Contacts of the helix formed by residues 89 - 112 (chain C) in PDB entry 2RD9
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 PRO 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ALA 3.2 7.8 - - - +
88C VAL* 1.3 87.8 - - + +
90C ILE* 1.3 67.0 + - - +
91C SER* 3.9 16.2 - - - +
92C GLU* 2.9 39.5 + - - +
93C ARG* 3.5 2.8 + - - +
303C GOL 3.7 15.5 - - - +
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Residues in contact with ILE 90 (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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23C LEU* 5.0 2.5 - - + +
24C GLU* 4.6 5.8 - - - +
25C GLY 5.9 0.2 - - - +
31C HIS* 3.6 51.1 - - + +
42C VAL* 5.3 0.2 - - + -
43C TYR* 3.9 36.8 - - + +
46C VAL* 4.7 8.1 - - + -
88C VAL 3.3 1.4 + - - -
89C PRO* 1.3 70.9 - - - +
91C SER* 1.3 65.1 + - - +
93C ARG* 2.9 23.2 + - + +
94C PHE* 3.0 46.9 + - + -
303C GOL 3.0 19.1 + - - +
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLU* 3.3 30.4 - - - +
89C PRO* 3.9 13.9 - - - +
90C ILE* 1.3 81.3 - - - +
92C GLU* 1.3 66.2 + - - +
94C PHE* 3.5 9.3 + - - +
95C LYS* 3.2 22.2 + - - +
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Residues in contact with GLU 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 3.4 19.7 - - + +
89C PRO* 2.9 33.4 + - + +
91C SER* 1.3 83.5 + - - +
93C ARG* 1.3 66.2 + - - +
95C LYS* 3.4 11.5 + - + +
96C GLU* 3.0 23.9 + - - +
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Residues in contact with ARG 93 (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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43C TYR* 3.0 24.8 + - + +
46C VAL* 3.9 13.5 - - + -
47C VAL* 3.9 20.3 - - + +
50C ILE* 3.4 27.8 - - + +
84C GLN* 3.7 35.5 - - - +
85C SER 2.9 28.5 + - - +
88C VAL* 3.6 28.8 - - - +
89C PRO 4.2 0.4 - - - +
90C ILE* 2.9 23.2 + - + +
92C GLU* 1.3 79.0 - - - +
94C PHE* 1.3 57.8 + - - +
96C GLU* 3.3 15.0 + - - -
97C PHE* 2.9 28.3 + - - +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C PRO* 5.1 5.2 - - - +
19C LEU* 4.0 18.2 - - + -
20C GLU* 3.6 40.4 - - + +
23C LEU* 3.6 25.4 - - + -
24C GLU* 3.7 32.1 - - + +
46C VAL* 4.3 25.4 - - + -
90C ILE* 3.0 52.1 + - + -
91C SER* 3.7 6.5 - - - +
92C GLU 3.3 0.2 - - - -
93C ARG* 1.3 76.5 - - - +
95C LYS* 1.3 57.3 + - - +
97C PHE* 3.6 8.5 + + - +
98C GLN* 3.0 30.1 + - - +
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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
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91C SER 3.2 12.9 + - - +
92C GLU* 3.5 14.4 - - + +
93C ARG 3.2 0.6 - - - -
94C PHE* 1.3 77.3 - - - +
96C GLU* 1.3 59.7 + - - +
98C GLN* 3.4 5.6 + - - +
99C GLN* 3.0 29.6 + - - +
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Residues in contact with GLU 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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50C ILE* 3.6 23.2 - - + +
54C LYS* 2.9 29.9 + - - -
84C GLN* 5.5 1.2 + - - -
92C GLU 3.0 16.8 + - - +
93C ARG* 3.7 19.5 + - - +
95C LYS* 1.3 74.2 - - - +
97C PHE* 1.3 65.0 + - - +
99C GLN* 3.2 6.6 + - + +
100C LEU* 3.0 36.9 + - + +
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Residues in contact with PHE 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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15C THR* 3.8 27.8 - - + -
16C PRO* 3.8 27.4 - - + -
19C LEU* 4.1 15.5 - - + -
