Contacts of the helix formed by residues 134 - 157 (chain T) 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 T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103T PHE* 3.8 1.6 - - - -
132T LEU* 3.3 3.1 - - - +
133T LYS* 1.3 78.7 - - - +
135T LYS* 1.3 63.8 + - - +
136T ALA 3.7 0.2 + - - -
137T LEU* 3.1 39.2 + - - +
138T SER* 2.8 30.7 + - - -
130U GLU* 2.8 27.3 + - - -
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Residues in contact with LYS 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96T VAL* 4.3 14.8 - - + -
103T PHE* 3.5 48.2 - - + -
105T VAL* 5.4 0.4 - - - +
134T SER* 1.3 72.0 + - - +
136T ALA* 1.3 59.7 + - - +
138T SER* 3.0 4.9 + - - -
139T LEU* 2.8 38.6 + - + +
95U PHE* 3.6 37.9 - - + +
97U ASP* 2.8 36.1 + - - +
130U GLU* 4.9 1.0 + - - -
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Residues in contact with ALA 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134T SER* 3.3 0.8 + - - +
135T LYS* 1.3 79.7 - - - +
137T LEU* 1.3 58.3 + - - +
139T LEU 3.3 0.2 + - - -
140T GLU* 2.9 30.9 + - - +
95U PHE* 3.3 25.3 - - + -
105U VAL 4.3 3.8 - - - +
106U GLY* 4.5 2.0 - - - -
126U TYR* 3.6 8.4 - - - -
128U VAL* 3.5 37.0 - - + -
130U GLU* 3.9 12.5 + - + +
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Residues in contact with LEU 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132T LEU* 4.1 16.7 - - + +
134T SER* 3.1 35.0 + - - +
136T ALA* 1.3 84.0 - - + +
138T SER* 1.3 61.8 + - - +
140T GLU* 3.6 22.7 - - - +
141T LYS* 3.2 24.3 + - - +
128U VAL* 4.6 8.7 - - + -
130U GLU* 3.8 15.7 - - - +
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Residues in contact with SER 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103T PHE* 3.7 16.1 + - - +
105T VAL* 3.8 21.5 - - - -
129T SER* 3.4 25.9 + - - -
132T LEU* 3.4 19.3 - - - +
134T SER 2.8 23.7 + - - -
135T LYS 3.3 4.5 - - - -
137T LEU* 1.3 75.8 - - - +
139T LEU* 1.3 65.8 + - - +
141T LYS 3.4 0.7 + - - -
142T ALA* 3.1 21.3 + - - +
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Residues in contact with LEU 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93T VAL* 4.4 17.7 - - + -
96T VAL* 4.0 21.3 - - + -
105T VAL* 3.6 26.2 - - + -
107T VAL* 4.7 2.0 - - + -
135T LYS* 2.8 30.7 + - + +
136T ALA 3.7 0.7 - - - +
138T SER* 1.3 69.5 - - - +
140T GLU* 1.3 67.4 + - - +
142T ALA 3.2 1.2 + - - -
143T ARG* 2.8 32.0 + - + +
94U ASP* 3.4 21.1 - - + +
95U PHE* 3.9 26.5 - - + -
126U TYR* 3.4 16.4 - - + +
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Residues in contact with GLU 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136T ALA 2.9 17.0 + - - +
137T LEU* 3.6 27.2 - - - +
139T LEU* 1.3 77.8 - - - +
141T LYS* 1.3 64.8 + - - +
143T ARG* 4.2 0.3 - - - +
144T LYS* 3.0 56.1 + - + +
126U TYR* 3.5 41.6 - - + +
128U VAL* 4.8 7.0 - - + +
149U ASP* 4.4 0.7 - - - +
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Residues in contact with LYS 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128T VAL 2.6 28.4 + - - +
129T SER* 3.8 14.5 - - - +
132T LEU* 5.1 7.4 - - + -
137T LEU 3.2 16.4 + - - +
138T SER 3.7 3.6 - - - +
140T GLU* 1.3 81.3 - - - +
142T ALA* 1.3 65.0 + - - +
144T LYS* 4.0 2.5 - - - +
145T GLU* 3.0 60.4 + - + +
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Residues in contact with ALA 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105T VAL* 3.9 15.5 - - + +
107T VAL* 3.7 17.5 - - + +
127T GLY* 3.2 35.0 - - - +
128T VAL* 4.0 7.9 - - - +
129T SER 4.3 0.2 - - - +
