Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 1E8O
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 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLN* 3.1 40.7 + - + +
56A ALA* 1.3 77.2 - - - +
58A ASP* 1.3 68.5 + - - +
60A LYS* 4.6 5.1 + - - +
61A LYS* 3.6 28.7 + - - +
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 5.0 0.5 - - - +
38A LEU* 5.2 1.6 - - + -
51A TYR* 2.9 33.6 + - + -
53A THR* 2.9 30.0 + - + +
55A GLN* 3.0 13.2 + - - +
56A ALA 2.7 3.4 + - - -
57A GLN* 1.3 87.9 + - - +
59A VAL* 1.3 64.9 + - - +
60A LYS 3.0 3.1 - - - -
61A LYS* 2.8 44.9 + - + +
62A ILE* 2.9 20.7 + - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.2 11.6 - - + +
56A ALA* 3.1 19.5 + - + +
58A ASP* 1.3 73.8 - - - +
60A LYS* 1.3 56.8 + - - +
62A ILE* 3.4 2.0 + - - +
63A GLU* 2.9 28.0 + - + +
87B LEU 4.3 8.7 - - - +
88B ARG* 4.6 13.7 - - + +
91B MET* 3.6 51.3 - - + +
94B LEU* 3.8 24.7 - - + -
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Residues in contact with LYS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 4.5 1.8 + - - -
57A GLN 4.9 6.1 - - - +
58A ASP 3.0 0.8 - - - -
59A VAL* 1.3 74.8 - - - +
61A LYS* 1.3 69.1 + - + +
62A ILE 3.0 1.6 - - - -
63A GLU* 3.5 8.2 - - + +
64A LYS* 2.9 48.2 + - + +
88B ARG* 2.9 44.2 - - + +
111E G 2.9 27.1 + - - -
112E U 2.8 31.0 + - - -
113E G 5.7 0.7 - - - -
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.5 54.6 + - + +
57A GLN* 3.6 28.3 - - - +
58A ASP* 2.8 30.2 + - + +
60A LYS* 1.3 77.5 - - + +
62A ILE* 1.3 58.3 + - + +
64A LYS* 3.4 10.6 - - - +
65A PHE* 3.2 18.9 + - - +
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Residues in contact with ILE 62 (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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7A TRP* 3.8 29.2 - - + -
29A LEU* 3.5 27.8 - - + -
38A LEU* 3.2 36.1 - - + -
40A VAL* 3.4 26.7 - - + -
51A TYR* 5.0 5.8 - - + -
53A THR* 6.0 0.9 - - - +
58A ASP* 2.9 20.7 + - + +
59A VAL* 3.7 6.3 - - + +
61A LYS* 1.3 74.1 - - - +
63A GLU* 1.3 67.4 + - - +
64A LYS 2.7 6.3 + - - -
65A PHE* 2.7 13.9 + - + +
66A HIS* 2.9 19.6 + - + +
87B LEU* 5.5 0.4 - - + -
91B MET* 5.8 2.0 - - + -
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Residues in contact with GLU 63 (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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59A VAL 2.9 17.5 + - - +
60A LYS* 3.5 18.3 - - - +
62A ILE* 1.3 72.7 - - - +
64A LYS* 1.3 72.6 + - + +
66A HIS* 3.6 3.8 - - - +
67A SER* 2.7 39.3 + - - -
83B TYR* 5.3 1.9 - - - -
84B SER* 2.8 39.1 + - - +
87B LEU* 4.3 34.5 - - + +
88B ARG* 4.3 19.5 + - + +
91B MET* 5.9 0.4 - - + +
113E G 3.7 16.6 + - - -
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Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LYS* 2.9 42.5 + - + +
61A LYS* 3.4 10.5 - - - +
62A ILE 2.7 1.0 + - - -
63A GLU* 1.3 85.6 - - + +
65A PHE* 1.3 54.3 + - - +
67A SER* 2.8 8.5 + - - -
68A GLN* 2.6 47.4 + - - +
111E G 5.6 3.0 + - - -
112E U 4.5 17.8 + - - +
113E G 2.9 34.9 - - - +
114E G 4.2 19.5 - - - -
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 3.4 37.9 - + + -
10A PHE* 5.1 2.2 - + - -
11A SER* 3.9 29.2 - - - -
14A ALA* 3.5 24.2 - - + -
15A GLU* 4.5 9.6 - - + -
27A VAL* 4.4 6.5 - - + -
40A VAL* 4.9 6.7 - - + -
42A VAL* 4.4 13.7 - - + -
61A LYS 3.2 1.4 + - - -
62A ILE* 2.7 12.9 + - + +
64A LYS* 1.3 73.9 - - - +
66A HIS* 1.3 61.4 + - - +
68A GLN* 2.9 24.3 + - - +
69A LEU* 2.7 67.0 + - + +
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A VAL* 4.5 26.5 - - + +
29A LEU* 3.4 38.7 - - + +
40A VAL* 5.3 2.2 - - + -
62A ILE* 2.9 15.5 + - + +
63A GLU* 3.6 10.1 - - - +
