Contacts of the helix formed by residues 108 - 129 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C LYS* 5.9 0.2 + - - -
106C ALA* 3.1 2.6 - - + +
107C ASN* 1.3 76.2 - - - +
109C ARG* 1.3 65.7 + - - +
110C ASP* 3.1 17.9 - - - +
111C VAL* 3.1 27.6 + - + +
112C ARG* 3.3 14.7 + - - +
334D ARG* 2.8 53.4 + - - +
337D GLN* 3.3 6.9 + - - +
365D ALA 5.3 3.8 - - - +
368D ARG* 4.4 5.1 + - - +
370D MET* 3.8 10.3 - - - +
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASP* 1.3 71.8 - - - +
110C ASP* 1.3 62.4 + - - +
112C ARG* 3.1 40.2 + - - +
113C ARG* 3.1 42.4 + - - +
337D GLN* 2.7 22.8 - - + +
340D GLU* 4.3 16.2 - - - -
341D PRO 2.8 24.1 + - - -
342D THR* 3.2 22.3 + - - +
343D ALA* 4.4 0.8 - - - +
344D ALA* 4.7 3.6 - - - +
345D ASP* 4.1 9.9 + - - -
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ASP* 3.1 23.8 - - - +
109C ARG* 1.3 76.0 + - - +
111C VAL* 1.3 69.3 + - - +
113C ARG* 3.7 10.8 + - - +
114C TYR* 3.3 20.6 + - - +
337D GLN* 4.4 3.2 + - - +
355D THR 5.4 3.8 - - - +
356D ALA* 5.5 0.9 - - - -
360D PHE* 3.5 31.8 - - + -
365D ALA* 4.5 7.4 - - - +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C VAL* 3.7 37.5 - - + +
99C PHE* 4.0 12.4 - - + -
102C GLY 3.8 7.4 - - - +
103C ALA 4.6 0.7 - - - +
106C ALA* 3.7 21.3 - - + -
108C ASP* 3.4 22.7 - - + +
109C ARG 3.1 0.6 - - - -
110C ASP* 1.3 95.6 + - - +
112C ARG* 1.3 59.0 + - - +
114C TYR* 3.3 3.9 + - + +
115C ALA* 3.0 25.5 + - - +
360D PHE* 4.2 9.2 - - + -
365D ALA* 4.6 6.7 - - + +
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ALA 3.2 19.0 - - - +
104C PHE* 3.3 23.6 - - - +
105C THR* 4.3 0.9 - - - +
106C ALA 2.8 44.4 + - - +
107C ASN 3.1 19.4 + - - -
108C ASP 3.5 2.7 - - - +
109C ARG* 3.1 33.2 + - - +
111C VAL* 1.3 77.6 - - - +
113C ARG* 1.3 61.3 + - - +
115C ALA* 3.2 5.2 + - - +
116C LEU* 3.2 24.4 + - - +
157C ARG* 3.3 17.1 - - - +
337D GLN 2.8 15.3 + - - -
338D LEU* 3.9 2.8 - - - +
340D GLU 2.6 29.9 + - - -
341D PRO 4.1 0.4 + - - -
342D THR* 2.9 30.4 + - + +
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Residues in contact with ARG 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG* 3.1 42.9 + - - +
110C ASP* 3.9 7.9 - - - +
111C VAL 3.3 0.2 - - - -
112C ARG* 1.3 73.5 - - - +
114C TYR* 1.3 66.5 + - - +
116C LEU* 3.2 6.6 + - - +
117C ARG* 3.2 25.1 + - - +
342D THR* 2.9 40.7 + - + +
343D ALA* 3.5 8.3 - - - +
345D ASP* 3.0 35.6 + - - -
350D LEU* 3.6 29.2 - - + +
353D ASP* 2.7 35.5 + - - +
355D THR* 5.1 2.2 + - - -
356D ALA* 4.1 13.6 - - + +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.1 34.6 - + - -
98C VAL* 4.3 4.5 - - + -
99C PHE* 3.6 35.9 - + - -
110C ASP 3.3 8.4 + - - +
111C VAL 3.3 7.5 + - - +
113C ARG* 1.3 79.3 - - - +
115C ALA* 1.3 57.4 + - - +
117C ARG* 3.2 1.6 + - - +
118C LYS* 2.9 42.3 + - + +
356D ALA 3.2 21.0 + - - +
357D TYR* 4.0 31.3 - + - -
360D PHE* 3.4 39.3 - + + -
362D VAL* 3.8 16.8 - - + +
