Contacts of the helix formed by residues 82 - 105 (chain C) in PDB entry 4BL5
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 TYR 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 4.7 6.5 - - + -
78C ARG* 3.2 47.0 + - + +
79C ASN 3.8 0.4 - - - -
80C ILE 3.3 1.2 - - - -
81C LYS* 1.3 109.4 - - + +
83C ASN* 1.3 62.2 + - - +
84C LEU 3.4 2.7 - - - -
85C ASP* 3.5 26.0 + - + +
86C PHE* 2.9 34.7 + + + -
184C ASP* 5.2 4.9 - - - -
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Residues in contact with ASN 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ASN* 2.9 21.8 + - - +
80C ILE* 3.8 9.7 + - - +
81C LYS 3.9 2.0 + - - -
82C TYR* 1.3 75.4 - - - +
84C LEU* 1.3 57.2 + - - +
86C PHE* 3.5 4.7 + - - +
87C TRP* 3.0 23.4 + - - +
138C ASN 4.1 1.6 + - - -
139C SER* 3.1 14.9 + - - +
140C ASN* 3.1 7.4 - - - -
141C PHE* 3.1 43.1 + - + -
142C GLY* 2.8 35.5 + - - +
143C TYR 4.4 1.0 + - - -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C TYR 3.4 0.4 - - - -
83C ASN* 1.3 74.7 - - - +
85C ASP* 1.3 64.1 + - - +
87C TRP* 3.2 12.6 + - + +
88C ARG* 2.7 68.2 + - + +
141C PHE* 5.8 0.2 - - - -
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Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET* 4.1 20.0 - - + -
82C TYR* 3.5 32.4 + - + +
84C LEU* 1.3 80.1 - - - +
86C PHE* 1.3 68.4 + - - +
87C TRP 2.9 1.6 - - - -
88C ARG* 4.3 2.7 - - - +
89C LYS* 2.8 43.7 + - + +
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Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C MET* 3.4 49.1 - - + -
73C VAL* 4.0 0.2 - - - -
74C GLY 3.9 9.9 - - - -
78C ARG* 3.7 32.5 - - + -
79C ASN* 3.3 52.9 - - - -
82C TYR* 2.9 31.8 + - + +
83C ASN* 3.6 7.2 - - - +
85C ASP* 1.3 80.2 - - - +
87C TRP* 1.3 60.1 + - - +
90C ASN* 2.9 31.8 + - - +
143C TYR* 3.8 25.7 - + - +
146C ALA* 4.2 2.9 - - - +
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Residues in contact with TRP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASN 3.0 14.8 + - - +
84C LEU* 3.4 16.8 - - + +
85C ASP 2.9 0.8 - - - -
86C PHE* 1.3 75.6 - - - +
88C ARG* 1.3 98.6 + - + +
90C ASN 3.3 1.4 + - - -
91C VAL* 3.0 66.0 + - + +
142C GLY* 3.8 15.5 - - - -
145C TYR* 3.9 14.8 - - + -
146C ALA* 3.5 27.6 - - - -
149C MET* 4.3 14.1 - - + -
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 2.7 46.9 + - + +
85C ASP* 4.2 2.5 - - - +
87C TRP* 1.3 93.7 - - + +
89C LYS* 1.3 63.6 + - + +
91C VAL* 4.1 1.5 - - - +
92C HIS* 3.0 59.1 + - + +
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C THR* 3.6 20.9 - - + +
72C MET* 3.9 26.9 - - + -
85C ASP* 2.8 29.0 + - - +
88C ARG* 1.3 80.0 - - + +
90C ASN* 1.3 56.4 + - - +
92C HIS* 3.5 2.8 + - - +
93C MET* 3.1 42.4 + - + +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 4.7 0.2 - - - +
71C ALA* 3.2 16.9 - - - +
72C MET* 2.9 50.3 + - - +
86C PHE* 2.9 25.0 + - - +
87C TRP 3.3 1.4 + - - -
89C LYS* 1.3 74.0 - - - +
91C VAL* 1.3 60.9 + - - +
92C HIS 3.1 2.0 - - - -
93C MET* 3.4 5.2 - - - +
94C ASN* 2.8 45.3 + - - +
143C TYR* 3.9 15.3 + - - +
146C ALA* 3.9 11.9 - - + -
147C LYS* 4.7 4.8 + - - +
