Contacts of the helix formed by residues 4 - 24 (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 GLN 4 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 5.7 1.0 + - - -
2A ASN* 3.3 10.0 + - - +
3A PHE* 1.3 88.5 + - - +
5A MSE 1.3 61.1 + - - +
6A ASN* 3.5 17.3 - - - +
7A GLU* 3.6 28.3 + - - +
8A ALA* 2.9 29.5 + - - +
115A GLU* 5.6 2.4 - - - +
157B ARG* 5.4 0.9 - - - +
158B TYR* 3.9 2.7 + - - -
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Residues in contact with MSE 5 (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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3A PHE* 3.7 18.1 - - + -
4A GLN* 1.3 69.4 + - - +
6A ASN* 1.3 66.3 + - - +
8A ALA* 3.3 3.0 + - - +
9A ILE* 3.1 48.5 + - + +
108A LEU* 4.0 20.6 - - + +
109A ARG* 5.1 3.4 - - + -
112A VAL* 3.5 40.4 - - + +
118A LEU* 4.3 7.0 - - + +
136A LEU* 4.0 22.9 - - - -
302A IMD 3.7 40.2 - - + +
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Residues in contact with ASN 6 (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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4A GLN* 3.5 18.0 - - - +
5A MSE 1.3 79.4 + - - +
7A GLU* 1.3 78.7 + - - +
9A ILE* 3.4 9.3 + - - +
10A GLN* 3.1 43.5 + - - +
306A GOL 3.7 30.7 - - - +
27B SER* 5.6 1.4 - - - -
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Residues in contact with GLU 7 (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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2A ASN 4.1 1.6 - - - +
4A GLN* 3.4 28.4 + - + +
5A MSE 3.3 0.8 - - - -
6A ASN* 1.3 93.0 + - - +
8A ALA* 1.3 65.6 + - - +
10A GLN* 3.5 17.1 - - - +
11A LEU 3.5 2.8 + - - -
27B SER* 3.3 32.9 + - - -
29B SER* 3.3 16.5 + - - -
30B TRP* 3.0 31.6 + - + +
157B ARG* 3.1 28.6 + - - -
158B TYR* 4.6 1.5 + - - +
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Residues in contact with ALA 8 (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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3A PHE* 3.4 27.6 - - + -
4A GLN 2.9 18.0 + - - +
5A MSE 3.5 6.3 - - - +
7A GLU* 1.3 77.6 - - - +
9A ILE* 1.3 59.7 + - + +
11A LEU* 3.3 6.4 + - - +
12A LEU* 3.1 34.5 + - + +
136A LEU* 5.4 0.9 - - + +
140A VAL* 3.8 14.9 - - + +
30B TRP* 4.8 1.6 - - - -
158B TYR* 3.9 10.3 + - - +
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Residues in contact with ILE 9 (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 3.1 45.3 + - + +
6A ASN* 3.8 7.4 - - - +
7A GLU 3.3 0.2 - - - -
8A ALA* 1.3 76.1 - - + +
10A GLN* 1.3 59.2 + - - +
12A LEU* 4.0 6.7 - - + +
13A GLU* 2.9 37.2 + - - +
105A LEU* 4.6 7.6 - - + -
108A LEU* 4.2 20.4 - - + -
109A ARG* 3.6 44.9 - - + +
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Residues in contact with GLN 10 (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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6A ASN* 3.1 33.1 + - - +
7A GLU* 3.5 8.7 - - - +
8A ALA 3.3 0.2 - - - -
9A ILE* 1.3 74.6 - - - +
11A LEU* 1.3 62.8 + - - +
13A GLU* 3.2 23.7 + - - +
14A ARG* 3.1 29.2 + - - +
25B GLY 4.2 8.0 + - - +
26B LEU* 3.8 16.2 - - + -
27B SER* 3.1 40.0 + - - +
30B TRP* 3.5 15.6 + - - -
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Residues in contact with LEU 11 (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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7A GLU 3.5 1.2 + - - +
