Contacts of the helix formed by residues 71 - 93 (chain C) in PDB entry 1CD9
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 GLN 71 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER* 3.4 15.4 + - - +
67C SER* 4.3 10.5 - - - -
68C GLN 4.3 0.4 + - - -
69C ALA 4.3 1.0 + - - -
70C LEU* 1.4 65.6 - - - +
72C LEU* 1.3 66.6 + - - +
73C ALA* 3.5 6.3 + - - +
127C MET* 3.9 5.9 - - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C SER* 5.5 4.5 - - - -
9C SER* 3.3 19.3 - - - +
10C LEU* 3.7 26.0 - - + -
66C PRO 4.8 7.6 - - - +
67C SER* 4.8 4.7 + - - +
70C LEU 2.7 12.6 + - - -
71C GLN* 1.3 72.8 - - - +
73C ALA* 1.3 64.3 + - - +
74C GLY 2.9 4.6 + - - -
75C CYS* 3.2 31.2 + - + +
76C LEU* 3.3 17.7 + - + +
127C MET* 3.8 12.8 - - + -
172C LEU* 3.6 41.1 - - + -
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Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 3.7 13.7 - - + +
71C GLN 3.5 4.1 - - - +
72C LEU* 1.3 76.3 - - - +
74C GLY* 1.3 59.6 + - - +
76C LEU* 5.6 0.2 - - - -
77C SER* 3.5 17.7 + - - -
122C MET* 4.2 4.5 - - - +
127C MET* 3.6 49.5 - - + +
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Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN* 6.0 3.6 - - - -
70C LEU* 3.2 17.4 - - - +
72C LEU 2.9 2.0 + - - -
73C ALA* 1.3 78.0 - - - +
75C CYS* 1.3 59.2 + - - +
76C LEU 3.2 2.0 - - - -
77C SER* 2.8 28.0 + - - -
78C GLN* 3.0 13.4 + - - +
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Residues in contact with CYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C CYS* 2.0 72.3 - - + +
67C SER* 5.7 1.8 - - - +
68C GLN* 5.8 4.4 - - - +
70C LEU* 5.3 1.2 + - - +
72C LEU* 3.2 27.5 + - + +
74C GLY* 1.3 73.4 - - - +
76C LEU* 1.3 65.8 + - - +
78C GLN* 3.1 5.9 + - - +
79C LEU* 3.0 25.6 + - - +
168C VAL* 3.6 16.8 - - - -
169C LEU* 6.1 0.7 - - - -
172C LEU* 5.3 2.0 - - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LEU* 4.0 36.3 - - + -
14C PHE* 4.0 26.5 - - + -
18C CYS* 6.0 0.4 - - - -
72C LEU* 3.3 17.5 + - + +
73C ALA* 4.3 0.7 - - - +
74C GLY 3.2 0.4 - - - -
75C CYS* 1.3 79.8 - - + +
77C SER* 1.3 65.3 + - - +
79C LEU* 3.1 21.4 + - + +
80C HIS* 2.8 24.4 + - - +
118C ILE* 4.2 9.0 - - + +
121C GLN* 5.3 0.7 - - + -
122C MET* 3.5 34.3 - - + +
127C MET* 4.7 7.2 - - - -
169C LEU* 4.7 10.5 - - + -
172C LEU* 5.4 1.3 - - + -
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Residues in contact with SER 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ALA 3.5 13.9 + - - -
74C GLY* 2.8 19.1 + - - -
76C LEU* 1.3 80.1 - - - +
78C GLN* 1.3 55.2 + - - +
80C HIS* 3.4 4.2 + - - +
81C SER* 3.0 31.1 + - - -
122C MET* 3.7 10.5 - - - -
129C PRO* 2.9 30.5 - - - +
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Residues in contact with GLN 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO* 3.8 26.0 + - - +
62C LEU* 3.8 14.8 - - + -
63C SER* 3.0 49.3 + - - +
65C CYS* 4.3 7.6 - - - +
74C GLY 3.0 15.2 + - - +
