Contacts of the helix formed by residues 9 - 26 (chain A) in PDB entry 2PG4
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 9 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 1.3 75.8 - - - +
10A PHE* 1.3 65.9 + - - +
11A GLY* 3.3 2.5 - - - -
12A HIS* 3.2 59.2 + - + +
13A LEU* 3.3 20.7 + - - +
15A ARG* 5.4 0.3 + - - -
95A CL 3.3 9.5 - - + +
98A EDO 4.6 2.4 + - - -
6B LEU* 3.2 22.8 + - - +
7B ARG* 3.9 26.3 + - - +
8B LEU 3.7 8.7 - - - +
9B GLN* 4.4 2.2 - - - +
10B PHE 4.4 0.2 - - - -
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 3.9 0.8 + - - -
9A GLN* 1.3 72.0 - - - +
11A GLY* 1.3 59.0 + - - +
13A LEU* 3.2 7.5 + - + +
14A ILE* 2.9 56.7 + - + +
85A LEU* 3.8 24.7 - - + -
88A CYS* 4.1 15.7 - - + -
92A LEU* 4.0 11.0 - - + -
5B THR* 3.6 36.8 - - + +
6B LEU* 4.4 4.5 - - + -
8B LEU 2.7 20.6 + - - +
10B PHE* 3.6 31.0 - + - +
13B LEU* 3.5 23.1 - - + -
81B LEU* 4.3 9.9 - - + -
85B LEU* 4.6 3.4 - - + -
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Residues in contact with GLY 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 3.3 4.2 + - - -
10A PHE* 1.3 76.5 - - - +
12A HIS* 1.3 56.0 + - - +
14A ILE* 3.3 10.6 - - - +
15A ARG* 3.0 46.4 + - - +
6B LEU* 2.8 35.7 + - - +
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Residues in contact with HIS 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.9 0.4 - - + -
9A GLN* 3.2 39.8 + - + +
10A PHE 3.5 0.2 - - - -
11A GLY* 1.3 73.7 - - - +
13A LEU* 1.3 58.0 + - + +
16A ILE* 3.1 36.9 + - - +
41A VAL* 4.4 7.2 - - + -
45A THR* 3.7 18.9 - - + +
50A LEU* 3.7 32.4 - - + +
53A ARG* 4.8 3.1 - - - -
54A LEU* 5.9 0.9 - - - -
95A CL 3.2 25.5 - - + +
98A EDO 3.2 39.6 - - - -
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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
----------------------------------------------------------
5A THR* 4.2 2.9 - - + +
8A LEU* 3.8 22.7 - - + -
9A GLN 3.3 10.8 + - - +
10A PHE* 3.2 8.8 + - + +
12A HIS* 1.3 79.4 - - - +
14A ILE* 1.3 61.9 + - - +
17A LEU* 3.1 45.6 + - + +
18A PRO* 3.4 0.7 - - - +
54A LEU* 4.2 7.2 - - + -
59A LEU* 3.7 30.1 - - + -
81A LEU* 4.8 3.8 - - + -
85A LEU* 4.0 11.4 - - + -
10B PHE* 3.4 52.9 - - + -
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Residues in contact with ILE 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 PHE* 2.9 54.2 + - + +
11A GLY* 3.3 20.9 - - - +
13A LEU* 1.3 72.6 - - - +
15A ARG* 1.3 61.5 + - + +
18A PRO* 3.3 24.0 - - - +
85A LEU* 3.6 15.2 - - + +
88A CYS* 3.3 25.6 - - + -
89A ARG* 3.5 34.1 + - + +
92A LEU* 4.2 5.6 - - + -
6B LEU* 4.2 18.2 - - + -
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Residues in contact with ARG 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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9A GLN* 5.4 0.4 + - - -
11A GLY* 3.0 24.7 + - - +
12A HIS 3.9 3.1 - - - +
14A ILE* 1.3 82.0 - - + +
16A ILE* 1.3 60.2 + - - +
17A LEU 3.5 0.2 - - - -
18A PRO* 4.5 0.3 - - - +
19A THR* 2.8 33.2 + - - -
39A SER* 3.3 27.4 + - - +
40A GLY* 4.1 9.9 + - - -
41A VAL* 3.9 12.8 - - + -
89A ARG* 5.5 1.0 + - - -
98A EDO 3.2 34.0 + - - -
6B LEU* 3.7 31.4 - - - +
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Residues in contact with ILE 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 HIS 3.1 15.9 + - - +
15A ARG* 1.3 77.7 - - - +
17A LEU* 1.3 71.8 + - + +
19A THR* 3.3 2.8 + - - -
20A LEU* 3.1 42.0 + - + +
35A ILE* 4.2 13.5 - - + -
39A SER* 4.2 12.3 - - - +
41A VAL* 4.0 16.6 - - + -
46A PHE* 4.3 12.6 - - + -
50A LEU* 3.4 34.3 - - + -
54A LEU* 3.5 28.0 - - + -
72A LEU* 5.0 3.6 - - + -
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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* 3.1 19.7 + - + +
16A ILE* 1.3 88.0 - - + +
18A PRO* 1.4 68.8 - - + +
20A LEU* 3.4 6.9 + - + +
21A LEU 3.1 17.5 + - - -
54A LEU* 4.3 22.7 - - + -
59A LEU* 3.9 19.3 - - + -
60A VAL* 4.6 10.5 - - + -
74A LEU* 4.3 14.0 - - + +
78A GLY 4.1 17.9 - - - +
