Contacts of the helix formed by residues 134 - 157 (chain S) in PDB entry 1H2I
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 SER 134 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S PHE* 3.8 1.8 - - - -
132S LEU* 3.3 2.7 - - - +
133S LYS* 1.3 78.4 - - - +
135S LYS* 1.3 62.6 + - - +
136S ALA 3.6 0.3 + - - -
137S LEU* 3.1 38.2 + - - +
138S SER* 3.0 27.9 + - - -
130T GLU* 2.9 25.3 + - - -
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Residues in contact with LYS 135 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96S VAL* 4.4 15.3 - - + -
103S PHE* 3.5 48.0 - - + -
133S LYS 3.7 0.2 + - - -
134S SER* 1.3 72.4 + - - +
136S ALA* 1.3 58.7 + - - +
138S SER* 3.0 5.0 + - - -
139S LEU* 2.8 39.1 + - + +
95T PHE* 3.8 36.7 - - + +
97T ASP* 2.9 34.1 + - - +
130T GLU* 4.9 1.0 + - - -
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Residues in contact with ALA 136 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134S SER* 3.3 0.8 + - - +
135S LYS* 1.3 79.8 - - - +
137S LEU* 1.3 59.6 + - + +
139S LEU* 3.3 1.8 + - - +
140S GLU* 2.9 30.8 + - - +
95T PHE* 3.6 24.0 - - + -
105T VAL 4.7 2.0 - - - +
126T TYR* 3.8 8.4 - - + -
128T VAL* 3.7 36.6 - - + -
130T GLU* 3.8 14.7 + - + +
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Residues in contact with LEU 137 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132S LEU* 4.1 17.5 - - + +
134S SER* 3.1 30.5 + - - +
136S ALA* 1.3 84.3 - - + +
138S SER* 1.3 61.2 + - - +
140S GLU* 3.6 22.5 + - - +
141S LYS* 3.1 23.9 + - - +
128T VAL* 5.0 8.1 - - + -
130T GLU* 4.0 14.1 - - - +
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Residues in contact with SER 138 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103S PHE* 3.7 16.6 + - - +
105S VAL* 3.8 20.9 - - - -
129S SER* 3.3 30.7 + - - -
132S LEU* 3.4 15.2 - - - +
134S SER 3.0 22.8 + - - -
135S LYS 3.0 4.9 + - - -
137S LEU* 1.3 74.8 - - - +
139S LEU* 1.3 66.8 + - - +
141S LYS 3.3 1.4 + - - -
142S ALA* 3.0 20.4 + - - +
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Residues in contact with LEU 139 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93S VAL* 4.4 19.5 - - + -
96S VAL* 4.0 22.7 - - + -
105S VAL* 3.7 24.7 - - + -
107S VAL* 4.7 2.7 - - + -
135S LYS* 2.8 27.5 + - + +
136S ALA 3.7 1.1 - - - +
138S SER* 1.3 78.0 - - - +
140S GLU* 1.3 64.2 + - - +
142S ALA* 3.2 1.6 + - - +
143S ARG* 2.9 32.6 + - + +
94T ASP* 3.5 20.2 - - + +
95T PHE* 4.1 23.6 - - + -
126T TYR* 3.4 14.8 - - + +
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Residues in contact with GLU 140 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136S ALA 2.9 17.4 + - - +
137S LEU* 3.6 26.6 - - - +
139S LEU* 1.3 76.9 - - - +
141S LYS* 1.3 65.4 + - - +
143S ARG* 4.1 0.6 - - - +
144S LYS* 3.0 61.5 + - + +
126T TYR* 3.8 35.3 - - + +
128T VAL* 5.0 7.5 - - + +
149T ASP* 4.4 1.2 - - - +
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Residues in contact with LYS 141 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S VAL* 2.6 27.6 + - - +
129S SER* 4.0 13.8 - - - +
132S LEU* 5.1 7.6 - - + -
137S LEU 3.1 15.7 + - - +
138S SER 3.8 3.4 - - - +
140S GLU* 1.3 80.8 - - - +
142S ALA* 1.3 65.1 + - - +
144S LYS* 4.0 2.6 - - - +
145S GLU* 3.0 60.7 + - + +
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Residues in contact with ALA 142 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105S VAL* 3.8 16.4 - - + +
107S VAL* 3.7 19.0 - - + +
127S GLY* 3.3 34.3 - - - +
128S VAL 4.1 6.5 - - - +
129S SER* 4.5 0.2 - - - -
138S SER 3.0 17.1 + - - +
139S LEU 3.9 1.3 - - - +