138T SER 3.1 15.5 + - - +
139T LEU 3.9 0.4 - - - +
141T LYS* 1.3 82.7 - - - +
143T ARG* 1.3 62.2 + - - +
146T ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91T GLN* 2.9 59.5 + - - +
93T VAL* 3.6 25.9 - - - +
107T VAL* 4.1 13.5 - - + -
139T LEU* 2.8 26.5 + - + +
140T GLU* 4.2 2.7 - - - +
142T ALA* 1.3 72.3 - - - +
144T LYS* 1.3 64.5 + - + +
146T ALA 3.4 0.9 + - - -
147T VAL* 3.3 12.1 + - - +
92U ASN* 4.9 4.6 + - - +
94U ASP* 2.6 45.5 + - - -
108U CYS* 3.3 26.3 - - - -
110U PHE* 4.5 5.9 - - - -
124U VAL* 4.1 9.0 - - + -
126U TYR* 3.8 23.3 - - + -
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Residues in contact with LYS 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140T GLU* 3.0 49.0 + - + +
141T LYS* 4.1 2.5 - - - +
143T ARG* 1.3 77.8 - - + +
145T GLU* 1.3 63.3 + - + +
147T VAL* 3.3 5.4 + - - +
148T THR* 3.1 23.8 + - - -
124U VAL* 4.1 14.4 - - + +
126U TYR* 4.0 11.4 - - + +
149U ASP* 2.6 36.2 + - - -
153U ARG* 3.4 40.4 + - - +
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Residues in contact with GLU 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126T TYR 4.1 3.1 - - - +
127T GLY* 4.1 9.1 - - - -
128T VAL* 3.8 10.2 + - - +
141T LYS* 3.0 61.6 + - + +
144T LYS* 1.3 74.0 - - + +
146T ALA* 1.3 60.8 + - - +
148T THR* 4.0 5.6 - - - +
149T ASP* 2.8 34.2 + - + +
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Residues in contact with ALA 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91T GLN* 3.8 11.9 - - - +
107T VAL* 3.5 25.1 - - + +
109T ALA* 3.7 16.1 - - + +
125T GLY* 3.4 8.9 - - - +
126T TYR 3.6 13.0 - - - +
127T GLY* 3.5 1.5 - - - +
142T ALA 3.1 19.4 + - - +
143T ARG 3.7 4.9 - - - +
144T LYS 3.3 0.4 - - - -
145T GLU* 1.3 76.6 - - - +
147T VAL* 1.3 57.5 + - - +
150T GLY* 2.9 24.8 + - - -
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Residues in contact with VAL 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86T HIS* 5.2 6.1 - - + +
88T ILE* 3.8 30.3 - - + -
91T GLN* 3.6 16.4 - - - +
109T ALA* 3.9 11.0 - - + -
111T VAL* 3.6 6.7 - - + +
143T ARG 3.3 0.6 + - - +
144T LYS 3.3 7.5 + - - +
145T GLU 3.2 0.4 - - - -
146T ALA* 1.3 78.2 - - - +
148T THR* 1.3 59.9 + - - +
150T GLY* 3.0 3.1 + - - -
151T LEU* 2.8 28.8 + - + +
110U PHE* 5.1 0.2 - - + -
122U GLU 4.6 3.1 - - - +
123U ASP* 3.5 25.8 - - - +
124U VAL* 3.3 26.7 - - + -
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Residues in contact with THR 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68T GLY* 4.0 27.4 - - - +
72T ILE* 6.5 0.9 - - + -
144T LYS 3.1 14.3 + - - -
145T GLU* 4.0 5.8 - - - -
147T VAL* 1.3 79.5 - - - +
149T ASP* 1.3 62.7 + - - +
151T LEU* 3.3 11.5 + - + +
152T LYS* 2.9 32.2 + - + +
123U ASP* 5.2 2.1 + - - -
153U ARG* 3.7 17.5 + - - -
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Residues in contact with ASP 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S GLU* 5.2 0.4 - - - -
144S LYS* 2.8 28.3 + - - -
125T GLY* 3.4 2.2 - - - -
126T TYR 2.8 32.1 + - - +
145T GLU* 2.8 24.2 + - + +
146T ALA 3.7 2.5 - - - +
148T THR* 1.3 73.9 - - - +
150T GLY* 1.3 57.3 + - - +
152T LYS* 3.3 19.9 + - - +
153T ARG* 2.9 37.9 + - - +
156T ARG* 5.2 4.2 + - - -
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Residues in contact with GLY 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111T VAL* 3.7 15.6 - - - +
123T ASP* 4.4 2.9 - - - +
124T VAL 4.0 5.2 - - - -
125T GLY* 3.3 22.4 - - - -
146T ALA 2.9 12.3 + - - -
147T VAL 3.5 2.7 - - - -
149T ASP* 1.3 75.8 - - - +
