Contacts of the helix formed by residues 89 - 112 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D ALA 3.6 6.7 - - - +
88D VAL* 1.3 92.8 - - + +
90D ILE* 1.3 65.0 + - - +
91D SER* 3.7 17.3 - - - +
92D GLU* 3.0 27.9 + - + +
93D ARG* 3.4 6.9 + - - +
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Residues in contact with ILE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.8 3.6 - - + +
24D GLU* 5.4 3.1 - - + -
25D GLY 5.7 1.1 - - - +
31D HIS* 3.5 52.0 - - + +
42D VAL* 5.0 0.7 - - + -
43D TYR* 3.9 35.5 - - + +
46D VAL* 4.5 14.6 - - + -
88D VAL 3.4 2.0 + - - -
89D PRO* 1.3 71.6 - - - +
91D SER* 1.3 61.5 + - - +
93D ARG* 2.9 26.8 + - + +
94D PHE* 3.0 49.8 + - + -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D GLU* 3.8 35.2 - - - +
89D PRO* 3.7 14.9 - - - +
90D ILE* 1.3 83.2 - - - +
92D GLU* 1.3 66.2 + - - +
94D PHE* 3.4 5.5 + - - +
95D LYS* 3.3 21.5 + - - +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 3.7 16.8 - - + -
89D PRO* 3.0 26.0 + - + +
91D SER* 1.3 82.8 + - - +
93D ARG* 1.3 65.9 + - - +
95D LYS* 3.4 35.4 + - - +
96D GLU* 3.0 23.8 + - - +
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Residues in contact with ARG 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TYR* 3.0 27.7 + - + +
46D VAL* 3.8 20.9 - - + -
47D VAL* 3.8 22.6 - - + +
50D ILE* 3.4 23.3 - - + +
54D LYS* 6.1 0.4 - - - +
82D LEU* 3.6 19.0 - - - +
86D ASN* 3.3 28.9 + - - -
88D VAL* 3.6 24.3 - - - +
89D PRO 3.4 6.0 + - - +
90D ILE* 2.9 16.5 + - + +
92D GLU* 1.3 78.8 - - - +
94D PHE* 1.3 57.0 + - - +
96D GLU* 3.2 20.0 + - - -
97D PHE* 2.9 26.8 + - - +
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Residues in contact with PHE 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PRO* 5.0 6.0 - - - +
19D LEU* 4.0 17.5 - - + -
20D GLU* 4.1 32.9 - - + +
23D LEU* 3.7 24.0 - - + -
24D GLU* 3.1 39.0 - - - +
46D VAL* 4.2 18.2 - - + -
90D ILE* 3.0 62.2 + - + -
91D SER* 3.7 6.1 - - - +
92D GLU 3.3 0.6 - - - -
93D ARG* 1.3 73.2 - - - +
95D LYS* 1.3 60.7 + - - +
97D PHE* 3.4 8.3 + + - +
98D GLN* 3.0 31.2 + - - +
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Residues in contact with LYS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D SER 3.3 11.1 + - - +
92D GLU* 3.5 39.1 + - - +
94D PHE* 1.3 76.8 - - - +
96D GLU* 1.3 64.8 + - - +
98D GLN* 3.4 6.4 + - - +
99D GLN* 3.1 23.4 + - - +
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Residues in contact with GLU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 3.7 18.1 - - + +
54D LYS* 2.7 33.9 + - - -
92D GLU 3.0 16.5 + - - +
93D ARG* 3.6 27.6 + - - +
95D LYS* 1.3 77.0 - - - +
97D PHE* 1.3 62.3 + - - +
99D GLN* 3.1 6.9 + - - +
100D LEU* 2.9 38.1 + - + +
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Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D THR* 3.9 19.7 - - + -
16D PRO* 3.8 32.1 - - + -
19D LEU* 4.2 10.3 - - + -
46D VAL* 5.3 7.0 - - + -
49D LEU* 4.0 37.2 - - + -
50D ILE* 3.8 15.9 - - + +
53D GLU* 3.7 22.2 - - + -
93D ARG 2.9 17.4 + - - +
94D PHE* 3.9 9.4 - + - +
96D GLU* 1.3 76.4 - - - +
98D GLN* 1.3 57.4 + - - +
100D LEU* 3.6 2.2 + - - -
101D ARG* 2.9 68.6 + - + +
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Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D GLU 4.8 8.3 + - - +
16D PRO* 3.7 31.4 - - + +
17D LYS* 4.2 15.2 + - - +
20D GLU* 5.4 7.1 - - - +
94D PHE 3.0 18.8 + - - +
95D LYS* 3.7 6.3 - - - +
97D PHE* 1.3 77.6 - - - +
99D GLN* 1.3 57.7 + - - +
101D ARG* 4.6 2.2 - - - +
102D LYS* 3.0 39.1 + - + +
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Residues in contact with GLN 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LYS 3.1 17.5 + - - +
96D GLU* 3.1 6.0 + - - +
98D GLN* 1.3 75.6 - - - +
100D LEU* 1.3 65.0 + - + +
102D LYS* 3.3 23.7 + - - +
103D GLU* 3.1 67.5 + - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 3.8 38.8 - - + +
53D GLU* 3.8 18.2 - - + +
54D LYS* 3.9 27.4 - - + -
96D GLU* 2.9 27.8 + - + +
97D PHE* 4.1 2.5 - - - +
99D GLN* 1.3 78.3 - - + +
101D ARG* 1.3 57.6 + - - +
103D GLU* 3.5 17.0 + - - +
104D ASN* 2.9 36.3 + - - +
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Residues in contact with ARG 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 2.8 49.1 + - - +
