136A GLN* 4.4 11.2 - - + +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 2.8 5.6 + - - -
132A VAL* 3.1 14.9 + - - -
133A SER 4.6 0.2 - - - -
134A ASP* 1.3 80.7 - - - +
136A GLN* 1.3 63.6 + - - +
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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