Contacts of the helix formed by residues 9 - 26 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU 3.1 20.6 + - - +
7A ARG* 3.8 22.1 + - - +
8A LEU 3.6 10.1 - - - +
9A GLN* 4.4 2.7 - - - +
7B ARG 3.9 0.6 + - - -
8B LEU* 1.3 74.2 - - - +
10B PHE* 1.3 65.2 + - - +
12B HIS* 3.1 45.5 + - + +
13B LEU* 3.3 20.7 + - - +
95B CL 3.4 8.7 - - + +
97B CIT 2.6 34.2 + - - +
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A THR* 3.7 32.1 - - + +
6A LEU* 4.7 2.0 - - + -
8A LEU 2.9 19.1 + - - +
10A PHE* 3.6 31.6 - + - -
13A LEU* 3.4 27.1 - - + -
81A LEU* 4.0 22.0 - - + -
85A LEU* 4.2 8.7 - - + -
8B LEU 3.6 2.2 + - - -
9B GLN* 1.3 71.6 - - - +
11B GLY* 1.3 58.6 + - - +
13B LEU* 3.2 6.0 + - + +
14B ILE* 2.9 48.4 + - + +
85B LEU* 3.7 24.0 - - + -
88B CYS* 4.1 13.7 - - + -
92B LEU* 4.2 7.4 - - + -
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Residues in contact with GLY 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 2.8 43.4 + - - +
9B GLN* 3.3 3.1 - - - -
10B PHE* 1.3 74.2 - - - +
12B HIS* 1.3 60.6 + - - +
14B ILE* 3.3 2.0 - - - +
15B ARG* 3.0 30.5 + - - +
97B CIT 3.4 15.9 - - - -
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Residues in contact with HIS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 6.0 0.4 - - + -
9B GLN* 3.1 24.5 + - + +
10B PHE 3.4 0.8 - - - -
11B GLY* 1.3 75.5 - - - +
13B LEU* 1.3 57.6 + - + +
15B ARG* 4.0 3.5 - - - +
16B ILE* 3.0 36.4 + - - +
41B VAL* 4.4 1.3 - - + -
45B THR* 3.6 18.2 - - + +
50B LEU* 3.6 29.3 - - + +
53B ARG* 4.3 0.9 - - - -
54B LEU* 5.4 1.2 - - + +
95B CL 3.1 25.1 - - + +
97B CIT 2.4 60.4 + - + -
99B EDO 4.3 7.9 - - - -
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Residues in contact with LEU 13 (chain B).
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* 3.5 51.6 - - + -
5B THR* 4.2 2.5 - - + +
8B LEU* 3.3 36.8 - - + -
9B GLN 3.3 7.9 + - - +
10B PHE* 3.2 10.2 + - - +
12B HIS* 1.3 75.8 - - + +
14B ILE* 1.3 66.7 + - - +
16B ILE* 5.2 0.4 - - - -
17B LEU* 3.1 38.4 + - + +
18B PRO* 3.2 5.5 - - - +
54B LEU* 4.0 9.6 - - + -
59B LEU* 3.7 17.5 - - + -
81B LEU* 4.6 6.1 - - + -
85B LEU* 3.9 11.8 - - + +
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.9 16.4 - - + -
10B PHE* 2.9 28.6 + - + +
11B GLY 3.3 12.1 - - - +
13B LEU* 1.3 78.1 - - - +
15B ARG* 1.3 64.4 + - + +
18B PRO* 3.1 24.6 - - - +
85B LEU* 3.9 31.2 - - + +
88B CYS* 4.4 0.9 - - + -
89B ARG* 3.6 43.6 + - + +
92B LEU* 3.9 27.6 - - + -
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.4 24.2 + - - +
6A LEU* 4.4 16.9 - - - +
11B GLY 3.0 18.2 + - - +
12B HIS 4.0 2.9 - - - +
14B ILE* 1.3 84.1 - - + +
16B ILE* 1.3 63.0 + - - +
19B THR* 2.9 28.8 + - - -
39B SER* 3.0 38.8 + - - +
40B GLY* 3.6 17.8 + - - -
41B VAL* 3.7 11.7 - - + +
89B ARG* 4.5 5.4 + - - +
97B CIT 3.0 39.9 + - - +
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Residues in contact with ILE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B HIS 3.0 19.5 + - - +
13B LEU* 4.6 0.7 - - - +
15B ARG* 1.3 81.6 - - - +
17B LEU* 1.3 68.6 + - + +
19B THR* 3.3 3.9 + - - +
20B LEU* 3.1 41.1 + - + +
35B ILE* 4.1 10.8 - - + -
39B SER* 3.6 23.6 - - - +
41B VAL* 3.8 18.4 - - + -
46B PHE* 4.1 21.3 - - + -
50B LEU* 4.0 14.6 - - + -
54B LEU* 3.7 24.7 - - + -
72B LEU* 4.8 3.4 - - + -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.1 17.6 + - + +