65A PHE* 1.3 82.6 - - - +
67A SER* 1.3 54.8 + - - +
68A GLN 2.9 0.5 + - - -
69A LEU* 3.0 6.8 + - - +
70A MET* 2.6 39.1 + - + +
28B ILE* 4.6 11.6 + - + +
30B LEU* 4.2 17.4 - - + +
58B LEU* 5.5 1.8 - - + -
83B TYR* 2.8 41.4 + + + -
87B LEU* 4.1 5.2 - - + -
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 2.7 24.3 + - - -
64A LYS 2.8 12.7 + - - -
66A HIS* 1.3 75.7 - - - +
68A GLN* 1.3 60.6 + - - +
70A MET* 3.7 10.7 + - - +
71A ARG* 3.5 12.1 + - - +
80B GLN* 3.1 29.1 + - - +
83B TYR* 5.1 6.3 - - - -
113E G 3.4 38.0 - - - +
136E A 4.9 2.3 - - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 5.1 4.9 + - - -
64A LYS* 2.6 27.3 + - - +
65A PHE* 3.1 34.7 - - + +
67A SER* 1.3 70.5 - - - +
69A LEU* 1.3 68.1 + - + +
70A MET 3.1 0.9 - - - -
71A ARG* 2.8 20.5 + - - +
72A LEU* 3.4 10.1 + - - +
113E G 3.9 25.1 - - - +
114E G 4.0 13.5 + - - -
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Residues in contact with LEU 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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14A ALA 6.1 0.4 - - - +
15A GLU* 5.3 6.5 - - + -
18A TYR* 3.8 39.5 - - + -
27A VAL* 4.4 20.6 - - + -
42A VAL* 5.3 4.0 - - + -
65A PHE* 2.7 57.9 + - + +
66A HIS* 3.7 3.6 - - - +
68A GLN* 1.3 73.4 - - + +
70A MET* 1.3 61.1 + - - +
71A ARG 3.0 1.0 + - - -
72A LEU* 3.3 19.4 + - + +
73A MET* 2.9 31.9 + - + +
30B LEU* 4.0 12.6 - - + -
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Residues in contact with MET 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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66A HIS* 2.6 22.0 + - + +
67A SER* 3.9 10.8 - - - +
69A LEU* 1.3 71.8 - - - +
71A ARG* 1.3 58.7 + - - +
73A MET* 4.0 9.7 + - - +
74A VAL* 3.0 24.3 + - + +
30B LEU* 4.2 10.5 - - + +
56B CYS* 3.9 16.8 - - - -
58B LEU* 3.5 39.9 - - + -
71B VAL* 4.5 9.2 - - + -
76B VAL* 4.5 14.8 - - + -
79B PHE* 3.6 26.7 - - + -
80B GLN* 5.3 8.5 - - - -
83B TYR* 4.6 14.8 - - + -
136E A 5.3 0.4 - - - +
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Residues in contact with ARG 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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67A SER 3.5 9.9 + - - +
68A GLN 2.8 11.6 + - - +
70A MET* 1.3 78.3 - - - +
72A LEU* 1.3 72.3 + - + +
74A VAL* 3.0 18.1 + - - +
75A ALA* 3.2 16.2 + - + +
113E G 3.3 33.5 + - - +
114E G 3.4 45.0 + - - -
136E A 3.7 21.8 - - + +
137E C 4.4 6.1 + - - -
138E U 4.0 23.2 + - - -
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Residues in contact with LEU 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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15A GLU* 5.5 10.3 - - + +
18A TYR* 3.7 36.6 - - + -
19A LEU* 4.4 14.4 - - + -
68A GLN 4.0 10.5 - - - +
69A LEU* 3.3 18.3 + - + +
71A ARG* 1.3 82.7 - - + +
73A MET* 1.3 61.4 + - - +
74A VAL 2.8 6.8 + - - -
75A ALA* 3.1 21.7 + - + +
32B LYS* 5.4 2.6 + - - +
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Residues in contact with MET 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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18A TYR* 3.8 30.1 - - + +
25A ALA 5.3 2.0 - - - +
27A VAL* 6.0 0.4 - - + -
69A LEU* 2.9 21.0 + - + +
70A MET 4.1 2.9 - - - +
72A LEU* 1.3 75.2 - - - +
74A VAL* 1.3 57.9 + - - +
75A ALA 3.7 0.7 - - - -
30B LEU* 3.3 40.4 - - + +
31B LYS* 3.3 13.7 - - - +
32B LYS* 3.2 50.1 - - + +
54B ASN* 4.1 5.2 - - - +
55B LYS 3.2 21.4 + - - +
56B CYS* 3.3 22.2 - - + -
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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
------------------------------------------------------------
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