Contacts of the helix formed by residues 108 - 129 (chain D) in PDB entry 4HHM
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 ASP 108 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334C ARG* 2.7 53.6 + - - +
337C GLN* 3.5 9.7 + - - +
365C ALA 5.5 0.5 - - - +
368C ARG* 3.4 23.7 + - - +
370C MET* 3.9 8.3 - - - +
101D ASP* 5.9 0.2 - - - +
106D ALA* 3.2 5.2 - - + +
107D ASN* 1.3 74.4 - - - +
109D ARG* 1.3 65.2 + - - +
110D ASP* 3.3 17.5 - - - +
111D VAL* 3.4 20.8 + - + +
112D ARG* 3.5 13.0 + - - +
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLN* 3.0 20.9 - - + +
340C GLU* 5.1 8.5 - - + -
341C PRO 3.1 23.7 + - - -
342C THR* 3.2 14.4 + - - +
343C ALA* 4.5 1.0 - - - +
344C ALA* 4.9 2.6 - - - +
345C ASP* 4.4 8.5 + - - -
107D ASN 3.5 2.0 + - - -
108D ASP* 1.3 68.7 - - - +
110D ASP* 1.3 67.7 + - - +
112D ARG* 3.1 27.7 + - - +
113D ARG* 3.0 60.9 + - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLN* 4.8 1.8 - - - +
355C THR 5.6 1.8 - - - +
356C ALA* 5.3 2.0 - - - +
360C PHE* 3.7 28.1 - - + -
365C ALA* 4.8 0.2 - - - +
368C ARG* 3.0 41.6 + - - -
108D ASP* 3.3 9.1 - - - +
109D ARG* 1.3 75.8 - - - +
111D VAL* 1.3 72.6 + - - +
113D ARG* 3.3 11.4 + - - +
114D TYR* 2.9 28.9 + - - +
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C PHE* 4.2 4.9 - - + -
365C ALA* 4.8 2.0 - - + +
368C ARG* 4.0 8.3 - - - +
98D VAL* 3.5 39.5 - - + +
99D PHE* 4.0 11.7 - - + -
102D GLY 3.7 18.6 - - - +
103D ALA 4.2 1.6 - - - +
106D ALA* 3.7 10.1 - - + -
108D ASP* 3.6 21.3 - - + +
109D ARG 3.2 0.4 - - - -
110D ASP* 1.3 94.0 + - - +
112D ARG* 1.3 53.4 + - - +
114D TYR* 3.2 8.3 + - + +
115D ALA* 2.8 33.1 + - - +
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLN 3.0 12.5 + - - -
338C LEU* 4.0 3.6 - - - +
340C GLU 2.9 27.7 + - - -
341C PRO 4.2 0.6 + - - -
342C THR* 2.7 31.3 + - + +
103D ALA 3.3 21.3 - - - +
104D PHE* 2.9 25.5 - - - +
105D THR* 4.1 0.4 - - - +
106D ALA 2.6 44.1 + - - +
107D ASN 2.8 20.8 + - - -
108D ASP 3.5 6.2 - - - +
109D ARG* 3.1 28.7 + - - +
111D VAL* 1.3 76.6 - - - +
113D ARG* 1.3 63.3 + - - +
115D ALA* 3.2 4.7 + - - +
116D LEU* 3.1 25.9 + - + +
157D ARG* 3.3 16.7 - - - +
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C THR* 2.9 35.7 + - + +
343C ALA* 3.7 17.0 - - - +
345C ASP* 4.0 11.1 + - - -
349C ALA 4.4 1.4 + - - -
350C LEU* 3.4 45.0 - - + +
353C ASP* 3.0 31.2 + - - +
355C THR* 5.0 1.0 + - - -
356C ALA* 3.9 11.2 - - + +
109D ARG* 3.0 56.0 + - - +
110D ASP* 3.7 9.9 - - - +
112D ARG* 1.3 75.3 - - - +
114D TYR* 1.3 62.5 + - - +
116D LEU* 3.3 5.6 + - - +
117D ARG* 3.1 26.3 + - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ALA 3.4 18.6 + - - +
357C TYR* 3.6 33.4 - + - -
360C PHE* 3.4 35.9 - + + -
362C VAL* 3.8 17.5 - - + +
61D PHE* 3.3 30.2 - + - -
98D VAL* 4.4 6.3 - - + -
99D PHE* 3.6 34.5 - + - -
110D ASP 2.9 14.1 + - - +
111D VAL 3.2 7.6 + - - +
113D ARG* 1.3 75.6 - - - +
115D ALA* 1.3 65.8 + - - +
117D ARG* 3.2 1.9 + - - -
118D LYS* 2.9 35.9 + - + +
