Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 1PG0
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 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A GLY 4.3 1.3 + - - +
67A ILE* 1.3 75.0 - - - +
69A PRO* 1.3 65.0 - - - +
70A GLU* 3.1 22.7 + - - +
71A GLN* 2.8 41.6 + - - +
72A MET* 3.0 10.6 + - - +
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Residues in contact with PRO 69 (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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58A ILE* 4.5 7.9 - - + -
59A MET* 4.0 22.9 - - + +
62A ALA* 3.4 25.4 - - + -
63A GLN* 5.5 1.8 - - + +
67A ILE 4.2 0.2 - - - +
68A THR* 1.3 85.6 - - - +
70A GLU* 1.3 71.3 - - - +
72A MET* 4.4 2.7 - - + +
73A ILE* 2.8 38.6 + - + +
238A PHE* 4.0 28.9 - - + -
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Residues in contact with GLU 70 (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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68A THR* 3.1 25.4 - - - +
69A PRO* 1.3 84.1 - - - +
71A GLN* 1.3 61.5 + - - +
73A ILE* 3.5 12.8 - - - +
74A GLY* 3.3 18.2 + - - -
98A HIS* 4.7 9.4 - - + +
238A PHE* 3.0 33.2 - - + -
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Residues in contact with GLN 71 (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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66A GLY 5.0 0.4 + - - -
67A ILE* 3.2 42.4 - - + +
68A THR* 2.8 22.0 + - - +
70A GLU* 1.3 79.5 - - - +
72A MET* 1.3 64.9 + - - +
74A GLY* 3.3 1.6 + - - -
75A GLU* 3.0 50.9 + - + +
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Residues in contact with MET 72 (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 ALA 3.3 24.7 - - - +
17A ASN* 4.5 0.2 - - - -
58A ILE* 3.4 40.4 - - + +
61A LYS* 3.8 38.6 - - + -
62A ALA* 4.2 9.2 - - + -
65A LEU* 4.7 4.9 - - + -
67A ILE* 3.5 26.4 - - + +
68A THR 3.0 9.4 + - - +
69A PRO* 3.8 7.2 - - + +
71A GLN* 1.3 77.8 - - - +
73A ILE* 1.3 62.4 + - + +
75A GLU* 3.2 7.0 + - - +
76A MET* 2.9 36.7 + - + +
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Residues in contact with ILE 73 (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 ALA* 4.1 11.0 - - + -
51A ASP* 4.6 2.1 - - + +
53A ALA* 3.8 39.5 - - + +
58A ILE* 4.0 17.9 - - + -
69A PRO 2.8 25.3 + - - +
70A GLU* 3.5 10.1 - - - +
72A MET* 1.3 74.0 - - + +
74A GLY* 1.3 61.9 + - - +
76A MET* 3.8 7.2 - - - +
77A SER* 2.9 30.3 + - - -
96A SER* 5.0 2.9 - - - +
98A HIS* 3.7 32.5 - - + -
238A PHE* 4.0 10.8 - - + -
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Residues in contact with GLY 74 (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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70A GLU 3.3 10.6 + - - -
71A GLN* 3.3 4.0 + - - -
72A MET 3.1 0.8 - - - -
73A ILE* 1.3 85.2 - - - +
75A GLU* 1.3 60.1 + - - +
77A SER* 3.7 5.4 - - - -
78A GLN* 3.3 24.1 + - - +
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Residues in contact with GLU 75 (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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67A ILE* 4.1 19.6 - - - +
71A GLN* 3.0 36.7 + - + +
72A MET* 3.7 4.4 - - - +
74A GLY* 1.3 76.3 - - - +
76A MET* 1.3 64.9 + - + +
78A GLN* 3.3 7.3 + - - +
79A GLU* 3.0 23.3 + - - +
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Residues in contact with MET 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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16A ALA* 3.3 23.8 - - - +
17A ASN* 4.1 2.0 - - - -
18A GLY* 3.5 42.2 - - - +
19A SER* 4.5 1.6 - - - +
51A ASP* 3.8 8.5 - - - +
61A LYS* 5.2 3.8 - - - -
72A MET* 2.9 28.1 + - + +
73A ILE* 3.9 4.7 - - - +
75A GLU* 1.3 74.2 - - + +
77A SER* 1.3 62.0 + - - +
79A GLU* 3.3 38.5 + - - +
80A HIS* 2.9 40.7 + - + +
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Residues in contact with SER 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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51A ASP* 3.4 20.3 + - - -
73A ILE 2.9 19.9 + - - -
74A GLY* 3.7 7.2 - - - -
75A GLU 3.3 0.2 - - - -
76A MET* 1.3 78.0 - - - +
78A GLN* 1.3 57.4 + - - +
80A HIS* 3.8 0.9 - - - +
81A GLN* 3.0 56.1 + - - +
94A TYR* 4.7 4.5 - - - -
95A HIS 4.9 4.7 + - - -
96A SER* 5.8 3.3 - - - -
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Residues in contact with GLN 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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74A GLY 3.3 11.3 + - - +