13D GLU* 4.8 1.6 - - - -
15D THR* 3.8 6.5 - - - -
16D PRO* 3.6 19.1 - - + -
49D LEU* 5.5 1.2 - - - +
53D GLU* 2.9 40.7 + - - +
57D TRP* 5.6 0.2 - - - +
97D PHE* 2.9 37.1 + - + +
98D GLN* 3.9 3.4 - - - +
100D LEU* 1.3 77.4 - - - +
102D LYS* 1.3 56.7 + - - +
104D ASN* 3.1 0.9 + - - +
105D LEU* 3.0 46.5 + - + +
139D TRP* 3.4 18.0 - - - +
143D ASP* 2.7 42.6 + - - -
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLN* 3.0 32.2 + - + +
99D GLN* 3.6 26.0 + - - +
101D ARG* 1.3 73.7 - - - +
103D GLU* 1.3 65.8 + - + +
105D LEU* 3.5 7.2 + - - +
106D ASN* 3.3 34.0 + - - +
109D ARG* 4.9 0.5 + - - -
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D GLN* 3.1 49.9 + - - +
100D LEU* 3.6 19.1 - - - +
102D LYS* 1.3 79.0 - - - +
104D ASN* 1.3 60.6 + - - +
106D ASN* 3.2 12.0 + - - +
107D THR* 3.1 31.0 + - - +
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Residues in contact with ASN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLU* 2.7 57.5 + - - +
57D TRP* 6.2 0.6 - - - +
58D ILE* 3.5 37.5 - - + +
100D LEU* 2.9 22.7 + - - +
101D ARG 3.1 5.1 + - - +
103D GLU* 1.3 78.3 - - - +
105D LEU* 1.3 60.5 + - - +
107D THR* 3.5 3.8 + - - -
108D LEU* 2.9 27.0 + - - +
139D TRP* 4.1 9.5 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 4.6 9.2 - - + +
12D LEU* 3.9 22.7 - - + -
13D GLU* 3.6 41.5 - - + +
101D ARG* 3.0 29.7 + - + +
102D LYS* 3.5 6.3 + - - +
104D ASN* 1.3 75.1 - - - +
106D ASN* 1.3 59.5 + - - +
108D LEU* 3.5 26.2 - - + +
109D ARG* 3.0 54.5 + - - +
139D TRP* 4.2 9.0 - - + -
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D LYS* 3.3 30.1 + - - +
103D GLU* 3.2 13.3 + - - +
105D LEU* 1.3 77.7 - - - +
107D THR* 1.3 60.0 + - - +
109D ARG* 2.9 24.9 + - - +
110D SER* 3.1 27.3 + - - -
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Residues in contact with THR 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ILE* 3.7 22.1 - - + +
62D ARG* 3.8 20.9 + - - +
103D GLU* 3.1 14.6 + - - +
104D ASN* 3.7 10.1 + - - -
106D ASN* 1.3 73.8 - - - +
108D LEU* 1.3 66.7 + - - +
110D SER* 3.1 6.9 + - - -
111D LEU* 2.9 45.7 + - + +
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D MSE 4.1 14.8 - - + -
8D ALA* 6.5 0.4 - - + -
9D ILE* 3.9 22.2 - - + -
12D LEU* 4.7 5.4 - - + -
58D ILE* 4.1 10.3 - - + +
61D LEU* 3.8 22.7 - - + -
104D ASN 2.9 18.6 + - - +
105D LEU* 3.5 27.8 - - + +
106D ASN 3.4 0.2 - - - -
107D THR* 1.3 73.6 - - - +
109D ARG* 1.3 57.1 + - - +
111D LEU* 3.0 2.9 + - - -
112D VAL* 2.8 39.1 + - + +
136D LEU* 3.8 27.8 - - + -
139D TRP* 4.2 12.1 - - + -
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Residues in contact with ARG 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D MSE 5.0 1.1 - - - -
9D ILE* 3.6 40.8 - - + +
13D GLU* 4.1 10.3 + - - +
102D LYS 4.9 0.8 + - - -
105D LEU* 3.0 36.8 + - - +
106D ASN* 2.9 33.8 + - - +
108D LEU* 1.3 80.5 - - - +
110D SER* 1.3 55.1 + - - +
112D VAL 3.5 9.2 - - - +
113D GLN* 3.3 20.4 + - - +
301D GOL 3.6 24.7 + - - +
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Residues in contact with SER 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ASN 3.1 15.0 + - - -
107D THR* 3.1 12.3 + - - -
109D ARG* 1.3 74.3 - - - +
111D LEU* 1.3 66.9 + - - +
113D GLN* 3.1 30.3 - - - +
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Residues in contact with LEU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ILE* 4.8 1.6 - - + +
61D LEU* 4.0 25.1 - - + -
62D ARG* 3.8 36.6 - - + +
65D LEU* 3.6 28.7 - - + +
107D THR* 2.9 38.5 + - + +
108D LEU 3.8 1.8 - - - +
110D SER* 1.3 83.4 - - - +
112D VAL* 1.3 62.9 + - - +
113D GLN* 3.7 3.9 + - - +
117D ASP* 4.3 8.0 - - - +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D MSE 3.7 33.9 - - + +
61D LEU* 3.9 17.0 - - + -
65D LEU* 4.4 4.7 - - + -
108D LEU* 2.8 26.5 + - + +
109D ARG* 3.5 10.7 - - - +
111D LEU* 1.3 73.6 - - - +
113D GLN* 1.3 61.5 + - - +
114D SER 3.6 17.7 - - - +
117D ASP* 4.2 11.2 - - + -
118D LEU* 4.1 20.2 - - + -
132D VAL* 3.8 24.0 - - + -
301D GOL 5.0 4.2 - - - -
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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