Contacts of the helix formed by residues 95 - 121 (chain P) in PDB entry 4G7Z
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 THR 95 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P LEU 3.9 2.7 + - - +
94P LEU* 1.3 75.0 - - - +
96P LEU* 1.3 66.1 + - - +
97P GLU* 2.3 32.2 + - - +
98P GLU* 2.9 34.4 + - - +
99P GLU* 3.0 20.7 + - - +
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Residues in contact with LEU 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349N PRO* 3.7 31.4 - - + -
350N HIS* 4.4 19.3 - - + +
95P THR* 1.3 74.1 - - - +
97P GLU* 1.3 68.6 + - + +
99P GLU* 3.1 18.9 + - - +
100P VAL* 2.9 35.6 + - + +
234P LYS* 4.8 21.8 - - + +
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Residues in contact with GLU 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207N PHE* 3.3 46.7 - - + -
209N ARG* 3.7 23.4 + - - +
349N PRO* 4.2 32.3 - - + +
391N ALA* 4.1 14.1 - - + +
95P THR* 2.3 35.7 + - - +
96P LEU* 1.3 77.8 - - + +
98P GLU* 1.3 56.2 + - - +
100P VAL* 3.2 4.0 + - - +
101P GLU 2.8 24.6 + - - -
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Residues in contact with GLU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168N THR* 5.4 5.4 - - - +
206N ARG* 4.7 7.8 - - - +
207N PHE* 3.5 27.5 - - + -
392N SER* 4.9 8.5 + - - -
93P LEU 4.1 2.9 - - - +
94P LEU* 3.3 23.5 - - + +
95P THR* 2.9 45.6 + - - +
96P LEU 3.2 0.2 - - - -
97P GLU* 1.3 75.5 - - - +
99P GLU* 1.3 63.2 + - - +
101P GLU* 3.2 2.1 + - - +
102P LEU* 3.0 34.6 + - + +
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Residues in contact with GLU 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P LEU* 4.2 25.5 - - + +
95P THR 3.0 13.8 + - - +
96P LEU* 3.4 18.3 - - + +
98P GLU* 1.3 76.9 - - - +
100P VAL* 1.3 62.0 + - + +
102P LEU* 4.3 1.3 - - - +
103P ALA* 3.2 27.8 + - + +
187P LEU* 4.8 6.8 - - + +
191P ASN* 4.7 4.5 + - - +
227P PHE* 5.5 2.8 - - + -
234P LYS* 3.5 22.5 - - - +
235P PHE* 2.9 40.6 + - + +
6R T 3.4 22.0 - - - +
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Residues in contact with VAL 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349N PRO 4.2 14.8 - - - +
350N HIS* 3.9 44.4 - - + +
351N MET* 5.9 1.6 - - - +
352N ASN* 6.5 0.4 - - + -
96P LEU* 2.9 26.8 + - + +
97P GLU 3.6 7.2 - - - +
99P GLU* 1.3 75.9 - - + +
101P GLU* 1.3 66.7 + - - +
103P ALA* 3.4 4.1 + - - +
104P ARG* 2.9 32.2 + - - +
229P TYR* 4.0 27.5 - - + -
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Residues in contact with GLU 101 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206N ARG* 2.7 38.2 + - - -
207N PHE* 2.9 20.2 - - + -
97P GLU 2.8 13.1 + - - +
98P GLU* 3.5 7.6 - - - +
100P VAL* 1.3 75.8 - - - +
102P LEU* 1.3 73.5 + - - +
104P ARG* 2.9 24.2 + - - +
105P LYS* 2.9 56.2 + - + +
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Residues in contact with LEU 102 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P LEU* 3.6 41.5 - - + -
98P GLU* 3.0 15.3 + - + +
99P GLU 4.3 1.8 - - - +
101P GLU* 1.3 93.4 - - + +
103P ALA* 1.3 62.5 + - - +
105P LYS* 3.4 1.7 + - + -
106P VAL* 3.1 29.9 + - - +
183P ALA* 3.5 38.1 - - + +
186P HIS* 4.2 21.1 - - + +
187P LEU* 4.2 19.5 - - + +
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Residues in contact with ALA 103 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P GLU* 3.2 21.5 + - + +
100P VAL* 3.9 2.9 - - - +
102P LEU* 1.3 76.5 - - - +
104P ARG* 1.3 61.2 + - - +
106P VAL* 3.5 6.9 - - - +
107P GLU* 3.3 26.3 + - - +
187P LEU* 4.3 16.5 - - + +
227P PHE* 4.1 21.9 - - + +