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 3.9 13.4 - - + +
99D PHE* 4.2 5.8 - - + -
103D ALA* 3.7 37.7 - - + -
104D PHE* 3.8 10.8 - - + -
111D VAL 2.8 16.5 + - - +
112D ARG 3.2 9.8 + - - +
114D TYR* 1.3 73.8 - - - +
116D LEU* 1.3 56.6 + - - +
118D LYS* 3.4 2.9 + - - +
119D THR* 2.9 32.4 + - - -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C THR* 3.7 23.3 - - + -
350C LEU* 3.6 28.9 - - + -
104D PHE* 3.7 25.8 - - + -
112D ARG* 3.1 12.8 + - + +
113D ARG* 3.6 6.7 - - - +
114D TYR 3.2 0.2 - - - -
115D ALA* 1.3 74.2 - - - +
117D ARG* 1.3 59.5 + - - +
119D THR* 3.2 3.8 + - - -
120D ILE* 2.8 38.1 + - + +
161D ALA* 3.7 31.4 - - + +
164D LEU* 3.7 22.0 - - + -
165D LEU* 4.2 11.4 - - + +
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Residues in contact with ARG 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LEU* 3.2 22.6 + - + +
351C LEU* 2.9 49.5 + - - +
353C ASP 3.1 26.3 + - - -
356C ALA* 3.4 29.6 - - + +
357C TYR* 3.7 39.2 - - + +
358C GLU* 3.8 13.7 + - - -
113D ARG 3.1 13.2 + - - +
114D TYR 3.8 2.0 - - - +
116D LEU* 1.3 73.1 - - - +
118D LYS* 1.3 66.3 + - - +
120D ILE* 3.3 5.1 + - - +
121D ARG* 3.1 23.7 + - - +
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Residues in contact with LYS 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C TYR* 4.6 13.4 - - + +
55D ASP* 2.5 34.1 + - - +
56D ASP* 3.1 21.1 + - - -
61D PHE* 4.0 23.1 - - - -
91D THR* 3.9 6.9 - - + +
92D ASN 2.9 26.3 + - - +
93D LEU* 4.3 2.9 - - + -
99D PHE* 4.1 21.1 - - + -
114D TYR* 2.9 34.5 + - + +
115D ALA 3.7 4.7 - - - +
117D ARG* 1.3 77.7 - - - +
119D THR* 1.3 63.8 + - - +
121D ARG* 3.7 4.7 + - - +
122D ASN* 3.5 15.2 + - - +
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Residues in contact with THR 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D THR* 3.6 21.3 + - - +
93D LEU* 3.5 22.7 - - - +
104D PHE* 3.8 6.2 - - + -
115D ALA 2.9 17.9 + - - -
116D LEU* 3.5 6.3 - - - -
118D LYS* 1.3 75.8 - - - +
120D ILE* 1.3 63.9 + - - +
122D ASN* 3.2 3.8 + - - -
123D ILE* 3.0 35.2 + - + +
134D TYR* 3.8 10.0 + - + -
165D LEU* 3.9 30.1 - - + -
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Residues in contact with ILE 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C LEU* 4.0 21.1 - - + -
350C LEU* 5.2 2.7 - - + -
351C LEU* 3.8 31.2 - - + -
116D LEU* 2.8 28.2 + - + +
117D ARG* 3.3 9.6 + - - +
119D THR* 1.3 76.6 - - - +
121D ARG* 1.3 63.0 + - - +
123D ILE* 3.2 16.9 + - + +
124D ASP* 3.3 15.2 + - - +
164D LEU* 5.7 1.6 - - + +
165D LEU* 4.1 19.1 - - + -
168D TYR* 3.7 38.8 - - + +
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Residues in contact with ARG 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C TYR* 2.9 43.6 + - + +
63D ALA 5.7 3.0 + - - -
65D ASP* 3.2 31.9 + - - +
68D ARG* 3.4 51.2 + - - +
117D ARG 3.1 15.6 + - - +
118D LYS* 4.1 5.2 - - - +
119D THR 3.3 0.2 - - - -
120D ILE* 1.3 79.9 - - - +
122D ASN* 1.3 62.3 + - - +
124D ASP* 3.3 12.3 + - - +
125D LEU* 3.3 17.2 + - - +
