Contacts of the helix formed by residues 9 - 23 (chain A) in PDB entry 1RJG
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 ASP 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A THR* 1.3 78.7 + - - +
10A TYR* 1.3 74.9 + - + +
11A ASP 3.2 0.4 - - - -
12A ALA* 3.2 11.8 + - - +
13A LEU* 3.3 12.0 + - - +
107A GLY* 3.3 20.2 - - - -
108A SER* 3.2 25.6 + - - -
132A SER* 5.6 4.4 - - - +
335A SAH 3.3 42.8 - - - +
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Residues in contact with TYR 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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8A THR 3.1 8.5 - - - +
9A ASP* 1.3 91.8 - - + +
11A ASP* 1.3 55.7 + - - +
12A ALA 3.2 0.2 - - - -
13A LEU* 4.1 7.0 - - + +
14A SER* 2.5 40.4 + - - +
52A LEU* 5.8 3.6 - - + -
59A ALA* 3.2 42.9 - - + +
62A LYS* 3.6 40.6 - - + -
63A VAL* 4.0 16.6 - - + +
108A SER* 6.5 0.2 - - - -
135A LEU* 4.1 17.5 - - + +
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Residues in contact with ASP 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A THR* 3.4 36.8 + - - +
9A ASP 3.2 0.8 - - - -
10A TYR* 1.3 78.6 - - - +
12A ALA* 1.3 59.4 + - - +
13A LEU 3.4 0.2 - - - -
14A SER* 4.3 4.1 - - - -
15A CYS* 3.3 32.8 + - - +
66A ALA* 5.5 6.6 - - - +
81A ARG* 5.3 2.1 + - - +
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Residues in contact with ALA 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 THR 3.7 2.9 + - - +
9A ASP* 3.2 11.3 + - - +
10A TYR 3.2 0.4 - - - -
11A ASP* 1.3 80.2 - - - +
13A LEU* 1.3 59.6 + - - +
15A CYS* 4.0 3.8 - - - +
16A LYS* 3.4 30.5 + - - +
81A ARG* 4.1 14.8 - - - +
108A SER* 6.0 0.4 - - - -
335A SAH 3.3 47.8 - - + +
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Residues in contact with LEU 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 ASP 3.3 11.5 + - - +
10A TYR* 3.5 9.8 + - + +
12A ALA* 1.3 77.0 - - - +
14A SER* 1.3 65.5 + - - +
16A LYS* 3.5 6.4 + - + +
17A LEU* 3.2 44.7 + - + +
45A HIS* 4.7 16.6 - - + +
48A TYR* 4.0 24.5 - - + -
49A LEU* 5.6 2.0 - - + +
52A LEU* 4.6 10.5 - - + -
63A VAL* 4.1 20.0 - - + -
108A SER* 3.6 38.8 - - - +
110A LEU* 5.8 0.2 - - + -
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Residues in contact with SER 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 TYR 2.5 24.4 + - - -
11A ASP* 4.3 5.6 - - - -
13A LEU* 1.3 74.8 - - - +
15A CYS* 1.3 65.7 + - - +
17A LEU* 3.5 0.7 + - - -
18A ALA* 3.1 23.9 + - - +
62A LYS 4.1 1.0 + - - -
63A VAL* 3.3 35.5 - - - +
66A ALA* 3.7 27.1 - - - +
67A MET* 3.6 10.5 - - - +
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Residues in contact with CYS 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 ASP* 3.3 24.8 + - - +
12A ALA* 4.0 5.2 - - - +
14A SER* 1.3 81.3 - - - +
16A LYS* 1.3 57.5 + - - +
18A ALA* 3.3 6.9 + - - +
19A ALA* 3.1 22.9 + - - +
70A SER* 5.3 5.6 - - - -
74A MET* 4.7 16.2 - - - -
75A ASN* 4.5 1.1 - - - +
78A THR* 3.2 36.1 + - + +
81A ARG* 5.6 8.3 - - - +
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Residues in contact with LYS 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 ALA 3.4 20.9 + - - +
13A LEU* 3.5 9.2 + - + +
14A SER 3.3 0.4 - - - -
15A CYS* 1.3 79.5 - - - +