151T LEU* 1.3 64.6 + - - +
153T ARG* 3.8 0.9 - - - +
154T ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 151 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T VAL* 5.5 1.3 - - + -
72T ILE* 4.4 26.0 - - + -
84T TRP* 3.9 11.0 - - + -
86T HIS* 3.8 48.5 - - + +
111T VAL* 3.8 13.1 - - + +
113T VAL* 4.7 5.4 - - + -
147T VAL* 2.8 17.6 + - + +
148T THR* 3.7 11.2 - - + +
150T GLY* 1.3 75.7 - - - +
152T LYS* 1.3 67.7 + - + +
154T ALA* 3.3 1.1 + - - +
155T LEU* 3.0 53.3 + - + +
123U ASP* 6.2 0.2 - - - +
157U SER* 5.3 0.4 - - - +
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Residues in contact with LYS 152 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65T TYR* 4.2 16.6 - - - +
66T ILE* 2.8 33.9 + - + +
67T GLU* 4.9 0.2 - - - +
68T GLY* 4.1 14.4 - - - +
71T VAL* 3.9 31.2 - - + -
148T THR* 2.9 27.9 + - + +
149T ASP* 3.7 19.6 + - - +
151T LEU* 1.3 81.0 - - + +
153T ARG* 1.3 63.7 + - - +
155T LEU* 3.3 6.2 + - - +
156T ARG* 3.1 44.2 + - - +
162T LEU 4.8 1.6 - - - +
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Residues in contact with ARG 153 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144S LYS* 3.5 56.9 + - - +
147S VAL* 4.8 0.2 - - - +
148S THR* 3.7 17.8 + - - -
123T ASP* 2.6 60.2 + - + +
124T VAL* 2.8 26.7 + - - +
149T ASP* 2.9 24.4 + - - +
150T GLY 3.9 1.3 - - - +
151T LEU 3.3 0.2 - - - -
152T LYS* 1.3 77.3 - - - +
154T ALA* 1.3 63.3 + - - +
156T ARG* 3.2 45.4 + - - +
157T SER* 3.9 4.7 + - - -
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Residues in contact with ALA 154 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86S HIS* 6.1 0.2 - - - -
111T VAL* 3.7 20.6 - - + +
113T VAL* 3.4 26.0 - - + +
121T HIS* 3.7 12.1 - - - +
122T GLU 4.9 0.7 - - - -
123T ASP* 3.8 12.9 - - - +
150T GLY 2.9 18.1 + - - +
151T LEU* 3.8 4.7 - - - +
153T ARG* 1.3 76.2 - - - +
155T LEU* 1.3 63.6 + - - +
157T SER* 3.1 25.2 + - - -
158T PHE* 4.5 1.2 + - - -
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Residues in contact with LEU 155 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T VAL* 3.8 20.0 - - + -
72T ILE* 6.0 0.2 - - - -
75T ALA* 4.7 8.1 - - + -
79T PHE* 5.0 4.5 - - + -
84T TRP* 4.2 15.7 - - + -
113T VAL* 3.5 29.4 - - + -
151T LEU* 3.0 45.2 + - + +
152T LYS 3.6 4.9 - - - +
154T ALA* 1.3 75.7 - - - +
156T ARG* 1.3 63.6 + - - +
158T PHE* 3.0 30.7 + - + -
162T LEU* 3.5 38.7 - - + +
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Residues in contact with ARG 156 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S ILE* 5.3 3.6 - - + -
65T TYR* 6.2 2.2 - - - +
66T ILE* 5.0 8.9 - - - +
71T VAL* 6.1 1.0 - - - +
149T ASP* 5.2 4.6 + - - -
152T LYS* 3.1 37.7 + - - +
153T ARG* 3.2 37.0 + - - +
155T LEU* 1.3 76.4 - - - +
157T SER* 1.3 63.3 + - - +
158T PHE 3.0 1.6 + - - -
159T GLY 3.1 11.8 + - - +
162T LEU 3.9 9.9 + - - +
163T GLY* 3.7 25.0 + - - +
164T ASN* 3.4 31.5 - - - +
166T ILE* 3.9 24.5 - - - +
167T LEU* 4.2 15.5 - - - +
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Residues in contact with SER 157 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72S ILE* 3.5 23.0 - - - +
76S ASN* 3.0 23.4 + - - +
84S TRP* 3.8 9.7 - - - -
86S HIS* 3.5 17.8 - - - -
151S LEU* 5.1 0.5 - - - +
121T HIS* 3.4 29.6 - - - -
123T ASP* 5.2 2.8 + - - -
153T ARG 4.0 4.9 + - - -
154T ALA* 3.2 15.3 + - - -
155T LEU 3.0 0.6 - - - -
156T ARG* 1.3 78.9 - - - +
158T PHE* 1.3 57.4 + - - +
159T GLY 3.3 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