Contacts of the helix formed by residues 66 - 80 (chain C) in PDB entry 4U2M
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 ASN 66 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A CYS 5.2 7.4 - - - +
25A ASP* 6.2 0.9 - - - -
36A LYS* 5.5 1.1 - - - +
30C VAL* 3.6 3.9 - - - +
31C ASP* 3.9 8.5 - - - +
65C SER* 1.3 76.7 - - - +
67C ALA* 1.3 59.8 + - - +
68C ALA* 3.7 11.4 - - + +
69C GLY* 3.8 8.6 - - - +
70C LEU* 3.0 29.6 + - - +
91C ASP* 3.8 29.2 - - - +
95C VAL* 4.7 2.0 - - - +
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 4.9 4.5 - - + -
191A ASN* 3.3 11.2 + - - +
30C VAL* 3.4 32.4 - - - +
31C ASP* 3.8 11.3 + - + -
33C VAL* 4.0 18.2 - - + -
35C PHE* 3.7 13.9 - - + -
66C ASN* 1.3 71.6 - - - +
68C ALA* 1.3 58.6 + - - +
71C GLY* 3.0 23.7 + - - -
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Residues in contact with ALA 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN* 3.1 21.2 + - - +
66C ASN* 3.2 10.0 - - + +
67C ALA* 1.3 78.8 - - - +
69C GLY* 1.3 60.1 + - - +
72C GLN* 3.3 28.2 + - - +
87C GLU 5.9 0.2 - - - +
88C ASN* 4.5 16.7 + - + -
91C ASP* 4.3 10.3 - - - +
92C VAL* 4.4 2.4 - - - +
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Residues in contact with GLY 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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66C ASN* 3.2 10.0 + - - +
68C ALA* 1.3 77.9 - - - +
70C LEU* 1.3 64.4 + - - +
72C GLN* 3.3 4.3 + - - +
73C VAL* 3.2 25.1 + - - +
91C ASP* 4.0 30.7 - - - +
92C VAL* 4.1 6.2 - - - +
95C VAL* 4.1 9.4 - - - -
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Residues in contact with LEU 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 3.9 27.4 - - + -
30C VAL* 3.6 28.3 - - + -
35C PHE* 4.2 10.1 - - + -
49C PHE* 4.9 11.0 - - + -
65C SER* 4.6 9.6 - - - -
66C ASN 3.0 15.5 + - - +
67C ALA 4.6 0.7 - - - +
69C GLY* 1.3 72.9 - - - +
71C GLY* 1.3 60.0 + - - +
73C VAL* 3.2 4.4 + - + +
74C LEU* 2.9 47.6 + - + +
95C VAL* 4.1 20.6 - - + +
99C LEU* 4.8 10.1 - - + -
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Residues in contact with GLY 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN 5.8 0.2 - - - -
191A ASN* 3.6 13.2 - - - -
18C ARG* 5.3 0.9 + - - -
35C PHE* 3.7 23.0 - - - -
67C ALA 3.0 19.5 + - - -
70C LEU* 1.3 77.0 - - - +
72C GLN* 1.3 57.6 + - - +
74C LEU* 3.5 3.0 + - - +
75C GLU* 3.0 29.0 + - - +
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Residues in contact with GLN 72 (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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191A ASN* 4.1 15.1 + - + +
68C ALA 3.3 17.8 + - - +
69C GLY 3.7 4.5 - - - +
70C LEU 3.1 0.8 - - - -
71C GLY* 1.3 75.5 - - - +
73C VAL* 1.3 59.4 + - - +
75C GLU* 3.3 16.2 + - - +
76C PHE* 3.0 27.2 + - - +
81C LYS 4.4 1.2 - - - +
82C LEU* 4.0 10.1 - - + +
83C SER* 3.0 54.0 + - - +
88C ASN* 3.7 15.8 - - - +
92C VAL* 3.8 12.8 - - + -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLY 3.2 14.9 + - - +
70C LEU* 3.2 9.5 + - + +
72C GLN* 1.3 72.1 - - - +
74C LEU* 1.3 67.8 + - + +
76C PHE* 3.2 7.8 + - - +
77C MET* 3.0 32.7 + - + +
82C LEU* 5.1 0.4 - - - -
92C VAL* 4.4 15.3 - - + +
95C VAL* 3.8 22.2 - - + -
96C ALA* 4.8 3.6 - - - +
99C LEU* 4.2 9.4 - - + -
101C MET* 3.7 29.4 - - - -
104C ILE* 4.0 16.6 - - + -
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 5.5 0.2 - - - +
