Contacts of the helix formed by residues 82 - 107 (chain C) in PDB entry 4U1D
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 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 4.4 7.8 - - - +
79C ILE* 3.6 3.8 + - - +
80C GLN 3.9 4.7 - - - +
81C GLY* 1.3 79.2 - - - +
83C THR* 1.3 64.1 + - - +
84C GLU* 3.3 17.7 + - - +
85C GLY* 2.8 25.5 + - - -
86C LEU* 3.1 19.9 + - - +
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Residues in contact with THR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 1.3 70.2 - - - +
84C GLU* 1.3 68.5 + - - +
86C LEU* 3.1 4.2 + - - +
87C VAL* 2.9 39.4 + - + +
174C LEU* 3.8 27.8 - - + +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 3.5 22.5 - - + +
46C SER* 6.5 0.2 - - - -
82C SER* 3.3 19.1 - - - -
83C THR* 1.3 84.3 + - - +
85C GLY* 1.3 56.8 + - - +
87C VAL* 3.5 10.7 - - - +
88C SER* 2.9 29.6 + - - -
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 3.9 4.5 - - - +
79C ILE* 3.2 45.7 - - - +
82C SER* 2.8 16.3 + - - -
83C THR 3.0 0.4 - - - -
84C GLU* 1.3 74.6 - - - +
86C LEU* 1.3 58.9 + - - +
88C SER* 3.1 2.6 + - - -
89C VAL* 2.9 25.7 + - - +
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Residues in contact with LEU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LYS* 4.9 2.5 - - - -
79C ILE 4.4 0.2 + - - -
80C GLN* 3.6 32.1 - - + +
82C SER 3.1 12.1 + - - +
83C THR 3.1 3.7 + - - +
85C GLY* 1.3 73.6 - - - +
87C VAL* 1.3 62.8 + - - +
89C VAL* 3.2 10.7 + - + +
90C GLY 2.9 19.4 + - - -
172C ASN* 3.4 39.9 - - - +
174C LEU* 3.5 33.9 - - + -
175C LEU* 3.5 19.4 - - + +
223C ASN* 3.4 25.8 - - - +
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Residues in contact with VAL 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C THR* 2.9 29.8 + - + +
84C GLU* 3.5 12.1 - - - +
86C LEU* 1.3 77.0 - - + +
88C SER* 1.3 58.3 - - - +
90C GLY* 3.2 3.0 + - - -
91C ALA* 2.9 32.1 + - + +
94C ARG* 4.4 5.2 + - - +
174C LEU* 5.6 2.2 - - + -
175C LEU* 5.6 0.2 - - - -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PRO* 3.7 12.9 + - - -
49C GLU* 3.2 32.0 + - - +
75C TYR* 2.7 28.6 + - - -
79C ILE* 4.6 0.4 - - - -
84C GLU 2.9 18.1 + - - -
85C GLY 3.1 4.9 + - - -
87C VAL* 1.3 77.3 - - - +
89C VAL* 1.3 63.2 + - - +
91C ALA* 3.7 2.4 - - - +
92C VAL* 2.9 26.7 + - - +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C TYR* 4.6 7.6 - - + -
76C LYS* 3.7 54.5 - - + +
79C ILE* 4.4 8.3 - - + -
80C GLN 5.1 0.2 - - - +
85C GLY 2.9 17.7 + - - +
86C LEU* 3.2 15.5 + - + +
88C SER* 1.3 75.4 - - - +
90C GLY* 1.3 65.2 + - - +
92C VAL* 3.1 8.2 + - - +
93C ALA* 2.9 20.6 + - - +
168C LEU* 4.9 6.4 - - + +
169C LEU* 4.6 9.4 - - + -
175C LEU* 4.0 17.5 - - + -
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU 2.9 11.3 + - - -
87C VAL* 3.7 2.9 - - - -
89C VAL* 1.3 78.3 - - - +
91C ALA* 1.3 56.4 + - - +
93C ALA* 3.3 8.4 + - - +
94C ARG* 3.0 43.9 + - - -
169C LEU* 5.2 0.9 - - - -
175C LEU* 3.8 17.9 - - - +
178C THR* 3.8 9.7 - - - +
