Contacts of the helix formed by residues 89 - 112 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 3.3 7.6 - - - +
88A VAL* 1.3 89.5 - - + +
90A ILE* 1.3 59.4 + - - +
91A SER* 3.7 17.0 - - - +
92A GLU* 2.9 52.1 + - + +
93A ARG* 3.6 2.4 + - - +
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.8 3.4 - - + +
24A GLU* 4.4 5.2 - - - +
25A GLY 5.8 0.4 - - - +
31A HIS* 3.6 48.9 - - + +
42A VAL* 5.2 0.2 - - + -
43A TYR* 4.1 34.8 - - + +
46A VAL* 4.7 9.9 - - + -
88A VAL 3.3 2.6 + - - -
89A PRO* 1.3 70.7 - - - +
91A SER* 1.3 66.0 + - - +
93A ARG* 3.0 26.6 + - + +
94A PHE* 3.1 49.1 + - + -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.3 32.4 - - - +
89A PRO* 3.7 15.4 - - - +
90A ILE* 1.3 82.4 - - - +
92A GLU* 1.3 65.9 + - - +
94A PHE* 3.5 6.0 + - - +
95A LYS* 3.2 22.0 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.6 17.3 - - + +
89A PRO* 2.9 37.7 + - + +
91A SER* 1.3 80.0 + - - +
93A ARG* 1.3 60.4 + - - +
95A LYS* 3.3 10.4 + - + +
96A GLU* 3.0 27.9 + - - +
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Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 3.0 23.3 + - + +
46A VAL* 3.9 14.8 - - + -
47A VAL* 3.7 18.7 - - + +
50A ILE* 3.2 30.4 - - + +
84A GLN* 3.5 36.9 + - - +
85A SER 3.0 27.5 + - - +
88A VAL* 3.6 26.8 - - - +
89A PRO 4.0 2.5 - - - +
90A ILE* 3.0 24.0 + - + +
92A GLU* 1.3 77.3 - - - +
94A PHE* 1.3 58.9 + - - +
96A GLU* 3.3 15.4 + - - -
97A PHE* 2.9 26.8 + - - +
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PRO* 5.1 4.9 - - - +
19A LEU* 4.1 17.9 - - + -
20A GLU* 3.8 37.7 - - + +
23A LEU* 3.7 25.8 - - + -
24A GLU* 3.7 31.6 - - + +
46A VAL* 4.2 23.1 - - + -
90A ILE* 3.1 50.8 + - + -
91A SER* 3.7 6.5 - - - +
93A ARG* 1.3 74.9 - - - +
95A LYS* 1.3 64.9 + - - +
97A PHE* 3.5 8.2 + + - +
98A GLN* 3.1 25.5 + - - +
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A SER 3.2 11.5 + - - +
92A GLU* 3.6 12.8 - - + +
94A PHE* 1.3 81.4 - - - +
96A GLU* 1.3 61.2 + - - +
98A GLN* 3.8 4.2 - - - +
99A GLN* 3.1 25.0 + - + +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.6 26.4 - - + +
54A LYS* 3.1 25.7 + - - -
84A GLN* 5.9 0.2 + - - -
92A GLU 3.0 16.3 + - - +
93A ARG* 3.6 19.4 + - - +
95A LYS* 1.3 76.5 - - - +
97A PHE* 1.3 55.8 + - - +
99A GLN* 3.3 5.8 + - + +
100A LEU* 2.9 43.0 + - + +
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Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 3.9 19.1 - - + -
16A PRO* 3.7 36.6 - - + -
19A LEU* 4.2 16.6 - - + -
46A VAL* 5.4 6.7 - - + -
49A LEU* 4.0 30.1 - - + -
50A ILE* 3.7 16.1 - - + +
53A GLU* 3.7 21.3 - - + -
93A ARG 2.9 17.0 + - - +
94A PHE* 3.9 10.3 - + - +
95A LYS 3.3 0.2 - - - -
96A GLU* 1.3 75.8 - - - +
98A GLN* 1.3 56.6 + - - +
100A LEU* 3.9 3.3 - - - +
101A ARG* 2.9 66.0 + - - +
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU 4.8 9.0 + - - +
16A PRO* 3.7 31.7 - - + +
17A LYS* 4.2 17.2 + - - +
20A GLU* 5.9 2.7 - - - +
94A PHE 3.1 18.8 + - - +
95A LYS* 3.8 4.9 - - - +
97A PHE* 1.3 73.2 - - - +
99A GLN* 1.3 65.8 + - - +
101A ARG* 4.5 2.0 - - - +
102A LYS* 3.0 32.2 + - + +
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Residues in contact with GLN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LYS* 3.1 18.8 + - + +
96A GLU* 3.7 6.3 - - + +
98A GLN* 1.3 78.9 - - - +
100A LEU* 1.3 64.3 + - + +
102A LYS* 3.4 21.9 + - - +
103A GLU* 2.6 64.5 + - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.7 35.4 - - + +
53A GLU* 3.9 17.3 - - + +
54A LYS* 3.7 30.7 - - + -
96A GLU* 2.9 28.1 + - + +
97A PHE* 4.0 2.9 - - - +
99A GLN* 1.3 75.7 - - + +
101A ARG* 1.3 60.6 + - - +
103A GLU* 3.6 19.8 + - - +
104A ASN* 2.9 38.2 + - - +
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Residues in contact with ARG 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 2.7 49.2 + - - +