46C VAL* 5.2 8.5 - - + -
49C LEU* 3.9 28.5 - - + -
50C ILE* 3.7 19.9 - - + +
53C GLU* 3.7 22.0 - - + -
93C ARG 2.9 21.0 + - - +
94C PHE* 3.8 8.3 - + - +
96C GLU* 1.3 73.5 - - - +
98C GLN* 1.3 62.4 + - - +
100C LEU* 3.5 2.9 + - - -
101C ARG* 3.0 58.3 + - - +
143C ASP* 4.7 0.7 - - - -
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Residues in contact with GLN 98 (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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13C GLU 4.6 8.8 + - - +
16C PRO* 3.8 30.9 - - + +
17C LYS* 4.1 17.7 + - - +
20C GLU* 5.7 4.9 - - - +
94C PHE 3.0 19.6 + - - +
95C LYS* 3.8 5.8 - - - +
97C PHE* 1.3 76.4 - - - +
99C GLN* 1.3 64.0 + - - +
101C ARG* 4.4 2.4 - - - +
102C LYS* 3.1 29.6 + - + +
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Residues in contact with GLN 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 LYS* 3.0 18.4 + - + +
96C GLU* 3.6 7.0 - - - +
98C GLN* 1.3 77.7 - - - +
100C LEU* 1.3 61.0 + - + +
102C LYS* 3.4 8.6 + - - +
103C GLU* 2.8 57.9 + - - +
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Residues in contact with LEU 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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50C ILE* 3.8 30.3 - - + +
53C GLU* 3.8 31.0 - - + +
54C LYS* 3.9 24.2 - - + -
96C GLU* 3.0 26.0 + - + +
97C PHE* 4.0 2.9 - - - +
99C GLN* 1.3 79.4 - - + +
101C ARG* 1.3 58.2 + - - +
103C GLU* 3.4 21.2 + - - +
104C ASN* 2.8 34.3 + - - +
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Residues in contact with ARG 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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12C LEU* 2.7 46.2 + - - +
13C GLU* 4.8 1.3 - - - -
15C THR* 3.9 5.9 - - - -
16C PRO* 3.7 18.3 - - + +
49C LEU* 5.7 0.4 - - - +
53C GLU* 2.9 40.7 + - - +
97C PHE* 3.0 33.1 + - + +
98C GLN* 4.0 4.3 - - - +
100C LEU* 1.3 76.7 - - - +
102C LYS* 1.3 57.5 + - - +
104C ASN 3.3 0.3 + - - -
105C LEU* 3.0 54.4 + - + +
139C TRP* 3.3 19.9 - - - +
143C ASP* 2.8 39.6 + - - -
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Residues in contact with LYS 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 GLN* 3.1 26.3 + - + +
99C GLN* 3.6 11.2 - - - +
101C ARG* 1.3 76.8 - - - +
103C GLU* 1.3 62.2 + - - +
105C LEU* 3.6 7.7 + - - +
106C ASN* 3.3 32.6 + - - +
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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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99C GLN* 2.8 47.2 + - - +
100C LEU* 3.6 24.1 - - - +
102C LYS* 1.3 77.6 - - - +
104C ASN* 1.3 59.9 + - - +
106C ASN* 3.1 10.1 + - - +
107C THR* 3.0 31.4 + - - +
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Residues in contact with ASN 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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53C GLU* 2.8 58.8 + - - +
57C TRP* 6.3 0.2 - - - +
58C ILE* 3.4 39.1 - - + +
100C LEU* 2.8 22.0 + - - +
101C ARG 3.3 2.4 + - - +
103C GLU* 1.3 76.3 - - - +
105C LEU* 1.3 57.5 + - - +
107C THR* 3.4 4.4 + - - -
108C LEU* 2.8 28.8 + - - +
139C TRP* 4.0 9.7 - - + -
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Residues in contact with LEU 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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9C ILE* 4.6 13.6 - - + +
12C LEU* 3.9 31.0 - - + -
13C GLU* 3.5 42.0 - - + +