16B ILE* 1.3 84.1 - - + +
18B PRO* 1.3 74.2 - - + +
20B LEU* 3.4 3.3 + - + +
21B LEU 3.0 18.2 + - - -
54B LEU* 4.6 8.7 - - + -
59B LEU* 4.1 18.2 - - + -
60B VAL* 4.0 20.0 - - + -
74B LEU* 3.9 19.1 - - + +
78B GLY* 3.6 23.6 - - - +
81B LEU* 4.0 26.5 - - + -
82B ALA* 3.5 20.1 - - + +
85B LEU* 4.2 6.5 - - + -
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Residues in contact with PRO 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU 3.2 15.3 - - - +
14B ILE* 3.1 16.2 - - - +
16B ILE 3.9 0.4 - - - -
17B LEU* 1.3 89.6 - - + +
19B THR* 1.3 62.7 + - - +
21B LEU* 3.4 4.1 + - + +
22B GLU* 3.0 31.3 + - - +
82B ALA* 4.1 8.7 - - + +
85B LEU* 3.9 24.5 - - + +
86B GLU* 3.6 24.7 - - - +
89B ARG* 3.4 21.8 - - - +
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG 2.9 23.0 + - - -
16B ILE 3.3 6.5 + - - +
18B PRO* 1.3 77.5 - - - +
20B LEU* 1.3 62.9 + - - +
22B GLU* 3.4 13.1 + - - +
23B PHE* 3.1 46.5 + - + -
35B ILE* 4.3 13.5 - - + +
38B ALA* 3.9 19.1 + - + +
39B SER* 3.6 18.6 + - - +
89B ARG* 4.5 6.6 + - - +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.1 28.7 + - + +
17B LEU* 3.7 7.0 - - + +
19B THR* 1.3 74.6 - - - +
21B LEU* 1.3 63.6 - - - +
23B PHE* 3.3 8.9 + - + +
24B GLU* 3.0 23.0 + - - +
30B PRO* 4.8 2.7 - - + -
35B ILE* 3.8 40.8 - - + -
60B VAL* 3.8 30.3 - - + -
72B LEU* 3.9 23.3 - - + +
74B LEU* 4.0 23.1 - - + +
96B CL 3.8 11.8 - - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 3.0 17.5 + - - +
18B PRO* 3.7 2.7 - - + +
20B LEU* 1.3 75.3 - - - +
22B GLU* 1.3 62.3 + - - +
24B GLU* 3.2 11.2 + - - +
25B LYS* 3.0 42.1 + - + +
74B LEU* 3.8 19.0 - - + +
79B ARG* 4.3 20.9 - - + +
82B ALA* 3.9 13.0 - - + -
83B GLU* 3.8 35.4 - - - +
86B GLU* 3.9 29.8 - - + +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PRO 3.0 21.4 + - - +
19B THR* 3.8 13.6 + - - +
21B LEU* 1.3 74.8 - - + +
23B PHE* 1.3 62.1 + - - +
25B LYS* 3.6 11.1 + - + +
26B LYS* 3.2 38.3 + - - +
86B GLU* 2.8 25.2 - - - +
89B ARG* 3.0 27.6 + - - -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 3.1 45.5 + - + -
20B LEU* 3.5 10.5 - - + +
22B GLU* 1.3 74.7 - - - +
24B GLU* 1.3 57.7 + - - +
26B LYS* 3.2 20.3 + - - +
27B GLY 3.0 7.1 + - - -
28B TYR* 2.9 70.7 + + + +
30B PRO* 3.6 31.9 - - + -
34B GLU* 4.3 12.1 - - + -
35B ILE* 4.7 2.2 - - - -
38B ALA* 3.9 20.4 - - + -
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Residues in contact with GLU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU 3.0 15.7 + - - +
21B LEU* 3.2 11.4 + - - +
23B PHE* 1.3 75.1 - - - +
25B LYS* 1.3 60.2 + - + +
27B GLY* 3.0 18.6 + - - +
28B TYR 4.6 4.9 - - - +
73B LYS* 5.6 4.9 - - - +
74B LEU* 4.1 23.4 + - - +
79B ARG* 3.0 46.1 + - - +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU* 3.0 41.9 + - + +
22B GLU* 3.9 10.8 - - + +
23B PHE 3.4 0.2 - - - -
24B GLU* 1.3 77.1 - - + +
26B LYS* 1.3 60.5 + - + +
27B GLY 3.6 0.3 + - - -
83B GLU* 2.9 31.5 + - - -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU* 3.2 31.2 + - - +
23B PHE* 3.2 27.4 + - - +
24B GLU 3.2 0.8 - - - -
25B LYS* 1.3 79.2 - - + +
27B GLY* 1.3 58.9 + - - +
28B TYR* 3.4 9.8 + - + +
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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
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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