75C CYS* 3.1 8.7 + - - +
77C SER* 1.3 74.6 - - - +
79C LEU* 1.3 66.1 + - - +
80C HIS 3.1 1.3 - - - -
81C SER* 3.1 8.3 + - - +
82C GLY* 2.9 22.7 + - - -
161C PHE* 4.2 2.3 - - - -
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 4.5 7.3 - - + +
65C CYS* 5.8 0.4 - - - -
75C CYS* 3.0 16.6 + - - +
76C LEU* 3.5 16.4 - - + +
78C GLN* 1.3 77.3 - - - +
80C HIS* 1.3 63.7 + - - +
82C GLY 3.4 0.2 + - - -
83C LEU* 3.1 46.0 + - + +
114C PHE* 4.7 6.7 - - + -
118C ILE* 4.0 17.3 - - + -
161C PHE* 3.6 13.4 - - + -
162C LEU* 5.6 0.4 - - + -
165C SER* 3.2 31.2 - - - +
168C VAL* 5.8 2.0 - - + -
169C LEU* 4.0 37.0 - - + -
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Residues in contact with HIS 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C LEU 2.8 12.8 + - - +
77C SER* 3.6 9.0 + - - +
79C LEU* 1.3 78.2 - - - +
81C SER* 1.3 60.8 + - - +
83C LEU* 3.8 4.5 - - - +
84C PHE* 2.9 44.5 + + + +
115C ALA* 3.2 37.3 + - + +
118C ILE* 4.1 16.7 - - + +
119C TRP* 3.9 34.4 - + + +
122C MET* 4.4 5.8 - - + -
133C PRO* 3.9 27.2 - - + +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PRO* 6.2 2.9 - - - -
77C SER* 3.0 19.8 + - - -
78C GLN* 3.1 9.8 + - - -
80C HIS* 1.3 81.3 + - - +
82C GLY* 1.3 64.4 + - - +
84C PHE* 3.2 8.9 + - - +
85C LEU* 2.9 23.1 + - - +
133C PRO* 5.0 8.6 - - - +
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Residues in contact with GLY 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ALA* 3.9 17.7 - - - -
61C PRO* 5.4 4.2 + - - +
78C GLN 2.9 11.4 + - - -
81C SER* 1.3 75.3 - - - +
83C LEU* 1.3 55.1 + - - +
85C LEU* 2.7 26.0 + - - +
86C TYR* 3.0 15.9 + - - -
161C PHE* 3.5 21.8 - - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 5.1 2.5 - - + -
79C LEU* 3.1 20.7 + - + +
80C HIS* 3.8 3.8 - - - +
82C GLY* 1.3 72.2 - - - +
84C PHE* 1.3 58.0 + - - +
86C TYR* 3.4 3.3 + - - +
87C GLN* 2.9 30.0 + - - +
111C VAL* 3.4 21.4 - - + +
114C PHE* 3.3 41.3 - - + -
115C ALA* 4.0 19.7 - - + +
118C ILE* 4.0 15.7 - - + -
158C LEU* 4.7 5.4 - - + -
161C PHE* 3.6 19.4 - - + -
162C LEU* 4.0 20.9 - - + -
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C HIS* 2.9 37.1 + + + +
81C SER* 3.3 8.5 - - - +
83C LEU* 1.3 79.4 - - - +
85C LEU* 1.3 61.1 + - - +
87C GLN* 3.1 42.7 - - - +
88C GLY 3.2 4.7 + - - -
115C ALA* 4.5 2.0 - - + +
133C PRO* 3.6 42.4 - - + -
134C THR 4.6 0.9 - - - -
135C GLN* 3.6 42.3 + - + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PRO* 3.9 28.5 - - + +
59C TRP 4.9 0.7 - - - +
60C ALA* 4.2 27.4 - - + +
61C PRO* 5.3 3.6 - - + -
81C SER 2.9 11.1 + - - +
82C GLY* 2.7 16.6 + - - +
84C PHE* 1.3 69.4 - - - +
86C TYR* 1.3 62.9 + - + +
87C GLN 3.0 1.1 - - - -
88C GLY* 2.9 4.2 + - - -
89C LEU* 2.8 35.3 + - + +
135C GLN* 4.1 10.3 - - - +
136C GLY* 5.8 1.3 - - - +
138C MET* 3.7 26.2 - - + +
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C PRO 4.6 3.4 - - - -
59C TRP* 4.1 0.7 - - - -
