Contacts of the helix formed by residues 108 - 129 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334G ARG* 2.8 52.6 + - - +
337G GLN* 3.8 8.4 + - - +
365G ALA 5.5 0.7 - - - +
368G ARG* 3.8 23.0 + - - -
370G MET* 3.7 10.4 - - - +
106H ALA* 3.2 2.0 - - + +
107H ASN* 1.3 75.1 - - - +
109H ARG* 1.3 65.6 + - - +
110H ASP* 3.3 17.9 - - - +
111H VAL* 3.3 23.2 + - + +
112H ARG* 3.3 15.9 + - - +
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Residues in contact with ARG 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLN* 3.0 23.2 - - + +
340G GLU* 4.4 16.1 - - - +
341G PRO 3.1 22.4 + - - -
342G THR* 3.4 14.1 + - - +
343G ALA* 4.8 0.4 - - - +
344G ALA* 4.8 4.8 - - - +
345G ASP* 4.2 8.9 + - - +
107H ASN 3.3 2.0 + - - -
108H ASP* 1.3 69.8 - - - +
110H ASP* 1.3 66.5 + - - +
112H ARG* 3.1 30.0 + - - +
113H ARG* 3.1 58.2 + - - +
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Residues in contact with ASP 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLN* 4.7 1.7 - - - +
355G THR 5.6 1.6 - - - +
356G ALA* 5.5 1.4 - - - -
360G PHE* 3.6 26.5 - - + -
368G ARG* 3.2 31.0 + - - -
108H ASP* 3.4 9.1 - - - +
109H ARG* 1.3 78.7 - - - +
111H VAL* 1.3 93.4 + - - +
113H ARG* 3.4 11.0 + - - +
114H TYR* 3.1 23.6 + - - +
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Residues in contact with VAL 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G PHE* 4.3 7.6 - - + -
365G ALA* 4.7 1.6 - - + +
368G ARG* 4.6 5.4 - - - +
98H VAL* 3.4 38.4 - - + +
99H PHE* 3.9 14.4 - - + -
102H GLY 3.9 7.4 - - - +
103H ALA 4.1 0.9 - - - +
106H ALA* 3.8 19.1 - - + -
108H ASP* 3.3 23.8 + - + +
109H ARG 3.2 0.6 - - - -
110H ASP* 1.3 91.5 + - - +
112H ARG* 1.3 66.8 - - - +
114H TYR* 3.3 3.3 + - + +
115H ALA* 3.0 22.3 + - - +
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Residues in contact with ARG 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLN 3.0 14.8 + - - -
338G LEU* 3.6 6.1 - - - +
340G GLU 2.9 25.7 + - - -
341G PRO 3.9 0.6 + - - -
342G THR* 2.6 32.0 + - + +
103H ALA 3.2 18.4 - - - +
104H PHE* 3.2 22.8 - - - +
106H ALA 2.9 36.8 + - - +
107H ASN 2.9 20.6 + - - -
108H ASP 3.4 2.9 - - - +
109H ARG* 3.1 34.6 + - - +
111H VAL* 1.3 77.2 - - - +
113H ARG* 1.3 61.0 + - - +
115H ALA* 3.5 3.6 + - - +
116H LEU* 3.4 25.5 + - - +
157H ARG* 3.4 16.1 - - - +
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Residues in contact with ARG 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G THR* 2.8 47.2 + - + +
343G ALA* 3.4 8.1 - - - +
345G ASP* 2.9 39.5 + - - -
350G LEU* 3.6 29.7 - - + +
353G ASP* 2.9 33.3 + - - +
355G THR* 5.3 0.8 + - - -
356G ALA* 4.1 11.2 - - + +
109H ARG* 3.1 47.7 + - - +
110H ASP* 3.8 9.0 - - - +
111H VAL 3.2 0.2 - - - -
112H ARG* 1.3 74.2 - - - +
114H TYR* 1.3 64.8 + - - +
116H LEU* 3.2 6.5 + - - +
117H ARG* 3.1 26.8 + - - +
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Residues in contact with TYR 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ALA* 3.3 21.2 + - - +
357G TYR* 4.1 27.4 - + - -
360G PHE* 3.4 34.5 - + + -
362G VAL* 3.7 19.7 - - + +
61H PHE* 3.0 34.7 - + - -
98H VAL* 4.3 6.7 - - + -
99H PHE* 3.5 35.7 - + - -
110H ASP 3.1 16.9 + - - +
