Contacts of the helix formed by residues 55 - 71 (chain C) in PDB entry 4IME
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 SER 55 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 1.3 73.1 - - - +
56C THR* 1.3 64.4 + - - +
57C GLU* 3.5 8.2 + - - +
58C GLU* 2.8 42.4 + - - +
59C LYS* 2.9 26.3 + - - +
87C GLU* 4.5 0.2 - - - -
269C ARG* 5.5 0.2 - - - -
84D ASN* 3.4 10.7 + - - -
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Residues in contact with THR 56 (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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55C SER* 1.3 71.5 - - - +
57C GLU* 1.3 60.5 + - - +
59C LYS* 3.1 6.8 + - - +
60C LYS* 2.9 33.2 + - - +
87C GLU* 2.5 36.3 + - + +
90C GLU* 3.9 28.9 - - - +
91C LEU* 4.0 18.6 - - + -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 3.2 7.6 + - - +
56C THR* 1.3 80.7 - - - +
58C GLU* 1.3 63.6 + - + +
60C LYS* 3.4 32.3 + - - +
61C GLU* 3.0 23.4 + - - +
64C ARG* 5.1 6.8 + - - -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY 4.4 2.8 - - - +
20C SER* 5.0 4.5 - - - -
21C ILE* 3.6 30.9 - - + +
54C LEU* 3.5 14.3 - - + -
55C SER* 2.8 46.0 + - - +
57C GLU* 1.3 76.5 - - + +
59C LYS* 1.4 65.2 + - - +
61C GLU* 3.2 5.0 + - - +
62C ILE* 3.1 21.5 + - - +
269C ARG* 3.1 38.0 + - - -
86D GLN* 4.3 5.5 - - - +
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Residues in contact with LYS 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ASN* 3.3 51.9 + - - +
52C PHE* 5.1 5.6 + - - +
54C LEU* 3.5 26.4 + - + -
55C SER 2.9 13.6 + - - +
56C THR* 3.6 4.7 - - - +
58C GLU* 1.4 75.3 - - - +
60C LYS* 1.3 63.7 + - - +
62C ILE* 3.2 11.1 + - - +
63C PHE* 3.1 33.5 + - + -
81C GLY 5.0 1.2 + - - -
82C SER* 4.7 7.1 + - - -
87C GLU* 3.2 33.6 + - - +
91C LEU* 3.7 29.3 - - + +
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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 THR* 2.9 23.0 + - + +
57C GLU* 3.6 33.4 + - - +
59C LYS* 1.3 77.0 - - - +
61C GLU* 1.3 58.2 + - - +
63C PHE* 3.1 4.5 + - - +
64C ARG* 2.9 29.0 + - - +
90C GLU* 2.7 40.8 + - - +
91C LEU* 3.8 11.4 - - + +
94C TYR* 3.4 58.6 - - + +
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Residues in contact with GLU 61 (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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21C ILE* 3.5 29.9 + - + +
23C GLU* 4.4 10.9 - - - +
57C GLU 3.0 17.8 + - - +
58C GLU* 3.2 7.7 + - - +
60C LYS* 1.3 75.6 - - - +
62C ILE* 1.3 59.0 + - - +
64C ARG* 3.2 31.5 + - - +
65C ILE* 2.8 51.7 + - + +
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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
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11C LEU* 4.8 3.8 - - + -
13C VAL* 3.9 36.1 - - + -
21C ILE* 3.7 19.5 - - + -
26C LEU* 4.2 18.9 - - + +
44C VAL* 3.7 21.1 - - + -
45C GLY* 5.0 7.2 - - - +
49C GLY 5.0 0.4 - - - +
54C LEU* 3.4 33.0 - - + -
58C GLU 3.1 13.9 + - - +
59C LYS* 3.7 7.9 - - - +
61C GLU* 1.3 75.0 - - - +
63C PHE* 1.3 64.9 - - + +
65C ILE* 3.9 0.9 - - - +
66C ALA* 3.0 23.7 + - - +
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Residues in contact with PHE 63 (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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44C VAL* 3.5 37.9 - - + -
45C GLY* 4.4 4.7 - - - -
51C ASN* 5.6 0.9 - - - -
59C LYS* 3.1 31.5 + - + -
60C LYS* 3.5 9.9 - - - +
62C ILE* 1.3 78.8 - - + +
64C ARG* 1.3 62.1 + - - +
67C LYS* 3.1 14.7 + - - +
78C ALA* 3.6 19.5 - - + -
79C GLN 3.2 23.6 - - - -
