Contacts of the helix formed by residues 75 - 92 (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 THR 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLY* 2.5 33.5 + - - +
59A LEU 3.2 8.3 + - - -
60A VAL 4.1 19.5 - - - +
61A LYS* 4.6 8.3 - - + +
74A LEU* 1.3 76.7 - - - +
76A GLU* 1.3 60.3 + - - +
77A LYS* 3.9 3.1 + - - -
78A GLY 3.1 12.3 + - - -
79A ARG* 2.8 30.1 + - - +
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Residues in contact with GLU 76 (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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75A THR* 1.3 73.4 - - - +
77A LYS* 1.3 56.9 + - - +
79A ARG* 3.5 21.5 + - - +
80A ARG* 2.9 40.5 + - + +
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Residues in contact with LYS 77 (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 ASP* 2.8 31.8 + - - -
5A THR* 3.8 7.6 - - - -
57A ALA 2.7 29.0 + - - -
58A GLY* 4.1 8.7 - - - +
59A LEU* 4.1 8.7 - - + -
75A THR* 4.0 8.0 - - - +
76A GLU* 1.3 76.5 - - - +
78A GLY* 1.3 60.8 + - - +
80A ARG* 3.8 7.7 - - - +
81A LEU* 3.0 28.1 + - - +
91B VAL* 3.9 17.6 - - + +
92B LEU* 3.8 13.9 - - + -
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Residues in contact with GLY 78 (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* 4.1 4.1 - - - +
59A LEU* 3.4 37.2 - - - -
74A LEU* 3.8 10.3 - - - +
75A THR* 3.1 13.0 + - - -
77A LYS* 1.3 76.7 - - - +
79A ARG* 1.3 56.9 + - - +
81A LEU* 3.8 1.8 - - - +
82A ALA* 2.8 29.6 + - - +
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Residues in contact with ARG 79 (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* 3.8 15.5 - - + -
24A GLU* 2.8 41.3 + - - -
73A LYS* 5.9 2.0 - - - +
74A LEU* 3.6 28.9 + - + +
75A THR 2.8 11.0 + - - +
76A GLU* 3.8 31.3 - - - +
78A GLY* 1.3 75.2 - - - +
80A ARG* 1.3 66.1 + - + +
82A ALA* 3.6 6.4 - - - +
83A GLU* 3.2 27.0 + - + +
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Residues in contact with ARG 80 (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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76A GLU* 2.9 30.6 + - + +
77A LYS* 3.8 2.2 - - - +
78A GLY 3.4 0.2 - - - -
79A ARG* 1.3 78.5 - - + +
81A LEU* 1.3 62.4 + - - +
83A GLU* 3.5 6.6 + - - +
84A CYS* 3.3 24.4 + - - -
90B ASP* 3.9 21.2 + - - +
91B VAL* 3.5 42.8 + - + +
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Residues in contact with LEU 81 (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 THR* 4.0 20.0 - - + -
13A LEU* 4.8 2.5 - - + -
17A LEU* 3.9 12.1 - - + -
59A LEU* 3.9 23.3 - - + -
77A LYS* 3.0 18.6 + - + +
78A GLY 3.9 3.1 - - - +
80A ARG* 1.3 74.1 - - - +
82A ALA* 1.3 54.4 + - - +
84A CYS* 3.0 5.5 + - - +
85A LEU* 2.8 48.4 + - + +
10B PHE* 4.0 14.8 - - + -
88B CYS* 3.7 46.0 - - + +
91B VAL* 4.0 8.6 - - + +
92B LEU* 4.9 7.2 - - + -
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Residues in contact with ALA 82 (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* 3.4 40.0 - - + +
18A PRO* 3.9 2.6 - - - +
21A LEU* 3.8 17.7 - - + -
74A LEU* 4.6 1.8 - - + -
78A GLY 2.8 23.0 + - - +
79A ARG* 3.6 9.2 - - - +
80A ARG 3.5 0.2 - - - -
81A LEU* 1.3 71.1 - - - +
83A GLU* 1.3 62.0 + - - +
85A LEU* 3.2 6.0 + - - +
86A GLU* 3.0 25.3 + - - +
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Residues in contact with GLU 83 (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* 3.6 22.6 - - + +
25A LYS* 3.3 25.4 + - - +
79A ARG* 3.2 18.1 + - + +
80A ARG* 3.7 10.1 - - - +
81A LEU 3.2 0.2 - - - -
82A ALA* 1.3 72.9 - - - +
84A CYS* 1.3 67.2 + - - +
86A GLU* 3.2 7.6 + - - +
87A LYS* 2.5 43.4 + - - +
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Residues in contact with CYS 84 (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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80A ARG 3.3 14.6 + - - -