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.2 23.8 - - - +
53C PHE* 4.0 4.9 - - + -
87C VAL* 2.9 21.5 + - + +
88C SER* 3.7 2.7 - - - +
90C GLY* 1.3 77.1 - - - +
92C VAL* 1.3 57.4 + - - +
94C ARG* 3.3 24.5 + - - +
95C LYS* 2.9 26.7 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.8 14.4 - - + -
52C VAL* 3.5 27.6 - - + -
53C PHE* 3.6 24.2 - - + -
56C LEU* 3.3 10.8 - - + +
72C LEU* 3.4 30.7 - - + -
75C TYR* 4.5 8.3 - - + -
88C SER* 2.9 22.7 + - - +
89C VAL* 3.6 5.8 - - - +
91C ALA* 1.3 75.4 - - - +
93C ALA* 1.3 63.1 + - - +
95C LYS 3.4 0.2 + - - -
96C PHE* 3.0 20.1 + - - +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 5.4 4.3 - - - -
89C VAL 2.9 12.9 + - - +
90C GLY 3.4 9.9 - - - +
92C VAL* 1.3 77.2 - - - +
94C ARG* 1.3 62.9 + - - +
96C PHE* 3.2 9.5 + - - +
97C ILE* 3.0 27.5 + - - +
165C VAL* 4.0 17.3 - - + +
168C LEU* 5.1 5.4 - - + +
169C LEU* 3.7 32.1 - - + -
178C THR* 4.5 1.3 - - + -
182C VAL* 6.1 0.4 - - - -
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Residues in contact with ARG 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C VAL* 4.4 4.9 + - - +
90C GLY* 3.0 37.3 + - - -
91C ALA* 3.3 26.1 + - - +
92C VAL 3.3 0.2 - - - -
93C ALA* 1.3 75.9 - - - +
95C LYS* 1.3 62.9 + - - +
97C ILE* 3.3 7.6 + - + +
98C ASP* 2.9 36.5 + - - +
178C THR* 3.6 31.4 + - + +
182C VAL* 6.0 2.9 - - + -
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE* 3.5 61.7 - - + -
56C LEU* 4.1 7.6 - - + -
57C GLU* 4.3 18.4 + - - +
91C ALA 2.9 10.1 + - - +
92C VAL 3.6 4.5 - - - +
93C ALA 3.3 0.2 - - - -
94C ARG* 1.3 76.1 - - - +
96C PHE* 1.3 62.7 + - - +
98C ASP* 3.1 9.1 + - + +
99C LEU* 2.9 55.7 + - + +
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Residues in contact with PHE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 3.5 23.4 - - + +
60C VAL* 3.8 18.2 - - + -
65C GLY* 5.9 1.3 - - - -
68C LEU* 3.4 38.4 - - + -
69C LYS* 5.8 1.3 - - - -
72C LEU* 3.8 21.1 - - + -
92C VAL 3.0 13.6 + - - +
93C ALA* 3.2 9.4 + - - +
95C LYS* 1.3 75.2 - - - +
97C ILE* 1.3 62.5 + - + +
99C LEU* 3.1 5.9 + - - +
100C VAL* 3.0 25.1 + - + +
157C PHE* 4.9 1.1 - + - -
161C SER* 3.4 37.7 - - - -
164C ALA* 4.9 7.2 - - + -
165C VAL* 3.4 27.8 - - + -
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Residues in contact with ILE 97 (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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93C ALA 3.0 16.4 + - - +
94C ARG* 3.8 9.4 - - - +
96C PHE* 1.3 74.7 - - + +
98C ASP* 1.3 59.4 + - - +
100C VAL* 3.2 10.7 - - + +
101C GLU* 2.9 44.0 + - - +
161C SER* 4.1 3.4 - - - +
162C TYR* 3.6 48.7 - - + +
165C VAL* 3.7 32.5 - - + -
182C VAL* 4.3 12.3 - - + -
185C LYS* 4.1 12.1 - - + -
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Residues in contact with ASP 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ARG* 2.9 28.6 + - - +
95C LYS* 3.1 9.3 + - + +
97C ILE* 1.3 76.2 - - - +
99C LEU* 1.3 60.4 + - + +
101C GLU* 3.5 16.3 + - - +
102C SER* 2.8 35.1 + - - +
185C LYS* 4.7 6.6 - - - -