13A GLU* 4.9 1.1 - - - -
15A THR* 3.9 5.1 - - - -
16A PRO* 3.7 18.8 - - + -
49A LEU* 5.4 1.4 + - - +
53A GLU* 2.8 45.6 + - - +
97A PHE* 2.9 34.8 + - + +
98A GLN* 4.0 3.6 - - - +
100A LEU* 1.3 75.4 - - - +
102A LYS* 1.3 65.6 + - - +
104A ASN 3.3 0.2 + - - -
105A LEU* 2.9 47.7 + - + +
139A TRP* 3.5 18.4 - - - +
143A ASP* 2.8 41.2 + - - -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.0 30.3 + - + +
99A GLN* 3.6 23.2 + - - +
101A ARG* 1.3 79.3 - - - +
103A GLU* 1.3 63.3 + - + +
105A LEU* 3.4 7.9 + - - +
106A ASN* 3.3 35.0 + - - +
109A ARG* 5.1 0.2 + - - -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLN* 2.6 51.9 + - - +
100A LEU* 3.6 21.3 - - - +
102A LYS* 1.3 76.5 - - + +
104A ASN* 1.3 59.0 + - - +
106A ASN* 3.2 12.8 + - - +
107A THR* 3.0 30.5 + - - +
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU* 2.8 57.4 + - - +
57A TRP* 6.3 0.4 - - - +
58A ILE* 3.6 37.1 - - + +
100A LEU* 2.9 20.5 + - - +
101A ARG 3.3 4.7 + - - +
103A GLU* 1.3 79.4 - - - +
105A LEU* 1.3 57.3 + - - +
107A THR* 3.6 4.4 + - - -
108A LEU* 2.9 27.7 + - - +
139A TRP* 4.2 10.3 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.5 9.4 - - + +
12A LEU* 3.9 27.4 - - + +
13A GLU* 3.5 42.2 - - + +
101A ARG* 2.9 28.9 + - + +
102A LYS* 3.8 6.5 - - - +
104A ASN* 1.3 75.0 - - - +
106A ASN* 1.3 63.9 + - - +
108A LEU* 3.4 25.5 + - + +
109A ARG* 3.1 48.9 + - - +
139A TRP* 4.4 4.7 - - + -
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LYS* 3.3 28.3 + - - +
103A GLU* 3.2 13.7 + - - +
105A LEU* 1.3 72.8 - - - +
107A THR* 1.3 66.3 + - - +
109A ARG* 3.1 28.6 + - - +
110A SER* 3.0 24.4 + - - -
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.0 13.8 - - + +
62A ARG* 3.3 32.2 + - - +
103A GLU* 3.0 14.8 + - - +
104A ASN* 3.7 13.1 + - - -
106A ASN* 1.3 76.0 - - - +
108A LEU* 1.3 64.3 + - - +
110A SER* 3.1 9.0 + - - -
111A LEU* 2.9 43.1 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MSE 4.0 14.1 - - + -
9A ILE* 4.2 19.7 - - + -
12A LEU* 4.4 6.1 - - + -
58A ILE* 4.2 9.8 - - + +
61A LEU* 3.9 8.7 - - + -
104A ASN 2.9 19.0 + - - +
105A LEU* 3.6 27.6 - - + +
106A ASN 3.2 0.4 - - - -
107A THR* 1.3 74.5 - - - +
109A ARG* 1.3 54.5 + - - +
112A VAL* 2.7 45.3 + - + +
136A LEU* 3.7 37.7 - - + -
139A TRP* 4.0 12.8 - - + -
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Residues in contact with ARG 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MSE 5.1 1.8 - - + -
9A ILE* 3.6 46.3 - - + +
13A GLU* 4.1 9.9 + - - -
102A LYS 5.1 0.4 + - - -
105A LEU* 3.1 33.2 + - - +
106A ASN* 3.1 32.9 + - - +
108A LEU* 1.3 76.7 - - + +
110A SER* 1.3 62.4 + - - +
112A VAL 3.7 9.3 - - - +
113A GLN* 3.5 20.8 + - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ASN 3.0 13.7 + - - -
107A THR* 3.1 13.0 + - - -
109A ARG* 1.3 75.8 - - - +
111A LEU* 1.3 65.9 + - - +
113A GLN* 3.3 27.8 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ILE* 5.1 0.4 - - + -
61A LEU* 4.0 23.3 - - + -
62A ARG* 3.8 37.0 - - + +
65A LEU* 3.5 30.0 - - + +
107A THR* 2.9 37.8 + - + +
108A LEU 4.0 1.6 - - - +
110A SER* 1.3 84.0 - - - +
112A VAL* 1.3 60.6 + - - +
113A GLN* 3.7 4.1 + - - +
117A ASP* 3.8 10.6 - - - +
120A ARG* 5.9 0.2 + - - -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MSE 3.5 33.2 - - + +
61A LEU* 3.9 26.2 - - + -
65A LEU* 4.5 3.4 - - + -
108A LEU* 2.7 34.6 + - + +
109A ARG* 3.7 6.9 - - - +
111A LEU* 1.3 73.4 - - - +
113A GLN* 1.3 59.9 + - - +
114A SER 4.1 3.6 - - - +
117A ASP* 4.0 17.3 - - + -
118A LEU* 3.8 27.1 - - + +
132A VAL* 3.9 10.1 - - + -
136A LEU* 4.5 0.4 - - + -
302A IMD 3.8 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
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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