229P TYR* 4.0 20.2 - - + +
235P PHE* 6.5 0.2 - - + -
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Residues in contact with ARG 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207N PHE* 5.4 3.2 - - - -
352N ASN* 3.8 46.3 + - - +
100P VAL* 2.9 21.4 + - - +
101P GLU* 3.3 37.3 - - - +
103P ALA* 1.3 73.2 - - - +
105P LYS* 1.3 76.9 + - - +
106P VAL 3.1 1.3 - - - -
107P GLU* 3.1 3.5 + - - +
108P GLU* 2.8 72.0 + - + +
229P TYR* 3.8 37.9 - - + +
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Residues in contact with LYS 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440N VAL* 6.3 1.0 - - - +
101P GLU* 2.9 51.3 + - + +
102P LEU* 5.1 1.1 - - + -
104P ARG* 1.3 93.0 - - - +
106P VAL* 1.3 52.8 + - - +
108P GLU* 3.7 10.3 + - - +
109P GLY* 2.7 28.2 + - - -
176P ILE* 4.2 1.6 - - - +
179P GLU* 3.6 44.7 + - + +
180P GLY* 3.2 12.3 + - - -
183P ALA* 3.6 23.8 - - + -
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Residues in contact with VAL 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P LEU 3.1 21.2 + - - +
103P ALA* 3.5 12.6 - - - +
104P ARG 3.1 0.2 - - - -
105P LYS* 1.3 76.4 - - - +
107P GLU* 1.3 62.5 + - + +
109P GLY* 3.1 2.9 + - - -
110P MET* 2.9 43.2 + - + +
180P GLY* 4.0 8.1 - - - -
183P ALA 4.1 0.7 - - - -
184P ARG* 3.5 46.9 - - + +
187P LEU* 4.8 7.9 - - + -
224P VAL* 4.4 18.8 - - + +
225P GLU* 5.6 2.0 - - - +
227P PHE 6.1 1.3 - - - +
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Residues in contact with GLU 107 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P ALA 3.3 8.2 + - - +
104P ARG 3.1 7.9 + - - +
106P VAL* 1.3 83.7 - - + +
108P GLU* 1.3 59.1 + - + +
110P MET* 3.1 14.7 + - - +
111P GLU* 2.9 40.5 + - + +
227P PHE* 3.3 24.0 - - - +
228P GLU* 4.2 13.2 - - - +
229P TYR* 3.2 40.0 + - + -
230P LYS* 4.1 17.8 - - - +
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Residues in contact with GLU 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352N ASN* 5.2 2.3 + - - -
104P ARG* 2.8 60.4 + - + +
105P LYS* 4.0 9.4 + - - +
107P GLU* 1.3 73.5 - - + +
109P GLY* 1.3 60.1 + - - +
111P GLU* 3.8 17.7 - - - +
112P ALA* 2.9 30.3 + - - +
176P ILE* 3.4 16.5 - - + +
229P TYR* 4.5 5.6 + - + +
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Residues in contact with GLY 109 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P LYS 2.7 19.4 + - - -
106P VAL 3.4 2.2 - - - -
108P GLU* 1.3 77.6 - - - +
110P MET* 1.3 51.3 + - - +
112P ALA* 3.2 3.6 + - - +
113P ILE* 2.8 43.3 + - - +
176P ILE* 3.5 19.7 - - - +
177P ALA* 3.7 8.5 - - - +
180P GLY* 4.3 4.3 - - - -
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Residues in contact with MET 110 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P VAL* 2.9 31.7 + - + +
107P GLU* 3.1 15.7 + - - +
109P GLY* 1.3 72.4 - - - +
111P GLU* 1.3 61.9 + - + +
113P ILE* 3.1 17.6 + - + +
114P LYS* 2.8 36.8 + - + +
128P ARG* 5.8 6.1 - - - -
181P GLU* 5.9 1.8 - - - +
225P GLU* 4.3 23.1 - - + +
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Residues in contact with GLU 111 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107P GLU* 2.9 28.7 + - + +
108P GLU* 3.8 19.5 - - - +
110P MET* 1.3 75.3 - - + +
112P ALA* 1.3 57.8 + - - +
114P LYS* 3.0 11.5 + - + +
115P LYS* 2.8 45.0 + - + +
230P LYS* 5.3 8.8 - - - -
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Residues in contact with ALA 112 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P GLU 2.9 19.7 + - - +
109P GLY 3.5 4.5 - - - +
111P GLU* 1.3 73.5 - - - +
113P ILE* 1.3 60.2 + - - +