111H VAL 3.7 3.6 - - - +
113H ARG* 1.3 76.2 - - - +
115H ALA* 1.3 56.7 + - - +
117H ARG* 3.3 0.9 + - - +
118H LYS* 2.9 41.8 + - + +
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H LEU* 4.1 12.9 - - + +
99H PHE* 4.2 6.1 - - + -
103H ALA* 3.7 32.1 - - + -
104H PHE* 3.8 14.4 - - + -
111H VAL 3.0 16.3 + - - +
112H ARG 3.6 6.7 - - - +
113H ARG 3.2 0.2 - - - -
114H TYR* 1.3 76.4 - - - +
116H LEU* 1.3 54.5 + - - +
118H LYS* 3.4 2.8 + - - +
119H THR* 2.8 37.2 + - - -
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342G THR* 3.9 24.2 - - + -
350G LEU* 4.0 17.9 - - + -
104H PHE* 3.5 23.3 - - + -
112H ARG 3.4 6.4 + - - +
113H ARG* 3.2 7.1 + - - +
115H ALA* 1.3 77.9 - - - +
117H ARG* 1.3 60.3 + - - +
119H THR* 3.2 3.1 + - - -
120H ILE* 2.9 39.2 + - + +
161H ALA* 3.6 32.1 - - + +
164H LEU* 3.7 30.3 - - + -
165H LEU* 3.8 16.8 - - + -
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Residues in contact with ARG 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350G LEU* 3.0 36.1 + - + -
351G LEU* 3.3 38.0 + - - +
353G ASP 2.9 28.9 + - - -
356G ALA* 3.5 25.1 - - + +
357G TYR* 3.6 41.3 - - + +
358G GLU* 4.1 9.1 + - - -
113H ARG 3.1 18.3 + - - +
114H TYR 3.7 2.7 - - - +
116H LEU* 1.3 76.8 - - - +
118H LYS* 1.3 61.2 + - - +
120H ILE* 3.3 6.9 + - - +
121H ARG* 3.1 23.9 + - - +
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Residues in contact with LYS 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G TYR* 4.3 12.7 - - + -
55H ASP* 2.8 30.8 + - - +
56H ASP* 2.9 27.6 + - - -
61H PHE* 3.7 29.6 - - - -
91H THR* 4.1 4.0 - - + +
92H ASN 3.0 23.2 + - - +
93H LEU* 3.9 11.0 - - + -
96H HIS* 6.1 0.4 - - - -
99H PHE* 4.0 13.2 - - + -
114H TYR* 2.9 33.8 + - + +
115H ALA* 3.7 5.6 - - - +
116H LEU 3.3 0.2 - - - -
117H ARG* 1.3 76.1 - - - +
119H THR* 1.3 60.8 + - - +
121H ARG* 3.7 5.3 + - - +
122H ASN* 3.5 19.6 + - - +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H THR* 3.5 22.6 + - - +
93H LEU* 3.6 13.2 - - + +
104H PHE* 3.6 17.0 - - + -
115H ALA 2.8 21.7 + - - -
116H LEU 3.6 4.0 - - - -
118H LYS* 1.3 73.1 - - - +
120H ILE* 1.3 61.9 + - - +
122H ASN 3.2 3.5 + - - -
123H ILE* 3.0 35.4 + - + +
134H TYR* 3.7 16.2 + - + -
165H LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347G LEU* 4.2 18.8 - - + -
350G LEU* 5.1 5.4 - - + -
351G LEU* 3.8 28.5 - - + -
116H LEU* 2.9 29.3 + - + +
117H ARG* 3.7 8.3 - - - +
119H THR* 1.3 76.9 - - - +
121H ARG* 1.3 62.7 + - - +
123H ILE* 3.0 19.1 + - + +
124H ASP* 3.1 16.0 + - - +
164H LEU* 6.0 0.7 - - + -
165H LEU* 3.7 21.3 - - + -
168H TYR* 3.6 38.4 - - + +
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Residues in contact with ARG 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357G TYR* 2.9 47.4 + - + +
63H ALA 5.7 1.8 + - - -
65H ASP* 3.4 31.3 + - - -
68H ARG* 3.4 48.2 + - - +
117H ARG 3.1 16.2 + - - +
118H LYS* 3.8 7.0 - - - +
120H ILE* 1.3 77.7 - - - +
122H ASN* 1.3 60.2 + - + +
124H ASP* 3.5 15.9 + - - +
125H LEU* 3.5 17.2 + - - +
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Residues in contact with ASN 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 3.6 10.3 - - - -
55H ASP* 3.2 35.1 - - + +
68H ARG* 5.4 3.5 + - - +
