Contacts of the helix formed by residues 58 - 75 (chain C) 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 ASP 58 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LEU* 5.5 0.2 - - - -
51C TYR* 3.1 19.8 + - + +
53C THR* 2.9 41.9 - - + +
55C GLN* 3.8 7.3 + - - +
56C ALA 2.9 1.8 + - - -
57C GLN* 1.3 97.9 + - - +
59C VAL* 1.3 66.9 + - - +
60C LYS 3.5 0.2 - - - -
61C LYS* 3.5 20.3 - - + +
62C ILE* 3.4 25.2 + - + +
94D LEU* 6.0 0.2 - - + -
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Residues in contact with VAL 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 6.1 0.4 - - + -
38C LEU* 4.1 24.7 - - + -
55C GLN 4.8 0.2 + - - -
56C ALA* 3.3 15.4 + - - +
58C ASP* 1.3 75.8 - - - +
60C LYS* 1.3 68.6 + - - +
62C ILE* 2.9 5.6 + - + +
63C GLU* 2.9 28.7 + - + +
87D LEU 5.1 0.9 - - - +
88D ARG* 5.0 16.6 - - + +
91D MET* 4.3 35.0 - - + +
94D LEU* 4.4 17.9 - - + -
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ALA 5.0 0.2 + - - -
57C GLN 4.4 9.1 + - - +
58C ASP 3.5 0.4 - - - -
59C VAL* 1.3 81.0 - - - +
61C LYS* 1.3 64.3 + - - +
63C GLU* 3.2 8.1 + - - +
64C LYS* 3.0 53.9 + - + +
88D ARG* 4.7 21.3 - - + +
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Residues in contact with LYS 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.4 54.0 - - + +
51C TYR* 5.8 0.7 - - + +
57C GLN 4.8 7.2 - - - -
58C ASP* 3.5 31.2 - - + +
60C LYS* 1.3 78.4 - - - +
62C ILE* 1.3 59.5 + - + +
64C LYS* 3.2 17.0 + - - +
65C PHE 2.9 24.6 + - - -
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.8 21.3 - - + -
29C LEU* 3.9 11.4 - - + -
38C LEU* 3.6 38.8 - - + -
39C CYS 5.2 0.7 - - - +
40C VAL* 3.1 34.8 - - + +
51C TYR* 4.0 20.9 - - + +
53C THR* 4.2 9.9 - - - +
58C ASP 3.4 13.9 - - - +
59C VAL 2.9 9.0 + - - +
61C LYS* 1.3 78.1 - - + +
63C GLU* 1.3 63.8 + - + +
65C PHE* 3.4 5.5 + - - +
66C HIS* 3.2 19.6 + - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 5.6 2.0 - - - -
59C VAL* 2.9 19.7 + - + +
60C LYS 3.3 12.1 - - - +
62C ILE* 1.3 79.3 - - - +
64C LYS* 1.3 80.7 + - - +
66C HIS* 3.1 8.8 - - - +
67C SER* 2.9 47.4 + - - -
84D SER* 3.1 29.5 + - - +
87D LEU* 4.3 22.3 - - + +
88D ARG* 3.7 30.2 + - + +
91D MET* 5.8 2.9 - - + -
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Residues in contact with LYS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LYS* 3.0 37.7 + - + +
61C LYS* 3.2 20.8 + - - +
63C GLU* 1.3 89.5 - - + +
65C PHE* 1.3 56.3 + - - +
66C HIS 3.0 4.9 - - - -
67C SER* 3.7 3.5 - - - +
68C GLN* 2.8 34.0 + - - +
71C ARG* 4.9 1.4 + - - -
88D ARG* 4.2 10.1 - - - +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C TRP* 3.7 23.1 - + + -
10C PHE* 4.3 7.4 - + - -
11C SER* 4.3 16.6 - - - -
14C ALA* 3.3 28.7 - - + -
15C GLU* 3.9 29.8 - - + -
27C VAL* 5.4 0.4 - - + -
40C VAL* 4.2 20.6 - - + -
42C VAL* 4.0 13.5 - - + -
61C LYS 2.9 17.1 + - - +
62C ILE 3.6 4.7 - - - +
64C LYS* 1.3 75.8 - - - +
66C HIS* 1.3 59.3 + - - +
68C GLN* 4.0 8.0 - - - +
69C LEU* 3.0 57.9 + - + +
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Residues in contact with HIS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C VAL* 4.9 12.5 - - + +
29C LEU* 4.1 22.3 - - + +
40C VAL* 6.5 0.9 - - + -
62C ILE 3.2 10.2 + - - +
63C GLU* 3.1 12.1 + - - +
65C PHE* 1.3 78.8 - - + +
67C SER* 1.3 68.9 + - - +
68C GLN 3.1 2.0 + - - -
69C LEU* 3.2 6.3 + - - +
70C MET* 3.1 21.4 + - + +
28D ILE* 4.4 13.0 - - + +
30D LEU* 3.4 43.8 - - + +
58D LEU* 4.5 0.9 - - + -
83D TYR* 2.7 46.2 + + - -
87D LEU* 3.8 13.5 - - + -