115P LYS* 3.8 7.8 - - - +
116P LEU* 3.0 33.4 + - - +
173P TYR* 3.5 37.2 - - + +
176P ILE* 3.8 18.4 - - + -
177P ALA 4.3 0.7 - - - +
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Residues in contact with ILE 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P GLY 2.8 20.9 + - - +
110P MET* 3.1 19.7 + - + +
112P ALA* 1.3 76.3 - - - +
114P LYS* 1.3 59.8 + - + +
116P LEU* 3.0 10.2 + - - +
117P SER* 2.9 26.7 + - - -
124P PRO* 3.5 29.8 - - + +
127P ILE* 4.2 16.4 - - + +
128P ARG* 3.6 34.5 - - + +
131P VAL* 5.0 2.7 - - + -
177P ALA* 3.6 21.1 - - + +
181P GLU* 4.4 9.2 - - - +
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Residues in contact with LYS 114 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110P MET* 2.8 20.1 + - + +
111P GLU* 3.3 14.4 - - + +
113P ILE* 1.3 78.6 - - + +
115P LYS* 1.3 61.6 + - + +
117P SER* 3.1 11.1 + - - +
118P GLU* 3.1 34.6 + - - +
124P PRO* 5.6 9.2 - - + -
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Residues in contact with LYS 115 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P GLU* 2.8 36.9 + - - +
112P ALA* 3.8 2.9 - - - +
114P LYS* 1.3 79.9 - - + +
116P LEU* 1.3 58.5 + - - +
118P GLU* 3.3 27.2 + - - +
119P ILE* 3.0 35.8 + - + +
173P TYR* 3.6 42.4 + - + +
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Residues in contact with LEU 116 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ALA 3.0 22.2 + - - +
113P ILE* 3.0 8.4 + - - +
115P LYS* 1.3 78.5 - - - +
117P SER* 1.3 54.8 + - - +
119P ILE* 4.5 5.2 - - + -
120P THR* 2.4 37.4 + - - +
127P ILE* 3.5 22.2 - - + +
131P VAL* 5.3 0.7 - - + -
163P LEU* 4.1 17.9 - - + -
166P LEU* 3.8 22.7 - - + -
170P HIS 3.7 12.6 - - - +
171P LYS* 5.6 0.4 - - - -
173P TYR* 3.4 40.2 - - + +
174P LEU* 3.9 15.3 - - + +
177P ALA* 4.8 4.3 - - + -
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Residues in contact with SER 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ILE 2.9 12.6 + - - -
114P LYS* 3.1 12.4 + - - +
115P LYS 3.2 0.2 - - - -
116P LEU* 1.3 75.4 - - - +
118P GLU* 1.3 65.5 + - - +
119P ILE 3.3 0.2 - - - -
121P GLY* 2.8 28.1 + - - -
122P LEU 3.3 25.4 + - - +
124P PRO* 4.0 25.1 - - - +
127P ILE* 3.8 6.9 - - - +
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Residues in contact with GLU 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P LYS* 3.1 19.3 + - - +
115P LYS* 3.5 35.0 + - - +
117P SER* 1.3 85.3 + - - +
119P ILE* 1.3 63.6 + - + +
121P GLY* 4.2 2.9 + - - -
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Residues in contact with ILE 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P LYS* 3.0 19.5 + - + +
116P LEU* 4.1 9.6 - - + +
118P GLU* 1.3 81.8 - - + +
120P THR* 1.3 61.2 + - - +
166P LEU* 3.9 23.6 - - + -
170P HIS* 3.4 57.7 - - + +
173P TYR* 4.0 21.1 - - + -
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Residues in contact with THR 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P LEU* 2.4 28.1 + - - -
119P ILE* 1.3 77.6 - - - +
121P GLY* 1.3 62.0 + - - +
122P LEU* 3.6 39.0 - - + +
127P ILE* 4.1 4.6 - - - +
162P LYS* 4.6 18.2 - - + +
163P LEU* 4.1 16.1 - - + +
166P LEU* 4.3 15.7 - - + +
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Residues in contact with GLY 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P SER 2.8 15.2 + - - -
118P GLU 4.2 2.2 + - - -
119P ILE 3.5 2.0 + - - -
120P THR* 1.3 79.5 - - - +
122P LEU* 1.3 67.4 + - - +
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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