81A LEU* 3.0 7.4 + - - +
83A GLU* 1.3 78.0 - - - +
85A LEU* 1.3 62.7 + - - +
86A GLU 3.2 1.0 + - - -
87A LYS* 3.3 18.5 + - - +
88A CYS* 3.4 13.0 + - - -
84B CYS* 4.6 5.3 - - - +
87B LYS* 3.7 26.9 - - + -
88B CYS* 3.3 25.5 - - - +
91B VAL* 3.7 22.0 - - - -
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Residues in contact with LEU 85 (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* 3.8 30.3 - - + -
13A LEU* 3.8 30.7 - - + +
14A ILE* 3.6 15.2 - - + +
17A LEU* 4.0 16.4 - - + -
18A PRO* 3.9 12.3 - - + +
81A LEU* 2.8 40.5 + - + +
82A ALA 3.2 5.6 + - - +
84A CYS* 1.3 71.4 - - - +
86A GLU* 1.3 61.6 + - - +
87A LYS 3.3 0.2 - - - -
88A CYS* 3.5 12.1 + - - +
89A ARG* 3.2 21.7 + - - +
10B PHE* 4.2 14.4 - - + -
88B CYS* 4.4 4.3 - - - -
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Residues in contact with GLU 86 (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* 3.8 14.6 - - + +
21A LEU* 3.9 18.5 - - + +
22A GLU* 3.0 40.1 - - - +
25A LYS* 4.9 5.7 + - - +
82A ALA 3.0 20.2 + - - +
83A GLU* 3.4 12.8 - - - +
84A CYS 3.2 0.8 - - - -
85A LEU* 1.3 77.2 - - - +
87A LYS* 1.3 73.3 + - + +
89A ARG* 3.4 24.4 + - - +
90A ASP* 3.4 19.7 + - - +
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Residues in contact with LYS 87 (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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83A GLU* 2.5 51.0 + - - +
84A CYS* 3.3 9.2 + - - +
85A LEU 3.3 0.2 - - - -
86A GLU* 1.3 86.9 - - + +
88A CYS* 1.3 65.2 + - - +
89A ARG 3.1 0.2 - - - -
90A ASP* 3.1 28.4 + - - +
91A VAL* 3.2 15.8 + - - +
84B CYS* 3.8 15.9 - - + -
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Residues in contact with CYS 88 (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* 4.2 10.1 - - - -
14A ILE* 3.3 23.8 - - + -
84A CYS 3.4 10.2 + - - -
85A LEU* 3.6 14.6 - - - +
87A LYS* 1.3 79.2 - - - +
89A ARG* 1.3 60.9 + - - +
91A VAL* 3.3 4.0 + - - +
92A LEU* 3.1 25.9 + - - +
81B LEU* 3.9 19.3 - - + -
84B CYS* 3.4 34.9 - - - -
85B LEU* 4.7 4.9 - - - -
88B CYS* 4.7 4.5 - - - -
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Residues in contact with ARG 89 (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 ILE* 3.5 39.4 + - + -
15A ARG 5.5 0.8 + - - -
18A PRO* 3.7 20.1 - - - +
19A THR* 5.0 3.4 + - - +
22A GLU* 3.1 31.5 + - - -
85A LEU 3.2 7.4 + - - +
86A GLU* 3.4 15.8 + - - +
87A LYS 3.1 0.8 - - - -
88A CYS* 1.3 78.9 - - - +
90A ASP* 1.3 63.8 + - - +
92A LEU* 3.3 24.8 - - + +
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Residues in contact with ASP 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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86A GLU 3.4 15.4 - - - +
87A LYS* 3.1 20.9 + - - +
89A ARG* 1.3 76.1 - - - +
91A VAL* 1.3 67.9 + - + +
92A LEU 3.8 4.0 - - - -
80B ARG* 4.3 5.4 + - - -
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Residues in contact with VAL 91 (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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87A LYS 3.2 2.8 + - - +
88A CYS* 3.4 8.5 - - - +
90A ASP* 1.3 81.0 - - + +
92A LEU* 1.3 75.6 + - + +
77B LYS* 4.1 14.1 - - + +
80B ARG* 3.4 67.0 + - + +
81B LEU* 3.9 11.9 - - + +
84B CYS* 3.7 27.6 - - - -
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Residues in contact with LEU 92 (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* 4.0 14.6 - - + -
14A ILE* 4.2 12.3 - - + -
88A CYS 3.1 15.5 + - - +
89A ARG* 3.3 18.6 - - + +
90A ASP 3.8 3.5 - - - +
91A VAL* 1.3 86.4 - - + +
3B ASP* 5.2 4.7 - - - +
5B THR* 4.4 10.8 - - + -
6B LEU* 3.7 30.3 - - + -
77B LYS* 4.8 16.6 - - + -
81B LEU* 3.8 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
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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