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C GLU* 2.9 38.1 + - - -
64C LYS* 3.3 4.2 + - - -
66C HIS* 1.3 81.3 - - - +
68C GLN* 1.3 63.8 + - - +
70C MET* 3.2 8.7 - - - +
71C ARG* 3.3 20.8 + - - -
80D GLN* 3.0 33.7 + - - +
83D TYR* 5.2 5.5 - - - -
84D SER* 4.3 5.7 + - - -
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Residues in contact with GLN 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 3.3 25.4 + - - +
64C LYS 2.8 18.3 + - - +
65C PHE* 4.1 9.7 - - - +
67C SER* 1.3 72.0 - - - +
69C LEU* 1.3 59.0 + - + +
70C MET 2.9 2.0 - - - -
71C ARG* 2.5 58.2 + - + +
72C LEU* 3.2 23.9 + - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA* 5.5 0.7 - - + +
15C GLU* 4.3 16.6 - - + +
18C TYR* 4.4 26.5 - - + -
27C VAL* 4.3 22.9 - - + -
42C VAL* 4.3 7.2 - - + -
65C PHE* 3.0 61.9 + - + +
66C HIS* 3.2 6.2 + - - +
68C GLN* 1.3 78.7 - - + +
70C MET* 1.3 62.3 + - - +
72C LEU* 3.4 15.7 + - + +
73C MET* 3.1 38.3 + - + +
30D LEU* 4.8 2.7 - - + -
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Residues in contact with MET 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C HIS* 3.1 18.2 + - + +
67C SER* 3.2 11.4 - - - +
68C GLN 2.7 4.6 + - - -
69C LEU* 1.3 74.2 - - - +
71C ARG* 1.3 56.5 + - - +
73C MET* 2.9 22.6 + - - +
74C VAL* 3.0 12.1 + - - +
30D LEU* 3.2 45.2 - - + +
56D CYS* 3.7 24.2 - - - -
58D LEU* 3.9 18.8 - - + -
71D VAL* 4.8 7.4 - - - -
76D VAL* 5.1 6.1 - - + -
79D PHE* 4.8 11.7 - - - -
80D GLN* 3.5 25.4 - - - +
83D TYR* 4.1 11.9 - - + -
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Residues in contact with ARG 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LYS 4.9 1.4 + - - -
67C SER* 3.3 36.1 + - - +
68C GLN* 2.5 51.9 + - + +
70C MET* 1.3 73.1 - - + +
72C LEU* 1.3 60.2 + - + +
74C VAL* 3.7 9.6 - - + +
75C ALA* 2.8 30.1 + - - +
76D VAL* 5.7 6.1 - - + -
77D ASN* 6.1 0.9 - - - -
80D GLN* 3.6 25.6 + - - +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 5.3 11.2 - - + +
18C TYR* 3.0 40.7 + - + -
19C LEU* 4.8 10.8 - - + -
68C GLN* 3.2 23.4 + - + +
69C LEU* 3.8 16.6 - - + +
70C MET 3.2 0.2 - - - -
71C ARG* 1.3 82.6 - - + +
73C MET* 1.3 60.5 + - - +
75C ALA* 3.9 17.2 + - + +
32D LYS* 4.1 5.9 + - - -
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Residues in contact with MET 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TYR* 3.0 36.3 - - + +
25C ALA 5.9 1.6 - - - +
26C ARG* 5.7 2.9 - - - -
27C VAL* 4.1 13.2 - - + +
69C LEU* 3.1 29.6 - - + +
70C MET 2.9 9.5 + - - +
72C LEU* 1.3 81.0 - - - +
74C VAL* 1.3 56.2 + - - +
75C ALA 3.5 0.2 - - - -
30D LEU* 3.9 24.0 - - + +
31D LYS* 3.3 15.3 - - - +
32D LYS* 3.2 52.5 + - + +
54D ASN* 3.6 8.1 - - - +
55D LYS 3.8 11.1 - - - +
56D CYS* 4.0 10.1 - - + -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C MET 3.0 12.3 + - - +
71C ARG* 3.4 7.4 + - - +
73C MET* 1.3 77.8 - - - +
75C ALA* 1.3 67.7 + - - +
54D ASN* 3.6 18.4 - - - +
55D LYS* 4.1 3.6 - - - -
56D CYS* 4.4 6.7 - - - +
71D VAL 3.3 26.5 - - - +
72D SER 3.5 2.2 - - - -
73D SER* 3.4 49.4 - - - +
76D VAL* 3.5 26.0 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG 2.8 17.6 + - - +
72C LEU* 4.1 19.7 - - + +
73C MET 3.5 0.9 - - - +
74C VAL* 1.3 86.3 + - - +
32D LYS* 4.6 2.3 + - - -
54D ASN* 3.6 22.4 + - - -
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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
------------------------------------------------------------
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