75A GLU* 3.7 9.6 - - - +
76A MET 3.2 0.2 - - - -
77A SER* 1.3 78.0 - - - +
79A GLU* 1.3 64.3 + - - +
81A GLN* 3.5 18.8 + - - +
82A THR* 2.9 34.7 + - - +
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Residues in contact with GLU 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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19A SER* 2.7 36.8 + - - -
75A GLU 3.0 16.6 + - - +
76A MET* 3.3 26.9 + - + +
78A GLN* 1.3 77.6 - - - +
80A HIS* 1.3 62.8 + - + +
82A THR* 3.3 7.4 + - - -
83A ASP* 3.2 33.6 + - - +
344A SER* 6.3 1.3 - - - -
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Residues in contact with HIS 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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14A PRO* 4.2 3.9 - - + +
15A TYR 3.3 26.2 - - - -
16A ALA* 4.2 4.7 - - - -
18A GLY 2.6 24.9 + - - -
19A SER* 4.5 0.9 - - - -
20A ILE* 3.5 38.9 - - + +
51A ASP* 2.8 35.8 + - - +
76A MET* 2.9 29.8 + - + +
77A SER 3.8 4.0 - - - +
79A GLU* 1.3 79.8 - - + +
81A GLN* 1.3 58.4 + - - +
83A ASP* 3.2 5.0 + - - +
84A PHE* 3.0 34.8 + - + -
94A TYR* 4.1 7.9 - - + +
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Residues in contact with GLN 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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77A SER* 3.0 39.1 + - - +
78A GLN* 4.0 17.6 + - - +
80A HIS* 1.3 72.3 - - - +
82A THR* 1.3 65.7 + - - +
84A PHE* 4.0 6.8 - - - +
85A ALA* 2.9 26.4 + - - +
91A TYR* 6.0 0.9 - - + -
94A TYR* 3.4 51.8 + - + +
95A HIS 5.3 0.6 + - - -
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Residues in contact with THR 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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78A GLN* 2.9 27.9 + - - +
79A GLU* 3.6 7.8 - - - -
80A HIS 3.2 0.2 - - - -
81A GLN* 1.3 75.8 - - - +
83A ASP* 1.3 62.8 + - - +
85A ALA* 3.5 6.6 + - - +
86A GLY* 3.0 23.2 + - - -
347A LEU* 5.5 0.5 - - - +
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Residues in contact with ASP 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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19A SER* 5.4 0.9 - - - -
20A ILE* 4.1 22.8 + - + +
79A GLU* 3.2 25.1 + - - +
80A HIS 3.6 7.6 - - - +
81A GLN 3.2 0.2 - - - -
82A THR* 1.3 80.6 - - - +
84A PHE* 1.3 67.1 + - - +
86A GLY* 3.0 11.9 + - - +
87A PHE* 3.2 19.7 + - - -
343A ALA* 4.0 17.4 - - + +
344A SER* 3.6 39.0 + - - -
347A LEU* 4.4 5.4 - - - +
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Residues in contact with PHE 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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14A PRO* 4.1 2.7 - - + -
20A ILE* 3.6 43.3 - - + -
24A HIS* 5.1 0.4 - - + -
25A MET* 3.7 17.3 - - + -
28A HIS* 3.4 39.3 - + - -
80A HIS* 3.0 24.8 + - + +
81A GLN* 4.0 4.3 - - - +
83A ASP* 1.3 75.5 - - - +
85A ALA* 1.3 62.5 + - - +
87A PHE* 3.0 11.3 + - - +
89A ILE* 3.1 27.5 + - + +
91A TYR* 2.8 36.6 - + + +
94A TYR* 3.6 35.0 - + - -
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Residues in contact with ALA 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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81A GLN 2.9 19.2 + - - +
82A THR* 3.7 7.4 - - - +
84A PHE* 1.3 76.2 - - - +
86A GLY* 1.3 57.5 + - - +
88A ASN* 3.0 27.0 + - - +
89A ILE 4.8 4.7 - - - +
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Residues in contact with GLY 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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82A THR 3.0 11.2 + - - -
83A ASP 3.0 10.4 + - - -
85A ALA* 1.3 78.7 - - - +
87A PHE* 1.3 57.1 + - - +
88A ASN* 3.2 5.6 + - - -
347A LEU* 3.9 24.3 - - - +
352A ALA* 3.5 13.9 - - - +
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Residues in contact with PHE 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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25A MET* 3.4 35.2 - - + -
29A ILE* 4.1 11.4 - - + -
83A ASP 3.2 18.8 + - - -
84A PHE 3.0 6.4 + - - +
86A GLY* 1.3 75.4 - - - +
88A ASN* 1.3 65.6 + - - +
89A ILE* 3.4 5.3 + - + +
343A ALA* 3.7 23.3 - - + -
346A TRP* 3.4 34.5 - + + -
347A LEU* 3.7 20.0 - - + -
352A ALA* 3.6 24.2 - - + -
355A LEU* 3.6 28.5 - - + -
356A ARG* 2.9 31.2 + - + -
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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