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Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.9 11.9 - - + +
99C PHE* 4.0 6.7 - - + -
103C ALA* 3.8 24.5 - - + -
104C PHE* 3.8 21.8 - - + -
111C VAL 3.0 13.0 + - - +
112C ARG 3.3 11.0 - - - +
114C TYR* 1.3 77.8 - - - +
116C LEU* 1.3 59.6 + - - +
118C LYS* 3.8 1.7 - - - +
119C THR* 2.9 29.8 + - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C PHE* 3.7 13.0 - - + -
112C ARG 3.2 9.9 + - - +
113C ARG* 3.2 8.2 + - - +
115C ALA* 1.3 76.1 - - - +
117C ARG* 1.3 58.8 + - - +
119C THR* 3.5 2.2 + - - -
120C ILE* 2.9 39.9 + - + +
161C ALA* 3.7 39.3 - - + +
164C LEU* 3.6 24.2 - - + -
165C LEU* 4.2 11.4 - - + +
342D THR* 3.8 22.0 - - + -
350D LEU* 3.6 28.7 - - + -
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Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ARG 3.2 9.9 + - - +
114C TYR 3.7 2.2 - - - +
116C LEU* 1.3 74.5 - - - +
118C LYS* 1.3 66.7 + - - +
120C ILE* 3.9 5.0 - - - +
121C ARG* 3.1 24.9 + - - +
350D LEU* 3.1 37.4 + - + -
351D LEU* 2.9 40.6 + - - +
353D ASP 3.1 22.2 + - - -
356D ALA* 3.4 26.0 - - + +
357D TYR* 3.5 32.0 - - + +
358D GLU* 3.8 21.2 + - - -
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ASP* 2.6 33.0 + - - +
56C ASP* 3.0 24.8 + - - -
61C PHE* 3.8 30.1 - - - -
91C THR* 4.2 3.4 - - + -
92C ASN 3.4 14.7 + - - -
93C LEU* 4.1 16.4 - - + -
96C HIS* 6.2 0.2 - - - -
99C PHE* 4.2 13.5 - - + -
114C TYR* 2.9 32.3 + - + +
115C ALA 3.8 5.4 - - - +
117C ARG* 1.3 79.1 - - - +
119C THR* 1.3 64.3 + - - +
121C ARG* 3.6 4.4 + - - +
122C ASN* 3.5 16.1 + - - +
357D TYR* 4.3 12.1 - - + +
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Residues in contact with THR 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C THR* 3.6 28.2 + - - +
93C LEU* 3.7 16.5 - - - +
104C PHE* 3.8 5.4 - - + -
115C ALA 2.9 18.5 + - - -
116C LEU* 3.7 4.9 - - - -
118C LYS* 1.3 75.5 - - - +
120C ILE* 1.3 57.5 + - - +
122C ASN* 2.7 26.3 + - - +
123C ILE* 2.9 15.0 + - + +
134C TYR* 3.7 16.1 + - + -
165C LEU* 3.9 28.7 - - + -
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 2.9 34.8 + - + +
117C ARG* 3.9 8.3 - - - +
119C THR* 1.3 75.0 - - - +
121C ARG* 1.3 65.2 + - - +
123C ILE* 3.0 21.6 + - - +
124C ASP* 3.2 14.4 + - - +
164C LEU* 5.7 1.1 - - + +
165C LEU* 3.9 19.3 - - + -
168C TYR* 3.6 39.5 - - + +
347D LEU* 4.3 17.0 - - + -
350D LEU* 5.1 1.6 - - + -
351D LEU* 3.6 31.4 - - + -
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Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ALA 5.6 4.0 + - - -
65C ASP* 3.3 31.3 + - - -
68C ARG* 3.2 52.7 + - - +
117C ARG 3.1 18.4 + - - +
118C LYS 3.8 6.3 - - - +
119C THR 3.1 0.4 + - - -
120C ILE* 1.3 78.3 - - - +
122C ASN* 1.3 59.2 + - - +
124C ASP* 3.7 12.3 + - - +
125C LEU* 3.6 16.1 + - - +
357D TYR* 2.7 52.1 + - + +
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Residues in contact with ASN 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE* 3.9 18.9 - - - -
55C ASP* 3.2 34.0 - - + +