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Residues in contact with VAL 91 (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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87C TRP* 3.0 58.5 + - + +
88C ARG* 4.1 2.7 - - - +
90C ASN* 1.3 76.0 - - - +
92C HIS* 1.3 64.8 + - + +
94C ASN* 4.1 5.7 - - - +
95C ASP* 3.0 30.7 + - + +
146C ALA* 3.5 23.1 - - + +
149C MET* 5.3 5.2 - - + -
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Residues in contact with HIS 92 (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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49C THR* 4.1 26.2 + - - +
88C ARG* 3.0 59.3 + - + +
89C LYS* 3.7 8.3 - - - +
90C ASN 3.1 0.8 - - - -
91C VAL* 1.3 83.3 - - + +
93C MET* 1.3 57.3 + - - +
95C ASP* 3.2 5.0 + - + -
96C ASN* 2.7 44.0 + - - +
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.7 21.5 + - + -
49C THR* 3.6 23.8 - - + +
68C HIS* 4.4 5.8 - - + -
70C ALA* 4.3 12.3 - - - +
71C ALA* 3.7 15.5 - - - -
72C MET* 3.3 34.5 - - + +
89C LYS* 3.1 25.3 + - + +
90C ASN* 3.4 17.3 - - - +
92C HIS* 1.3 77.8 - - - +
94C ASN* 1.3 58.9 + - - +
96C ASN* 3.6 0.7 - - - +
97C VAL* 2.7 42.3 + - - +
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Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C HIS* 2.8 34.0 + - + +
70C ALA 4.6 3.5 - - - +
71C ALA* 6.0 0.2 - - - +
90C ASN* 2.8 40.6 + - - +
91C VAL* 4.1 4.4 - - - +
93C MET* 1.3 72.2 - - - +
95C ASP* 1.3 67.7 + - - +
98C LEU* 2.9 36.1 + - + +
146C ALA 3.9 11.5 + - - -
147C LYS* 5.1 4.9 + - - +
149C MET 6.3 0.2 - - - -
150C ILE* 3.3 41.0 - - + +
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Residues in contact with ASP 95 (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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91C VAL* 3.0 22.9 + - + +
92C HIS* 3.7 5.8 - - + +
94C ASN* 1.3 75.2 - - - +
96C ASN* 1.3 70.8 + - - +
98C LEU* 4.4 2.0 - - - +
99C HIS* 3.0 40.0 + - - +
157C TYR* 4.7 3.8 + - - -
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Residues in contact with ASN 96 (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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48C LEU 2.7 27.9 + - - +
49C THR* 3.0 24.2 + - - +
51C THR* 3.1 38.6 + - - +
54C THR* 3.7 13.0 - - + +
92C HIS* 2.7 24.7 + - - +
93C MET 3.6 0.9 - - - +
95C ASP* 1.3 82.8 - - - +
97C VAL* 1.3 62.4 + - - +
99C HIS* 4.2 1.5 - - - +
100C SER* 3.0 30.9 + - - -
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C THR* 4.5 5.2 - - + -
48C LEU* 3.7 33.7 - - + -
54C THR* 4.2 6.7 - - + -
58C PHE* 3.7 16.5 - - + -
66C VAL* 4.4 8.5 - - + -
68C HIS* 3.3 50.3 - - + +
93C MET 2.7 22.8 + - - +
94C ASN 4.1 0.2 - - - +
96C ASN* 1.3 72.2 - - - +
98C LEU* 1.3 67.4 + - + +
101C ALA* 3.2 23.4 + - - +
109C VAL* 5.2 0.2 - - + -
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C HIS* 5.1 2.9 - - + -
94C ASN* 2.9 28.8 + - + +
95C ASP* 4.4 2.0 - - - +
97C VAL* 1.3 79.2 - - + +
99C HIS* 1.3 58.3 + - - +
101C ALA* 3.8 2.3 - - - +
102C PHE* 3.1 24.8 + - - +
109C VAL* 3.6 31.4 - - + -
111C SER* 3.8 10.5 - - - +
150C ILE* 4.2 16.2 - - + -
153C GLN* 4.0 22.2 - - + -
154C ASN* 3.7 20.0 - - - +