8A ALA 3.3 8.8 + - - +
9A ILE 3.3 0.2 - - - -
10A GLN* 1.3 78.4 - - - +
12A LEU* 1.3 65.9 + - + +
14A ARG* 3.0 14.7 + - + +
15A THR* 3.2 17.4 + - - +
140A VAL* 3.5 30.5 - - + -
143A ASP* 5.2 0.2 - - - -
144A LEU* 3.9 15.5 - - + -
22B PHE* 4.5 15.7 - - + +
26B LEU* 3.7 18.8 - - + -
30B TRP* 3.5 32.1 - - + +
154B MSE 3.0 35.0 - - + -
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Residues in contact with LEU 12 (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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8A ALA* 3.1 25.1 + - + +
9A ILE* 4.0 2.7 - - - +
11A LEU* 1.3 79.8 - - + +
13A GLU* 1.3 61.5 + - - +
14A ARG 3.4 0.5 + - - -
15A THR 3.8 4.0 + - - -
101A ARG* 2.7 40.5 + - - +
105A LEU* 3.9 25.8 - - + -
108A LEU* 4.4 8.1 - - + -
136A LEU* 5.1 2.9 - - + +
139A TRP* 3.7 53.6 - - + +
140A VAL* 3.8 30.1 - - + -
143A ASP* 3.9 6.7 - - - +
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Residues in contact with GLU 13 (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* 2.9 28.7 + - - +
10A GLN* 3.2 26.4 - - - +
11A LEU 3.1 0.2 - - - -
12A LEU* 1.3 76.7 - - - +
14A ARG* 1.3 80.4 + - + +
15A THR 3.6 0.6 + - - -
16A PRO* 3.9 6.8 - - - +
17A LYS* 5.3 2.4 + - - +
98A GLN* 4.8 10.7 + - - +
101A ARG* 4.9 1.1 - - - -
105A LEU* 3.5 19.0 - - + +
109A ARG* 4.1 8.5 + - - -
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Residues in contact with ARG 14 (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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10A GLN* 3.1 23.3 + - - +
11A LEU* 3.0 10.6 + - - +
13A GLU* 1.3 107.2 + - + +
15A THR* 1.3 63.2 + - - +
16A PRO* 3.4 2.0 - - - -
17A LYS* 3.5 6.9 + - - +
18A THR* 2.8 34.9 + - - +
21B VAL* 3.8 14.8 + - + +
22B PHE* 3.3 26.8 + - + +
24B GLU 3.0 27.9 + - - -
25B GLY* 3.8 15.0 + - - -
26B LEU* 3.5 16.9 - - - +
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Residues in contact with THR 15 (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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11A LEU* 3.2 13.7 + - - +
12A LEU 3.8 0.2 + - - -
14A ARG* 1.3 76.9 - - - +
16A PRO* 1.4 70.1 - - - +
18A THR* 3.4 6.4 + - - -
19A LEU* 3.0 32.1 + - + +
49A LEU* 5.0 2.0 - - + -
97A PHE* 3.9 16.4 - - + -
101A ARG* 3.9 3.4 - - - -
143A ASP* 2.7 41.8 + - + +
147A ILE* 4.1 24.2 - - + +
22B PHE* 5.3 4.3 - - - -
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Residues in contact with PRO 16 (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 3.8 11.0 - - - +
13A GLU 3.9 7.0 - - - +
14A ARG 3.5 3.8 - - - -
15A THR* 1.4 92.9 - - - +
17A LYS* 1.3 56.3 + - - +
19A LEU* 3.2 3.2 + - + +
20A GLU* 3.0 30.5 + - - +
94A PHE* 5.1 4.1 - - - +
97A PHE* 3.7 27.7 - - + -
98A GLN* 3.7 35.7 - - + +
101A ARG* 3.7 28.7 - - + -
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Residues in contact with LYS 17 (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 5.4 1.8 - - - +
14A ARG* 3.5 9.1 + - - +
15A THR 3.4 0.4 - - - -
16A PRO* 1.3 78.9 - - - +
18A THR* 1.3 56.0 + - - +
20A GLU* 3.5 27.0 + - - +
21A VAL* 2.9 46.5 + - - +
98A GLN* 4.2 13.5 + - - +
21B VAL* 3.8 23.0 - - + +