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Residues in contact with ASN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 3.7 10.1 - - - -
55D ASP* 3.3 33.8 - - + +
68D ARG* 4.8 6.0 + - - +
89D ALA* 4.5 1.4 - - - +
90D THR 2.8 30.9 + - - +
91D THR* 4.7 0.7 - - - +
118D LYS 3.5 8.9 + - - +
119D THR 3.2 3.4 + - - +
121D ARG* 1.3 77.4 - - - +
123D ILE* 1.3 59.6 + - - +
125D LEU* 3.3 25.0 + - - +
126D ALA* 2.8 27.2 + - - +
134D TYR* 2.9 22.0 + - - +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D THR* 3.0 32.3 + - + +
120D ILE* 3.2 12.5 + - - +
122D ASN* 1.3 77.7 - - - +
124D ASP* 1.3 62.7 + - - +
126D ALA* 3.3 2.5 + - - +
127D VAL* 3.0 25.0 + - + +
134D TYR* 3.9 26.7 - - + -
165D LEU* 4.1 11.0 - - + +
168D TYR* 4.3 9.9 - - + -
169D VAL* 4.1 22.0 - - + -
174D TYR* 4.3 12.3 - - + -
176D ILE* 4.7 7.0 - - + -
178D PHE* 3.8 31.0 - - + -
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ILE* 3.3 11.1 + - - +
121D ARG* 3.5 12.7 - - + +
123D ILE* 1.3 75.0 - - - +
125D LEU* 1.3 63.7 + - - +
127D VAL* 3.3 5.4 + - - +
128D GLU* 3.2 25.6 + - - +
168D TYR* 2.5 31.0 + - - -
174D TYR* 2.8 31.3 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 4.0 13.9 - - + -
58D LEU* 4.1 5.6 - - + -
59D ILE* 3.8 27.6 - - + -
68D ARG* 4.0 14.8 - - - +
72D VAL* 3.9 22.4 - - + -
121D ARG 3.3 9.1 + - - +
122D ASN* 3.3 24.0 + - - +
124D ASP* 1.3 75.8 - - - +
126D ALA* 1.3 67.6 - - - +
128D GLU* 3.3 19.0 + - - +
129D LEU* 3.1 39.6 + - + +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 5.0 2.5 - - - -
89D ALA* 3.4 29.6 - - + -
122D ASN 2.8 14.3 + - - +
123D ILE 3.3 10.5 - - - +
124D ASP 3.2 0.2 - - - -
125D LEU* 1.3 76.9 - - - +
127D VAL* 1.3 63.7 + - - +
129D LEU* 3.1 7.5 + - - +
130D GLY 3.1 4.5 + - - -
131D ALA* 2.9 32.5 + - + +
134D TYR* 3.9 12.3 - - + -
176D ILE* 4.3 4.7 - - + -
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ILE* 3.0 18.4 + - + +
124D ASP 3.3 6.9 + - - +
126D ALA* 1.3 75.0 - - - +
128D GLU* 1.3 60.0 + - + +
130D GLY* 2.8 22.2 + - - -
131D ALA 4.4 7.6 + - - -
174D TYR* 3.5 54.7 - - + -
175D ASP 5.7 2.5 - - - +
176D ILE* 4.7 11.7 - - + -
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 3.3 34.2 + - - +
124D ASP 3.2 11.7 + - - +
125D LEU* 3.6 25.5 - - + +
126D ALA 3.3 0.2 - - - -
127D VAL* 1.3 80.0 - - + +
129D LEU* 1.3 61.0 + - + +
130D GLY* 3.0 5.7 + - - -
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Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D PHE* 3.6 36.6 - - + -
58D LEU* 4.3 3.1 - - + -
72D VAL* 5.6 2.7 - - + +
75D PHE* 3.9 22.0 - - + -
76D ARG* 3.6 37.5 - - + +
79D LEU* 4.9 8.7 - - + -
86D VAL* 4.0 29.0 + - + +
125D LEU* 3.1 27.6 + - + +
126D ALA* 3.1 7.4 + - - +
128D GLU* 1.3 74.8 - - + +
130D GLY* 1.3 59.9 + - - +
131D ALA 3.4 0.6 + - - -
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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) + - + + + + + -
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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