141S LYS* 1.3 78.9 - - - +
143S ARG* 1.3 61.9 + - - +
146S ALA* 3.1 21.5 + - - +
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Residues in contact with ARG 143 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S GLN* 2.9 63.9 + - - +
93S VAL* 3.5 27.6 - - - +
107S VAL* 4.1 12.6 - - + -
139S LEU* 2.9 23.1 + - + +
140S GLU* 4.2 2.9 - - - +
142S ALA* 1.3 76.7 - - - +
144S LYS* 1.3 64.4 + - + +
147S VAL* 3.3 13.2 + - - +
92T ASN* 5.0 3.2 + - - +
94T ASP* 2.7 44.8 + - - -
108T CYS* 3.5 24.4 - - - -
110T PHE* 4.5 4.6 - - - -
124T VAL* 4.3 9.6 - - + -
126T TYR* 3.8 22.7 - - + -
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Residues in contact with LYS 144 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S GLU* 3.0 49.1 + - + +
141S LYS* 4.1 3.1 - - - +
143S ARG* 1.3 78.3 - - + +
145S GLU* 1.3 62.4 + - + +
147S VAL* 3.4 4.0 + - - +
148S THR* 3.2 24.3 + - - -
124T VAL* 4.3 9.0 - - + +
125T GLY 4.6 0.2 - - - -
126T TYR* 4.1 10.8 - - + +
149T ASP* 2.8 34.0 + - - -
153T ARG* 3.5 47.1 + - - +
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Residues in contact with GLU 145 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126S TYR 3.9 4.0 - - - +
127S GLY* 4.2 7.6 - - - -
128S VAL* 3.7 10.9 + - - +
141S LYS* 3.0 62.7 + - + +
144S LYS* 1.3 73.8 - - + +
146S ALA* 1.3 61.4 + - - +
148S THR* 4.1 5.6 - - - +
149S ASP* 2.8 34.1 + - + +
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Residues in contact with ALA 146 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S VAL* 3.6 17.5 - - + +
109S ALA* 3.7 22.9 - - + +
125S GLY* 3.4 8.1 - - - -
126S TYR 3.5 12.3 - - - -
127S GLY* 3.6 12.3 - - - +
142S ALA 3.1 19.8 + - - +
143S ARG 3.7 4.5 - - - +
144S LYS 3.3 0.4 - - - -
145S GLU* 1.3 77.7 - - - +
147S VAL* 1.3 52.5 + - - +
150S GLY* 2.8 31.4 + - - -
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Residues in contact with VAL 147 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S HIS* 5.1 6.3 - - + +
88S ILE* 3.8 27.4 - - + -
91S GLN* 3.5 17.5 - - - +
109S ALA* 3.9 11.7 - - + -
111S VAL* 3.6 5.9 - - + +
143S ARG 3.3 1.0 + - - +
144S LYS 3.7 6.7 - - - +
145S GLU 3.2 0.4 - - - -
146S ALA* 1.3 77.6 - - - +
148S THR* 1.3 60.1 + - - +
150S GLY* 3.0 2.6 + - - -
151S LEU* 2.8 30.0 + - + +
110T PHE* 5.1 0.2 - - + -
122T GLU 4.6 3.6 - - - +
123T ASP* 3.3 28.7 - - - +
124T VAL* 3.2 27.8 - - + -
153T ARG* 4.9 0.2 - - - +
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Residues in contact with THR 148 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S GLY* 4.1 26.9 - - - +
72S ILE* 6.5 0.7 - - + -
144S LYS 3.2 15.1 + - - -
145S GLU* 4.1 5.2 - - - -
147S VAL* 1.3 79.6 - - - +
149S ASP* 1.3 64.1 + - - +
151S LEU* 3.3 10.2 + - + +
152S LYS* 2.9 33.4 + - + +
123T ASP* 5.1 2.4 + - - -
153T ARG* 3.7 17.5 + - - -
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Residues in contact with ASP 149 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140R GLU* 5.2 0.7 - - - -
144R LYS* 2.7 33.7 + - - -
125S GLY* 3.3 2.3 - - - -
126S TYR 2.9 26.0 + - - +
145S GLU* 2.8 24.3 + - + +
146S ALA 3.5 3.1 - - - +
148S THR* 1.3 74.6 - - - +
150S GLY* 1.3 57.9 + - - +
152S LYS* 3.4 18.8 + - - +
153S ARG* 3.0 38.8 + - - +
156S ARG* 5.2 4.3 + - - -
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Residues in contact with GLY 150 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111S VAL* 3.7 16.6 - - - +
123S ASP* 4.4 3.1 - - - +
124S VAL 4.0 4.3 - - - -
125S GLY* 3.3 21.9 - - - -
146S ALA 2.8 13.3 + - - -
147S VAL 3.5 3.1 - - - -