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Residues in contact with THR 18 (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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14A ARG 2.8 22.3 + - - -
15A THR* 3.6 5.8 - - - -
17A LYS* 1.3 77.1 - - - +
19A LEU* 1.3 65.3 + - + +
21A VAL* 3.7 4.4 - - - +
22A PHE* 3.1 27.0 + - + +
147A ILE* 5.5 9.0 - - + -
18B THR* 4.0 18.2 - - + +
21B VAL* 3.8 11.0 - - - +
22B PHE* 3.5 55.3 - - + -
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Residues in contact with LEU 19 (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* 3.0 23.8 + - + +
16A PRO* 3.9 3.6 - - + +
18A THR* 1.3 79.4 - - + +
20A GLU* 1.3 56.7 + - - +
22A PHE* 3.4 11.6 + - + -
23A LEU* 2.9 42.4 + - + +
46A VAL* 4.4 9.6 - - + -
49A LEU* 3.6 31.0 - - + -
94A PHE* 4.2 13.0 - - + -
97A PHE* 4.2 15.3 - - + -
147A ILE* 4.0 25.8 - - + -
150A ILE* 3.9 27.8 - - + -
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Residues in contact with GLU 20 (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 3.0 17.2 + - - +
17A LYS* 3.8 28.3 + - - +
19A LEU* 1.3 77.9 - - - +
21A VAL* 1.3 57.8 + - - +
24A GLU* 2.9 56.5 + - + +
94A PHE* 3.8 41.3 - - + +
98A GLN* 5.9 2.8 - - - +
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Residues in contact with VAL 21 (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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17A LYS* 2.9 35.1 + - - +
18A THR* 3.7 9.2 - - - +
20A GLU* 1.3 75.2 - - - +
22A PHE* 1.3 65.1 + - - +
24A GLU* 4.6 0.9 + - - +
14B ARG* 3.8 21.5 + - - +
17B LYS* 4.1 34.9 + - + +
18B THR* 3.5 33.1 + - - +
21B VAL* 4.3 13.7 - - + -
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Residues in contact with PHE 22 (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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18A THR* 3.1 18.7 + - + +
19A LEU* 3.7 11.7 - - + +
21A VAL* 1.3 79.3 - - - +
23A LEU* 1.3 71.1 + - + +
26A LEU* 3.4 11.1 - - - +
147A ILE* 6.2 1.6 - - + -
150A ILE* 4.3 6.7 - - + -
151A VAL* 4.0 19.3 - - + -
154A MSE 3.8 23.1 - - + -
11B LEU* 3.7 19.4 - - + +
14B ARG* 3.3 24.6 - - + +
15B THR* 5.3 4.0 - - - -
18B THR* 3.4 30.3 - - + +
144B LEU* 3.8 24.2 - - + -
147B ILE* 4.0 22.0 - - + -
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Residues in contact with LEU 23 (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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19A LEU* 2.9 24.3 + - + +
22A PHE* 1.3 98.8 - - + +
24A GLU* 1.3 65.0 + - - +
26A LEU* 3.3 26.3 + - + +
30A TRP 5.9 0.2 - - - +
31A HIS* 2.6 32.8 + - + +
42A VAL* 3.8 28.9 - - + -
46A VAL* 4.1 20.9 - - + -
90A ILE* 4.8 1.1 - - + -
94A PHE* 3.7 15.9 - - + -
150A ILE* 4.2 11.4 - - + -
154A MSE 3.8 15.5 - - - -
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Residues in contact with GLU 24 (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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20A GLU* 2.9 46.4 + - + +
21A VAL* 4.8 1.4 - - - +
23A LEU* 1.3 74.7 - - - +
25A GLY* 1.3 61.7 + - - +
26A LEU 3.2 0.2 - - - -
31A HIS* 5.3 0.7 - - - -
90A ILE* 4.4 3.1 - - - +
91A SER* 3.3 38.7 + - - +
94A PHE* 3.7 16.1 - - + +
14B ARG* 3.0 25.5 + - - -
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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