18C ARG* 4.1 15.7 - - - +
28C PHE* 4.6 8.7 - - + -
35C PHE* 3.6 41.3 - - + -
36C LYS 5.1 6.3 - - - +
37C ALA* 4.6 7.4 - - + -
42C LEU* 3.9 30.7 - - + -
49C PHE* 5.5 1.6 - - + -
70C LEU* 2.9 37.5 + - + +
71C GLY* 3.8 4.3 - - - +
73C VAL* 1.3 76.7 - - + +
75C GLU* 1.3 63.7 + - - +
77C MET* 3.0 20.4 + - + -
78C TYR* 3.1 24.6 + - + +
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Residues in contact with GLU 75 (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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187A GLN 5.7 1.2 - - - +
188A LEU* 5.3 5.7 - - - +
15C ASN* 5.2 0.5 + - - -
18C ARG* 3.0 30.3 + - - +
19C GLN* 6.0 0.2 + - - -
71C GLY 3.0 17.2 + - - +
72C GLN* 3.5 20.9 - - - +
73C VAL 3.2 0.2 - - - -
74C LEU* 1.3 78.6 - - - +
76C PHE* 1.3 58.1 + - - +
78C TYR 3.4 1.0 + - - -
79C THR* 2.7 55.5 + - - +
81C LYS* 4.5 6.5 - - + +
83C SER* 6.2 0.2 - - - +
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Residues in contact with PHE 76 (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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72C GLN 3.0 14.6 + - - +
73C VAL* 3.5 7.2 - - - +
74C LEU 3.2 0.2 - - - -
75C GLU* 1.3 78.3 - - - +
77C MET* 1.3 66.7 + - - +
79C THR* 4.2 0.4 - - - -
80C ALA* 2.8 34.6 + - - -
81C LYS 3.3 15.8 + - - +
82C LEU* 4.0 18.8 - - + -
101C MET* 3.8 21.8 - - + -
103C ASP* 4.9 9.6 - - + -
104C ILE* 3.6 26.7 - - + -
134C PHE* 3.4 41.3 - + + -
137C HIS* 3.5 34.5 + + - -
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Residues in contact with MET 77 (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* 3.5 10.2 - - - +
41C VAL* 4.8 3.5 - - + +
42C LEU* 3.6 29.2 - - - +
45C CYS* 3.8 33.4 - - + -
46C SER* 4.3 2.0 - - - -
49C PHE* 4.2 25.4 - - + -
73C VAL* 3.0 23.5 + - + +
74C LEU* 3.0 17.4 + - + +
76C PHE* 1.3 78.4 - - - +
78C TYR* 1.3 67.5 + - + +
101C MET* 3.6 37.5 - - + -
137C HIS* 2.8 25.2 + - - -
141C VAL* 4.4 0.3 - - - +
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Residues in contact with TYR 78 (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* 3.4 21.5 - - + +
12C GLU* 5.3 0.2 - - - -
14C LEU* 3.5 36.3 - - + -
15C ASN* 3.5 39.8 - - - +
18C ARG* 3.6 31.4 - - + +
37C ALA* 3.7 4.9 - - + -
38C HIS* 2.6 48.9 + - - +
41C VAL* 3.7 23.3 - - + +
42C LEU* 4.3 14.4 - - + -
74C LEU* 3.1 25.1 + - + +
75C GLU 4.2 0.7 - - - +
77C MET* 1.3 83.9 - - + +
79C THR* 1.3 58.1 + - - +
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Residues in contact with THR 79 (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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8C GLN* 5.5 3.5 + - - +
11C LEU* 4.0 8.6 - - - +
15C ASN* 3.7 21.8 - - - +
75C GLU* 2.7 45.5 + - - +
78C TYR* 1.3 81.7 - - + +
80C ALA* 1.3 68.6 + - - +
81C LYS* 3.0 30.3 + - - +
133C GLN* 5.6 1.4 - - - +
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Residues in contact with ALA 80 (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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8C GLN* 5.6 3.4 - - - +
11C LEU* 4.4 5.4 - - + -
76C PHE* 2.8 22.7 + - - -
79C THR* 1.3 79.4 - - - +
81C LYS* 1.3 56.8 + - - +
132C ILE 3.5 1.6 - - - +
133C GLN* 3.5 8.1 - - + -
134C PHE* 2.9 50.2 + - - +
137C HIS* 3.7 23.2 - - + -
138C ALA 5.0 2.0 - - - +
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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