149S ASP* 1.3 74.5 - - - +
151S LEU* 1.3 58.8 + - - +
153S ARG* 3.1 2.3 + - - +
154S ALA* 2.8 31.7 + - - +
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Residues in contact with LEU 151 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S VAL* 5.5 1.6 - - + -
72S ILE* 4.4 20.9 - - + -
84S TRP* 3.9 14.8 - - + -
86S HIS* 3.8 50.3 - - + +
111S VAL* 3.7 14.2 - - + +
113S VAL* 4.7 5.4 - - + -
147S VAL* 2.8 20.2 + - + +
148S THR* 3.6 11.7 - - + +
150S GLY* 1.3 72.9 - - - +
152S LYS* 1.3 65.6 + - + +
154S ALA* 3.3 0.9 + - - +
155S LEU* 3.0 48.5 + - + +
157T SER* 5.1 0.4 - - - +
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Residues in contact with LYS 152 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65S TYR* 4.1 16.6 - - - +
66S ILE* 2.7 33.2 + - + +
67S GLU* 4.9 0.4 - - - +
68S GLY* 4.1 11.8 - - - +
71S VAL* 3.9 31.4 - - + -
148S THR* 2.9 33.2 + - + +
149S ASP* 3.7 19.8 + - - +
151S LEU* 1.3 78.1 - - + +
153S ARG* 1.3 62.1 + - - +
155S LEU* 3.4 6.9 + - - +
156S ARG* 3.1 45.7 + - - +
162S LEU 4.7 1.9 - - - +
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Residues in contact with ARG 153 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144R LYS* 3.4 57.6 + - - +
148R THR* 3.8 17.6 + - - -
123S ASP* 2.4 58.8 + - + +
124S VAL* 2.9 22.9 + - - +
149S ASP* 3.0 24.2 + - - +
150S GLY 3.8 2.9 - - - +
152S LYS* 1.3 73.2 - - + +
154S ALA* 1.3 70.0 + - - +
156S ARG* 3.3 42.0 + - - +
157S SER* 3.9 4.7 + - - -
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Residues in contact with ALA 154 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111S VAL* 3.8 15.0 - - + +
113S VAL* 3.3 26.8 - - + +
121S HIS* 3.7 16.4 + - - +
122S GLU 4.8 1.1 - - - -
123S ASP* 3.7 12.0 - - - +
150S GLY 2.8 20.4 + - - +
151S LEU* 3.7 6.3 - - - +
153S ARG* 1.3 76.4 - - - +
155S LEU* 1.3 63.2 + - - +
157S SER* 3.1 23.2 + - - -
158S PHE* 4.5 0.7 + - - -
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Residues in contact with LEU 155 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S VAL* 3.9 20.2 - - + +
72S ILE* 6.0 0.2 - - - -
75S ALA* 4.6 7.6 - - + -
79S PHE* 5.0 4.7 - - + -
84S TRP* 4.2 15.9 - - + -
113S VAL* 3.5 29.8 - - + -
151S LEU* 3.0 45.8 + - + +
152S LYS 3.7 4.7 - - - +
154S ALA* 1.3 76.7 - - - +
156S ARG* 1.3 63.3 + - - +
157S SER 3.0 1.2 + - - -
158S PHE* 3.0 29.0 + - + +
162S LEU* 3.5 38.8 - - + +
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Residues in contact with ARG 156 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ILE* 5.3 3.1 - - + -
65S TYR* 6.2 2.0 - - - +
66S ILE* 4.9 8.9 - - - +
71S VAL* 6.2 1.0 - - - +
149S ASP* 5.2 4.6 + - - -
152S LYS* 3.1 41.4 + - - +
153S ARG* 3.6 34.5 - - - +
154S ALA 3.2 0.8 + - - -
155S LEU* 1.3 75.4 - - - +
157S SER* 1.3 64.0 + - - +
158S PHE 3.0 1.4 + - - -
159S GLY 3.0 11.8 + - - +
162S LEU 3.8 11.7 + - - +
163S GLY* 3.7 22.6 + - - +
164S ASN* 3.3 29.5 - - - +
166S ILE* 3.9 26.0 - - - +
167S LEU* 4.2 17.4 - - - +
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Residues in contact with SER 157 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72R ILE* 3.4 23.1 - - - +
76R ASN* 2.9 24.8 + - - +
84R TRP* 3.9 9.3 - - - -
86R HIS* 3.5 18.7 + - - -
151R LEU* 5.2 1.0 - - - +
121S HIS* 3.4 30.2 - - - -
123S ASP* 5.2 2.4 + - - -
153S ARG 4.0 5.0 + - - -
154S ALA* 3.1 16.4 + - - -
155S LEU 3.0 0.8 + - - -
156S ARG* 1.3 79.1 - - - +
158S PHE* 1.3 56.5 + - - +
159S GLY 3.2 0.4 - - - -
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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