80C VAL* 4.0 13.5 - - + -
91C LEU* 4.4 20.0 - - + -
94C TYR* 4.5 7.0 - + + -
95C ALA* 4.6 8.1 - - + -
98C LEU* 3.7 15.2 - - + +
100C TYR* 2.7 33.5 + + + +
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 5.1 6.5 + - - -
60C LYS* 2.9 20.0 + - - +
61C GLU* 3.5 46.3 - - - +
63C PHE* 1.3 78.1 - - - +
65C ILE* 1.3 60.8 + - + +
67C LYS* 3.9 1.2 - - - +
68C ASP* 2.9 33.1 + - + +
94C TYR* 2.8 37.5 + - - +
98C LEU* 3.8 20.3 - - + +
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Residues in contact with ILE 65 (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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21C ILE* 4.2 6.5 - - + -
23C GLU* 3.8 30.5 - - + +
26C LEU* 3.9 32.1 - - + -
27C ARG* 3.6 37.2 + - + +
30C VAL* 5.8 0.4 - - + -
61C GLU* 2.8 52.0 + - + +
62C ILE 4.0 0.2 - - - +
64C ARG* 1.3 75.3 - - + +
66C ALA* 1.3 64.4 + - - +
68C ASP* 3.2 5.1 + - - +
69C GLU* 2.9 23.0 + - + +
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.1 25.4 - - + -
26C LEU* 4.9 1.7 - - + +
30C VAL* 4.3 14.9 - - + +
42C LEU* 5.4 1.3 - - + -
44C VAL* 4.1 11.7 - - + -
62C ILE 3.0 17.9 + - - +
65C ILE* 1.3 76.4 - - - +
67C LYS* 1.3 57.8 + - - +
69C GLU* 3.9 1.0 - - - +
70C ALA* 2.9 33.1 + - - +
76C LEU* 4.8 4.5 - - + -
100C TYR* 3.5 13.7 - - - +
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Residues in contact with LYS 67 (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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63C PHE 3.1 19.0 + - - +
64C ARG* 4.0 2.5 - - - +
66C ALA* 1.3 74.2 - - - +
68C ASP* 1.3 61.0 + - - +
71C LYS* 2.8 43.3 + - - +
72C ASP* 2.9 29.2 + - - -
74C ILE 5.8 0.4 + - - -
76C LEU* 3.4 24.0 - - + +
98C LEU* 3.4 37.2 - - + +
99C GLY* 3.9 16.7 + - - +
100C TYR* 3.7 14.1 + - + -
101C ASP* 5.6 3.6 + - - -
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Residues in contact with ASP 68 (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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27C ARG* 2.8 36.2 + - - +
64C ARG* 2.9 20.7 + - + +
65C ILE 3.2 3.6 + - - +
67C LYS* 1.3 77.5 - - - +
69C GLU* 1.3 61.6 + - - +
71C LYS* 2.9 43.9 + - - +
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Residues in contact with GLU 69 (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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27C ARG* 2.9 61.0 + - + +
30C VAL* 3.8 22.9 - - + -
31C ARG* 3.0 56.4 + - + +
65C ILE 2.9 16.4 + - - +
66C ALA 4.0 2.2 - - - +
68C ASP* 1.3 80.9 - - - +
70C ALA* 1.3 60.9 + - - +
71C LYS* 3.7 4.7 + - - +
73C GLU* 3.7 1.9 - - - +
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Residues in contact with ALA 70 (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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30C VAL* 4.2 5.6 - - + -
34C ILE* 3.9 22.0 - - + -
42C LEU* 5.1 0.2 - - + -
66C ALA 2.9 18.0 + - - +
69C GLU* 1.3 75.4 - - - +
71C LYS* 1.3 69.0 + - - +
72C ASP 3.2 0.2 + - - -
73C GLU* 3.1 33.7 + - - +
74C ILE* 4.1 15.0 - - + -
76C LEU* 4.3 19.1 - - + -
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Residues in contact with LYS 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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67C LYS* 2.8 41.9 + - - +
68C ASP* 2.9 44.4 + - - +
69C GLU 4.3 4.3 - - - +
70C ALA* 1.3 79.6 - - - +
72C ASP* 1.3 66.0 + - - +
73C GLU* 3.9 2.9 + - + +
74C ILE 4.5 2.6 - - - +
76C LEU* 4.2 6.2 - - - +
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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