60C ALA* 3.0 47.1 + - + +
82C GLY 3.0 19.9 + - - -
83C LEU 4.0 5.2 - - - +
85C LEU* 1.3 78.4 - - + +
87C GLN* 1.3 66.6 + - - +
89C LEU* 3.9 24.9 - - + -
90C LEU* 2.9 37.0 + - + +
111C VAL* 4.8 2.7 - - + -
154C VAL* 4.0 12.8 - - + -
157C HIS* 3.3 41.8 + - + +
158C LEU* 3.4 33.0 - - + -
161C PHE* 3.8 20.8 - + + +
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Residues in contact with GLN 87 (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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83C LEU 2.9 13.4 + - - +
84C PHE* 3.1 37.1 - - - +
86C TYR* 1.3 77.4 - - - +
88C GLY* 1.3 60.6 + - - +
90C LEU* 3.8 2.1 + - - +
91C GLN* 3.3 27.3 + - - +
108C GLN* 3.1 39.4 + - - +
111C VAL* 4.1 9.4 - - + +
112C ALA* 3.6 31.2 + - - +
115C ALA* 4.0 13.7 - - - +
116C THR* 5.6 0.6 + - - -
135C GLN* 6.1 0.2 - - - -
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PHE 3.2 3.2 + - - -
85C LEU 2.9 7.1 + - - -
87C GLN* 1.3 79.6 - - - +
89C LEU* 1.3 65.8 + - - +
91C GLN* 2.8 19.8 + - - +
92C ALA* 2.9 13.2 + - - +
135C GLN* 3.9 18.8 - - - +
138C MET* 3.8 12.8 - - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ILE* 4.2 21.1 - - + -
58C PRO* 4.2 20.2 - - + +
85C LEU* 2.8 25.9 + - + +
86C TYR* 3.4 31.2 + - + +
88C GLY* 1.3 70.3 - - - +
90C LEU* 1.3 62.6 + - - +
92C ALA* 3.0 16.8 + - - +
93C LEU* 3.4 15.7 + - - +
138C MET* 3.9 11.8 - - + -
139C PRO* 3.6 37.5 - - + -
141C PHE* 4.1 5.4 - - + -
154C VAL* 4.0 17.9 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.9 3.8 - - + -
86C TYR 2.9 28.2 + - - +
87C GLN* 4.1 3.6 - - - +
89C LEU* 1.3 76.2 - - - +
91C GLN* 1.3 60.4 + - - +
93C LEU* 3.5 23.2 + - + +
94C GLU 4.4 0.9 + - - -
95C GLY 5.0 0.5 + - - -
104C LEU* 3.9 34.4 - - + +
107C LEU* 3.9 33.0 - - + -
108C GLN* 4.2 21.4 - - + +
111C VAL* 4.0 20.6 - - + -
151C GLY 5.9 0.2 - - - +
154C VAL* 3.6 27.6 - - + -
155C ALA 5.2 0.4 - - - +
158C LEU* 4.5 6.3 - - + -
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C GLN* 3.3 29.8 + - - +
88C GLY* 2.8 13.9 + - - +
90C LEU* 1.3 79.1 - - - +
92C ALA* 1.3 62.1 + - - +
94C GLU* 3.1 20.1 + - - +
108C GLN* 3.6 31.2 + - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C GLY 2.9 10.2 + - - +
89C LEU* 3.0 12.1 + - - +
91C GLN* 1.3 73.2 - - - +
93C LEU* 1.3 56.0 + - - +
94C GLU* 2.9 33.0 + - - +
138C MET* 4.9 11.4 - - + -
139C PRO* 3.7 11.4 - - + +
140C ALA* 5.7 0.2 - - - -
141C PHE* 3.5 33.0 + - + +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU 3.7 10.1 - - - +
90C LEU* 3.6 27.8 - - + +
91C GLN 3.2 0.6 - - - -
92C ALA* 1.3 75.1 - - - +
94C GLU* 1.3 53.9 + - - +
95C GLY 3.1 0.9 - - - -
96C ILE* 2.6 50.4 + - + -
104C LEU* 4.1 11.2 - - + -
141C PHE* 3.8 28.0 - - + -
147C ARG* 3.4 32.6 - - - +
150C GLY 3.9 7.2 - - - +
151C GLY* 3.5 31.2 - - - +
154C VAL* 4.5 4.0 - - + -
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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