101C ARG* 3.0 35.4 + - + +
102C LYS* 4.1 6.3 - - - +
104C ASN* 1.3 73.4 - - - +
106C ASN* 1.3 65.8 + - - +
108C LEU* 3.5 17.3 - - + +
109C ARG* 3.1 42.1 + - - +
139C TRP* 4.5 4.0 - - + -
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Residues in contact with ASN 106 (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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102C LYS* 3.3 24.2 + - - +
103C GLU* 3.1 12.3 + - - +
105C LEU* 1.3 75.6 - - - +
107C THR* 1.3 63.6 + - - +
109C ARG* 3.2 18.1 + - - +
110C SER* 3.2 22.5 + - - -
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Residues in contact with THR 107 (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 ILE* 3.8 9.9 - - + -
62C ARG* 3.7 27.9 + - - +
103C GLU* 3.0 14.2 + - - +
104C ASN* 3.7 12.1 + - - -
106C ASN* 1.3 77.4 - - - +
108C LEU* 1.3 57.0 + - - +
110C SER* 3.1 7.7 + - - +
111C LEU* 2.9 51.4 + - + +
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Residues in contact with LEU 108 (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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5C MSE 4.1 13.0 - - + -
9C ILE* 4.1 30.3 - - + -
12C LEU* 4.8 4.7 - - + -
58C ILE* 4.3 8.9 - - + +
61C LEU* 3.6 27.4 - - + -
104C ASN 2.8 21.0 + - - +
105C LEU* 3.5 19.1 - - + +
106C ASN 3.3 0.2 - - - -
107C THR* 1.3 73.8 - - - +
109C ARG* 1.3 58.1 + - - +
111C LEU 4.5 0.2 - - - +
112C VAL* 2.8 45.2 + - + +
136C LEU* 3.8 18.4 - - + -
139C TRP* 4.3 11.9 - - + -
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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
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5C MSE 6.5 0.2 - - - -
9C ILE* 3.4 48.7 - - + +
13C GLU* 4.4 8.7 + - - -
105C LEU* 3.1 34.8 + - - +
106C ASN* 3.7 16.8 + - - +
107C THR 3.2 0.6 - - - -
108C LEU* 1.3 80.1 - - - +
110C SER* 1.3 60.1 + - - +
112C VAL 3.8 7.2 - - - +
113C GLN* 3.4 20.4 - - - +
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Residues in contact with SER 110 (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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106C ASN 3.2 10.4 + - - -
107C THR* 3.1 11.4 + - - -
109C ARG* 1.3 77.6 - - - +
111C LEU* 1.3 65.1 + - - +
113C GLN* 3.0 27.2 + - - +
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Residues in contact with LEU 111 (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 ILE* 4.5 4.5 - - + -
61C LEU* 3.9 26.9 - - + -
62C ARG* 4.0 36.8 - - + +
65C LEU* 3.7 29.0 - - + +
107C THR* 2.9 41.5 + - + +
108C LEU 4.1 1.8 - - - +
110C SER* 1.3 79.2 - - - +
112C VAL* 1.3 61.5 + - - +
113C GLN* 3.9 1.6 - - - +
117C ASP* 3.8 11.6 - - - +
120C ARG* 5.5 1.0 + - - -
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Residues in contact with VAL 112 (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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5C MSE 3.8 21.0 - - + +
61C LEU* 3.9 16.8 - - + -
65C LEU* 4.6 2.7 - - + -
108C LEU* 2.8 41.7 + - + +
109C ARG* 3.8 6.4 - - - +
111C LEU* 1.3 75.4 - - - +
113C GLN* 1.3 61.3 + - - +
114C SER 4.0 4.7 + - - +
117C ASP* 3.7 18.8 - - + +
118C LEU* 3.6 30.5 - - + +
132C VAL* 3.9 18.2 - - + -
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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
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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