17A LEU* 1.3 59.0 + - - +
19A ALA* 3.8 2.8 + - - +
20A ILE* 3.2 34.8 + - + +
25A LEU* 4.4 4.4 - - + +
41A TYR* 4.3 13.5 - - - +
45A HIS* 4.0 28.1 + - + +
78A THR* 4.0 10.5 - - + +
81A ARG* 6.5 1.8 - - - +
82A THR* 3.6 30.1 - - - +
108A SER 5.0 3.8 + - - -
109A ASP* 4.3 22.0 + - - +
111A ARG* 5.9 2.7 - - - +
201A GLU* 5.5 7.4 - - - -
335A SAH 4.1 17.2 + - - -
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Residues in contact with LEU 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 LEU* 3.2 35.5 + - + +
14A SER 3.5 3.3 + - - +
15A CYS 3.3 0.2 - - - -
16A LYS* 1.3 74.6 - - + +
18A ALA* 1.3 59.6 + - - +
19A ALA 3.3 0.9 - - - -
20A ILE* 3.9 4.0 - - + +
21A SER* 3.2 26.9 + - - -
45A HIS* 3.4 41.3 - - + +
46A ARG* 4.3 17.6 + - + +
49A LEU* 4.0 26.9 - - + -
63A VAL* 3.6 25.4 - - + -
67A MET* 3.5 19.2 - - + +
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Residues in contact with ALA 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 SER 3.1 17.1 + - - +
15A CYS 3.3 4.5 + - - +
17A LEU* 1.3 76.2 - - - +
19A ALA* 1.3 62.4 + - - +
21A SER* 4.0 3.7 - - - -
22A VAL* 3.5 27.7 + - - +
67A MET* 3.2 30.7 - - - +
70A SER* 3.7 9.9 - - - +
75A ASN* 3.3 20.9 - - - +
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Residues in contact with ALA 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 CYS 3.1 16.0 + - - +
16A LYS 4.0 4.5 - - - +
17A LEU 3.3 0.2 - - - -
18A ALA* 1.3 77.7 - - - +
20A ILE* 1.3 63.2 + - - +
22A VAL 3.8 0.2 + - - -
23A GLY 3.2 3.3 + - - -
24A TYR* 3.0 49.4 + - + +
25A LEU* 3.3 17.1 + - + -
75A ASN* 4.0 6.7 + - - +
78A THR* 4.1 19.3 - - + -
79A TYR 5.2 0.4 - - - +
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Residues in contact with ILE 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 LYS* 3.2 22.2 + - + +
17A LEU* 3.7 4.0 + - + +
18A ALA 3.4 0.2 - - - -
19A ALA* 1.3 77.1 - - - +
21A SER* 1.3 63.7 + - - +
23A GLY* 3.6 8.1 + - - -
25A LEU* 3.4 21.8 - - + +
41A TYR* 3.6 24.7 - - + +
42A THR* 3.6 30.9 - - + +
45A HIS* 3.4 43.5 - - + +
46A ARG* 3.4 23.2 + - - +
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Residues in contact with SER 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 LEU 3.2 19.8 + - - -
18A ALA* 4.0 7.0 - - - -
19A ALA 3.3 0.2 - - - -
20A ILE* 1.3 79.4 - - - +
22A VAL* 1.3 63.1 + - - +
46A ARG* 3.7 24.6 + - - +
67A MET* 5.2 7.0 - - - -
68A ARG* 6.1 0.7 - - - -
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Residues in contact with VAL 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 ALA 3.5 14.6 + - - +
20A ILE 3.4 0.2 - - - -
21A SER* 1.3 80.1 - - - +
23A GLY* 1.3 56.9 + - - +
24A TYR* 3.3 35.7 - - + +
75A ASN* 4.4 5.6 - - - +
305A LEU* 3.7 25.2 - - + +
306A GLN* 3.6 41.3 - - + +
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Residues in contact with GLY 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 ALA 3.2 4.7 + - - -
20A ILE 3.6 7.6 + - - -
21A SER 3.4 2.2 - - - -
22A VAL* 1.3 79.4 - - - +
24A TYR* 1.3 67.6 + - - +
25A LEU 3.2 11.5 + - - +
26A PRO 5.0 1.4 - - - +
301A ARG* 3.4 17.3 + - - -
305A LEU* 3.6 14.5 - - - +
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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