81A LEU* 3.9 28.5 - - + -
82A ALA* 3.4 15.9 - - + +
85A LEU* 4.0 8.3 - - + -
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Residues in contact with PRO 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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13A LEU 3.4 4.5 - - - +
14A ILE* 3.3 26.2 - - - +
17A LEU* 1.4 91.1 - - + +
19A THR* 1.3 65.2 + - - +
21A LEU* 3.3 4.9 + - + +
22A GLU* 3.0 31.0 + - - +
82A ALA* 3.9 16.1 - - + +
85A LEU* 3.9 21.8 - - + +
86A GLU* 3.9 15.0 - - - +
89A ARG* 3.7 23.8 - - - +
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Residues in contact with THR 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 ARG 2.8 22.7 + - - -
16A ILE 3.3 6.9 + - - +
18A PRO* 1.3 76.8 - - - +
20A LEU* 1.3 64.0 + - - +
22A GLU* 3.2 4.6 + - - -
23A PHE* 3.1 47.5 + - + -
35A ILE* 4.2 11.0 - - + +
38A ALA* 3.7 16.6 + - + -
39A SER* 3.4 20.8 + - - +
89A ARG* 5.0 3.4 + - - +
100A EDO 3.4 15.6 + - - +
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Residues in contact with LEU 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 ILE* 3.1 31.9 + - + +
17A LEU* 3.8 4.9 - - + +
19A THR* 1.3 76.7 - - - +
21A LEU* 1.3 63.2 + - - +
23A PHE* 3.6 6.1 + - + +
24A GLU* 3.1 23.9 + - - +
30A PRO* 4.6 7.0 - - + -
35A ILE* 3.6 42.4 - - + -
60A VAL* 3.5 32.3 - - + -
72A LEU* 4.1 20.6 - - + +
74A LEU* 3.8 23.6 - - + +
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Residues in contact with LEU 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 3.1 16.2 + - - +
18A PRO 3.7 4.5 - - - +
19A THR 3.3 0.2 - - - -
20A LEU* 1.3 77.0 - - - +
22A GLU* 1.3 55.9 + - - +
24A GLU* 3.3 15.0 + - - +
25A LYS* 2.9 50.6 + - + +
74A LEU* 3.7 8.0 - - + +
79A ARG* 3.8 31.6 - - + +
82A ALA* 3.8 8.3 - - + -
83A GLU* 3.6 51.4 - - + +
86A GLU* 3.9 14.6 - - - +
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Residues in contact with GLU 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 PRO 3.0 19.2 + - - +
19A THR* 3.2 5.1 + - - +
21A LEU* 1.3 73.4 - - - +
23A PHE* 1.3 63.8 + - - +
25A LYS* 3.5 13.5 + - - +
26A LYS* 3.2 37.4 + - - +
86A GLU* 3.0 27.4 - - - +
89A ARG* 3.1 30.7 + - - -
100A EDO 3.6 26.5 + - - +
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Residues in contact with PHE 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 THR* 3.1 44.8 + - + -
20A LEU* 3.8 8.1 - - - +
22A GLU* 1.3 75.2 - - - +
24A GLU* 1.3 61.6 + - - +
26A LYS* 3.1 13.7 + - + +
27A GLY 3.1 0.2 + - - -
28A TYR* 3.0 68.1 + + + +
30A PRO* 3.6 33.2 - - + -
34A GLU* 4.2 13.5 - - + -
35A ILE* 4.5 3.6 - - + -
38A ALA* 3.7 21.1 - - + -
100A EDO 3.5 21.9 + - - -
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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 LEU 3.1 13.8 + - - +
21A LEU* 3.5 13.9 - - - +
23A PHE* 1.3 77.3 - - - +
25A LYS* 1.3 65.2 + - - +
27A GLY* 3.1 14.1 + - - +
28A TYR 4.5 5.2 - - - +
73A LYS* 5.1 7.9 - - + +
74A LEU* 3.7 22.8 + - - +
79A ARG* 2.8 47.4 + - - -
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Residues in contact with LYS 25 (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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21A LEU* 2.9 45.5 + - + +
22A GLU* 3.9 11.2 - - - +
23A PHE 3.4 0.2 - - - -
24A GLU* 1.3 73.3 - - + +
26A LYS* 1.3 61.5 + - + +
27A GLY 3.5 0.7 + - - -
83A GLU* 3.3 33.7 + - - +
86A GLU* 4.9 7.9 + - - +
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Residues in contact with LYS 26 (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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22A GLU* 3.2 22.7 + - - +
23A PHE* 3.1 14.0 + - + +
25A LYS* 1.3 78.4 - - + +
27A GLY* 1.3 58.5 + - - +
28A TYR* 4.6 7.3 - - + +
100A EDO 3.3 29.8 + - - +
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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
------------------------------------------------------------
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