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C PHE 4.7 0.4 - - - +
56C LEU* 3.4 47.1 - - + +
57C GLU* 3.4 18.4 - - + +
60C VAL* 4.0 13.4 - - + +
95C LYS* 2.9 55.4 + - + +
96C PHE* 3.1 9.2 + - - +
98C ASP* 1.3 77.2 - - + +
100C VAL* 1.3 65.2 + - - +
102C SER* 3.1 8.5 + - - -
103C LYS* 3.0 25.4 + - - +
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C VAL* 4.5 6.5 - - + +
96C PHE* 3.0 14.9 + - + +
97C ILE* 3.2 24.9 - - + +
99C LEU* 1.3 74.1 - - - +
101C GLU* 1.3 58.7 + - + +
103C LYS* 3.0 24.4 + - + +
104C ILE* 3.0 14.7 + - - +
154C TRP* 6.0 0.4 - - + -
157C PHE* 4.1 17.3 - - + -
158C THR* 3.2 43.5 - - + +
161C SER* 4.0 24.7 - - - +
162C TYR* 5.9 0.9 - - + -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 2.9 23.8 + - - +
98C ASP* 3.8 12.5 - - - +
100C VAL* 1.3 78.6 - - + +
102C SER* 1.3 57.5 + - - +
104C ILE* 3.1 32.4 - - + +
105C ALA* 3.5 7.3 + - - +
158C THR* 5.6 1.8 - - + -
162C TYR* 2.4 33.2 + - + +
185C LYS* 3.1 41.8 - - - +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 2.8 21.6 + - - +
99C LEU* 3.1 8.3 + - - -
101C GLU* 1.3 75.6 - - - +
103C LYS* 1.3 62.6 + - - +
105C ALA* 3.1 9.2 + - - +
106C SER* 2.9 26.7 + - - -
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Residues in contact with LYS 103 (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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60C VAL* 3.6 25.1 - - + -
61C GLU* 3.3 34.7 + - - +
99C LEU 3.0 10.1 + - - +
100C VAL* 3.0 12.1 + - + +
102C SER* 1.3 74.8 - - - +
104C ILE* 1.3 66.0 + - + +
106C SER* 3.1 12.7 + - - +
107C GLU* 2.9 46.2 + - - +
154C TRP* 3.4 43.2 - - + -
158C THR* 6.0 0.2 - - - +
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Residues in contact with ILE 104 (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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100C VAL 3.0 10.4 + - - +
101C GLU* 3.1 33.7 - - + +
103C LYS* 1.3 76.9 - - - +
105C ALA* 1.3 76.8 + - + +
106C SER 3.5 0.2 + - - -
107C GLU* 3.5 19.2 + - - +
154C TRP* 4.7 7.2 - - + +
155C LEU* 4.4 17.7 - - + -
158C THR* 3.1 37.0 - - + +
189C PHE* 5.1 3.6 - - + -
192C LYS* 6.0 1.8 - - - +
193C TYR* 3.5 28.6 + - + +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C GLU 3.5 9.2 + - - +
102C SER* 3.1 13.6 + - - +
104C ILE* 1.3 90.5 - - + +
106C SER* 1.3 63.0 + - - +
107C GLU 3.6 4.2 - - - +
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER 2.9 13.3 + - - -
103C LYS* 3.1 21.9 + - - -
104C ILE 3.3 0.2 - - - -
105C ALA* 1.3 78.1 - - - +
107C GLU* 1.3 86.4 + - - +
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 2.9 33.2 + - - +
104C ILE* 3.5 13.3 + - - +
105C ALA 3.6 7.1 - - - +
106C SER* 1.3 98.9 + - - +
151C ILE* 4.1 39.5 - - + +
154C TRP* 3.9 40.6 + - + -
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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) + - + + + + + -
------------------------------------------------------------
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