68C ARG* 5.5 4.2 + - - +
89C ALA* 4.4 1.0 - - - +
90C THR 3.1 21.8 + - - +
91C THR* 5.0 0.2 - - + -
118C LYS 3.5 7.5 + - - +
119C THR* 2.7 8.9 + - - +
121C ARG* 1.3 71.8 - - - +
123C ILE* 1.3 60.1 + - - +
124C ASP 3.2 2.0 - - - -
125C LEU* 3.7 14.5 - - - +
126C ALA* 2.9 28.4 + - - +
134C TYR* 2.9 32.2 + - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C THR* 2.9 27.2 + - + +
120C ILE* 3.0 13.4 + - - +
122C ASN* 1.3 79.0 - - - +
124C ASP* 1.3 59.9 + - - +
126C ALA* 3.6 2.2 - - - +
127C VAL* 3.1 26.6 + - + +
134C TYR* 3.9 26.0 - - + -
165C LEU* 4.2 12.1 - - + -
168C TYR* 4.3 8.7 - - + -
169C VAL* 4.2 13.2 - - + -
174C TYR* 3.9 25.6 - - + -
176C ILE* 4.6 7.0 - - + -
178C PHE* 3.8 30.7 - - + -
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Residues in contact with ASP 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE* 3.2 12.0 + - - +
121C ARG* 3.8 12.4 - - - +
122C ASN 3.2 0.4 - - - -
123C ILE* 1.3 75.6 - - - +
125C LEU* 1.3 59.3 + - - +
127C VAL* 3.4 2.3 + - - +
128C GLU* 2.9 31.3 + - - +
168C TYR* 2.5 32.3 + - - -
174C TYR* 2.7 28.8 + - - +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 4.4 4.9 - - + -
55C ASP* 6.0 0.7 - - - -
58C LEU* 4.1 11.7 - - + -
59C ILE* 3.7 30.5 - - + -
68C ARG* 4.4 11.7 - - - +
72C VAL* 3.9 22.9 - - + -
121C ARG 3.6 8.7 + - - +
122C ASN* 3.3 25.6 + - - +
124C ASP* 1.3 75.8 - - - +
126C ALA* 1.3 60.1 + - - +
128C GLU* 3.2 23.0 + - - +
129C LEU* 2.9 46.9 + - + +
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Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 4.7 3.5 - - - -
89C ALA* 3.5 30.5 - - + -
122C ASN 2.9 17.6 + - - +
123C ILE 3.6 5.4 - - - +
125C LEU* 1.3 77.5 - - - +
127C VAL* 1.3 62.5 + - - +
129C LEU* 3.0 11.2 + - - -
131C ALA* 3.0 32.8 + - + +
134C TYR* 4.0 12.8 - - + -
176C ILE* 4.2 5.4 - - + -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ILE 3.1 17.8 + - - +
124C ASP 3.8 4.7 - - - +
126C ALA* 1.3 75.2 - - - +
128C GLU* 1.3 62.5 + - - +
130C GLY* 3.0 14.1 + - - -
131C ALA 4.1 7.6 - - - +
174C TYR* 3.7 52.7 - - + -
175C ASP 5.3 4.9 - - - +
176C ILE* 4.2 18.4 - - + -
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C VAL* 5.3 7.4 - - - +
76C ARG* 3.6 29.4 + - - +
124C ASP* 2.9 19.7 + - - +
125C LEU* 3.5 24.8 - - + +
126C ALA 3.2 0.2 - - - -
127C VAL* 1.3 78.5 - - - +
129C LEU* 1.3 58.6 + - + +
130C GLY 3.3 0.4 + - - -
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Residues in contact with LEU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE* 3.8 33.2 - - + -
58C LEU* 4.6 3.8 - - + -
72C VAL* 5.6 4.0 - - + +
75C PHE* 4.2 27.6 - - + -
76C ARG* 3.6 38.1 - - + +
79C LEU* 5.1 6.3 - - + -
85C THR* 5.5 1.2 + - - -
86C VAL* 4.5 20.9 + - + +
125C LEU* 2.9 31.2 + - + +
126C ALA* 3.0 6.2 + - - +
128C GLU* 1.3 76.3 - - + +
130C GLY* 1.3 59.2 + - - +
131C ALA 3.4 2.3 + - - +
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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