157C TYR* 3.8 14.0 - - + -
165C PHE* 3.6 25.2 - - + -
166C THR 5.9 0.2 - - - +
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Residues in contact with HIS 99 (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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95C ASP* 3.0 27.3 + - - +
96C ASN* 4.2 2.2 - - - +
98C LEU* 1.3 75.0 - - - +
100C SER* 1.3 60.6 + - - +
102C PHE* 3.2 23.0 - + - +
103C GLU* 3.1 51.2 + - - +
157C TYR* 2.6 36.3 + + - +
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Residues in contact with SER 100 (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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51C THR* 4.9 2.6 + - - +
54C THR* 3.9 3.3 - - - +
55C ARG* 3.9 28.4 + - - +
58C PHE* 3.7 30.5 - - - -
96C ASN* 3.0 19.6 + - - -
97C VAL 4.0 1.3 - - - -
99C HIS* 1.3 74.5 - - - +
101C ALA* 1.3 54.7 + - - +
103C GLU* 3.0 13.5 + - - +
104C VAL* 2.8 38.3 + - - +
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Residues in contact with ALA 101 (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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58C PHE* 3.5 21.6 - - + -
66C VAL* 4.2 3.1 - - + -
97C VAL 3.2 17.2 + - - +
98C LEU* 3.8 5.2 - - - +
100C SER* 1.3 73.8 - - - +
102C PHE* 1.3 62.5 + - - +
104C VAL* 4.3 2.0 - - - +
105C GLY 3.4 1.6 + - - -
106C ALA* 2.8 41.3 + - + +
109C VAL* 3.8 28.5 - - + -
165C PHE* 4.4 1.1 - - - -
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Residues in contact with PHE 102 (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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98C LEU 3.1 17.1 + - - +
99C HIS* 3.2 26.5 - + - +
100C SER 3.1 0.6 - - - -
101C ALA* 1.3 78.6 - - - +
103C GLU* 1.3 68.1 + - + +
105C GLY* 3.1 19.4 + - - -
106C ALA 4.9 0.2 - - - +
157C TYR* 3.8 22.4 - + + -
161C TYR* 3.4 53.6 - + + -
163C CYS* 3.6 23.3 - - - -
165C PHE* 3.9 9.2 - - + -
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Residues in contact with GLU 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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55C ARG* 2.2 45.7 + - - +
99C HIS* 3.1 41.5 + - - +
100C SER* 3.0 15.1 + - - +
102C PHE* 1.3 84.0 - - + +
104C VAL* 1.3 61.9 + - + +
105C GLY 3.3 0.4 - - - -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C ARG* 5.6 5.6 - - - +
58C PHE* 3.2 39.3 - - + +
59C GLU* 4.5 3.6 - - + +
62C GLN* 3.4 29.2 - - - +
63C PRO* 4.1 25.8 - - + +
100C SER* 2.8 17.9 + - - +
101C ALA* 4.4 5.4 - - - +
103C GLU* 1.3 80.3 - - + +
105C GLY* 1.3 58.7 + - - +
106C ALA* 4.7 1.6 - - + +
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Residues in contact with GLY 105 (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 PRO 4.9 1.7 - - - +
64C THR* 5.7 0.5 - - - -
102C PHE 3.1 15.6 + - - -
103C GLU 3.3 0.6 - - - -
104C VAL* 1.3 81.7 - - - +
106C ALA* 1.3 66.9 + - - +
107C ARG* 3.5 3.6 + - - +
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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
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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