89H ALA* 4.3 1.0 - - - +
90H THR 2.9 29.7 + - - +
91H THR* 4.8 0.2 - - - +
118H LYS 3.5 7.3 + - - +
119H THR 3.2 4.1 + - - +
121H ARG* 1.3 78.6 - - + +
123H ILE* 1.3 60.7 + - - +
124H ASP 3.2 0.4 - - - -
125H LEU* 3.6 23.8 - - - +
126H ALA* 3.0 26.5 + - - +
134H TYR* 3.0 23.4 + - - +
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Residues in contact with ILE 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H THR* 3.0 30.1 + - + +
120H ILE* 3.0 13.2 + - + +
122H ASN* 1.3 75.7 - - - +
124H ASP* 1.3 66.9 + - - +
126H ALA* 3.3 2.9 + - - +
127H VAL* 3.2 22.7 + - + +
134H TYR* 3.9 24.0 - - + -
165H LEU* 4.0 13.9 - - + +
168H TYR* 4.6 7.0 - - + -
169H VAL* 4.2 20.9 - - + -
174H TYR* 4.2 15.9 - - + -
176H ILE* 4.4 11.2 - - + -
178H PHE* 3.7 30.1 - - + -
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Residues in contact with ASP 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H ILE* 3.1 13.5 + - - +
121H ARG* 3.7 17.0 - - - +
122H ASN 3.2 0.2 - - - -
123H ILE* 1.3 77.2 - - - +
125H LEU* 1.3 57.7 + - - +
127H VAL* 3.3 5.4 + - - +
128H GLU* 2.9 28.7 + - - +
168H TYR* 2.7 29.3 + - - -
174H TYR* 2.9 30.2 + - - +
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Residues in contact with LEU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 3.9 17.0 - - + -
55H ASP* 5.8 0.2 - - - -
58H LEU* 4.1 7.6 - - + -
59H ILE* 3.8 26.5 - - + -
68H ARG* 4.8 4.5 - - - +
72H VAL* 3.7 32.1 - - + -
121H ARG 3.5 11.0 + - - +
122H ASN* 3.6 23.8 - - - +
123H ILE 3.3 0.2 - - - -
124H ASP* 1.3 79.0 - - - +
126H ALA* 1.3 53.3 + - - +
128H GLU* 3.0 21.3 + - - +
129H LEU* 2.8 47.4 + - + +
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Residues in contact with ALA 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H PHE* 5.1 2.4 - - - -
89H ALA* 3.8 25.1 - - + -
122H ASN 3.0 15.2 + - - +
123H ILE* 3.3 10.8 - - - +
124H ASP 3.2 0.2 - - - -
125H LEU* 1.3 77.9 - - - +
127H VAL* 1.3 56.0 + - - +
129H LEU* 3.2 6.0 + - - +
130H GLY 3.1 4.3 + - - -
131H ALA* 2.8 41.3 + - + +
134H TYR* 3.9 12.3 - - + -
176H ILE* 4.4 7.6 - - + -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H ILE* 3.2 16.7 + - + +
124H ASP 3.6 6.3 - - - +
126H ALA* 1.3 72.5 - - - +
128H GLU* 1.3 60.1 + - - +
130H GLY* 2.8 23.5 + - - +
131H ALA 4.2 8.3 - - - +
174H TYR* 3.7 52.7 - - + -
175H ASP 5.3 4.5 - - - +
176H ILE* 4.8 12.3 - - + -
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Residues in contact with GLU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H VAL* 3.8 18.9 - - - +
76H ARG* 3.2 34.1 + - - +
124H ASP 2.9 14.4 + - - +
125H LEU* 3.0 27.8 + - + +
127H VAL* 1.3 77.3 - - - +
129H LEU* 1.3 59.7 + - + +
130H GLY 3.5 0.5 + - - -
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H PHE* 3.8 34.1 - - + -
58H LEU* 4.4 11.2 - - + -
72H VAL* 4.8 5.8 - - + -
75H PHE* 4.6 10.3 - - + -
76H ARG* 4.4 31.0 - - + +
79H LEU* 4.5 18.8 - - + +
86H VAL* 4.1 25.1 + - + +
125H LEU* 2.8 33.7 + - + +
126H ALA* 3.8 4.7 - - - +
127H VAL 3.0 0.4 - - - -
128H GLU* 1.3 78.4 - - + +
130H GLY* 1.3 61.3 + - - +
131H ALA 3.4 1.5 + - - +
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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