Contacts of the helix formed by residues 79 - 88 (chain C) in PDB entry 5O9G
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 ILE 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C LYS* 5.8 2.9 - - + -
77C ARG* 4.0 10.3 - - + +
78C ILE* 1.3 78.0 - - - +
80C PRO* 1.3 73.1 - - + +
81C ARG* 3.7 20.6 - - + +
82C HIS* 2.9 50.1 + - + +
83C LEU* 3.3 14.4 - - - +
52D SER* 5.1 3.8 - - - -
55D ALA* 4.6 0.4 - - - -
58E THR* 5.5 3.4 - - + -
58J C 6.5 0.4 - - - -
59J A 5.3 8.7 - - - +
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Residues in contact with PRO 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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78C ILE 4.7 0.7 - - - +
79C ILE* 1.3 88.7 - - + +
81C ARG* 1.3 55.8 + - - +
83C LEU* 3.0 16.3 + - + +
84C GLN* 2.9 26.0 + - - +
102C ILE* 4.4 3.1 - - - +
103C ALA 3.5 23.6 - - - +
104C GLN* 3.6 15.5 - - + +
105C GLY* 4.8 0.2 - - - -
52D SER* 4.8 8.1 - - - -
54D LYS* 4.1 12.1 - - + -
55D ALA* 3.7 26.2 - - + +
58D ILE* 4.1 7.6 - - + -
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Residues in contact with ARG 81 (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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73C ASN* 6.2 0.4 - - - +
79C ILE* 3.1 19.8 - - + +
80C PRO* 1.3 77.1 - - - +
82C HIS* 1.3 59.3 + - + +
84C GLN* 3.3 4.6 + - - +
85C LEU* 2.9 62.4 + - + +
104C GLN 4.0 5.1 + - - -
105C GLY 4.3 0.2 - - - -
106C GLY* 4.1 25.4 - - - +
107C VAL 3.2 20.2 + - - -
109C PRO* 5.1 3.6 - - - +
55E GLN* 2.4 31.5 + - - +
56E LYS* 3.6 18.1 + - - +
57E SER 3.4 20.2 + - - -
58E THR* 3.6 29.7 - - + +
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Residues in contact with HIS 82 (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 ALA* 4.1 9.4 - - - +
69C ALA* 3.6 19.4 + - + +
70C ALA* 3.4 31.5 - - + +
73C ASN* 3.9 22.3 + - - +
75C LYS* 3.7 27.6 - - + +
77C ARG 4.2 3.1 - - - -
78C ILE* 3.6 11.8 - - + -
79C ILE* 2.9 49.4 + - + +
81C ARG* 1.3 80.4 - - + +
83C LEU* 1.3 57.5 + - - +
85C LEU* 4.6 4.5 - - + +
86C ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 83 (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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62C ILE* 3.9 24.5 - - + +
63C LEU* 5.7 3.4 - - + -
66C ALA* 3.7 20.6 - - + -
78C ILE* 3.7 17.0 - - + -
79C ILE 3.3 16.8 - - - +
80C PRO* 3.0 10.6 + - + +
82C HIS* 1.3 75.0 - - - +
84C GLN* 1.3 59.9 + - - +
86C ALA* 3.2 2.5 + - + +
87C VAL* 2.9 37.4 + - + +
102C ILE* 4.0 16.6 - - + -
51D ILE* 4.0 4.3 - - + -
55D ALA* 3.8 25.6 - - + -
58D ILE* 5.8 4.0 - - + -
59D MET* 4.4 14.6 - - + -
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Residues in contact with GLN 84 (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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80C PRO 2.9 12.6 + - - +
81C ARG* 3.6 11.7 - - - +
83C LEU* 1.3 75.4 - - - +
85C LEU* 1.3 60.4 + - + +
88C ARG* 2.9 71.3 + - + +
102C ILE* 3.3 38.2 + - + +
105C GLY* 4.2 5.8 - - - -
106C GLY 2.7 48.2 + - - +
107C VAL* 4.9 2.5 - - - +
108C LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 85 (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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69C ALA* 4.9 8.6 - - + +
73C ASN* 4.7 16.2 - - - +
81C ARG* 2.9 60.7 + - + +
82C HIS* 4.3 7.2 - - + +
84C GLN* 1.3 77.1 - - + +
86C ALA* 1.3 56.5 + - - +
87C VAL 3.5 0.2 - - - -
88C ARG 4.3 0.7 - - - -
89C ASN* 3.2 27.4 + - - +
107C VAL 4.3 5.4 - - - +
108C LEU* 3.7 27.3 - - + +
109C PRO* 4.8 5.6 - - + -
56E LYS* 5.7 6.5 - - - +
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Residues in contact with ALA 86 (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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62C ILE* 5.0 2.5 - - + +
65C LEU* 3.5 54.8 - - + +
66C ALA* 3.9 5.2 - - + +
69C ALA* 4.1 3.4 - - + -
82C HIS 2.9 22.1 + - - +
83C LEU* 3.7 6.3 - - + +
84C GLN 3.1 0.2 - - - -
85C LEU* 1.3 80.0 - - - +
87C VAL* 1.3 63.4 + - + +
89C ASN* 4.3 2.3 - - - +
90C ASP* 4.3 7.1 + - - +
93C LEU* 4.2 3.2 - - - +
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Residues in contact with VAL 87 (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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62C ILE* 4.2 28.9 - - + -
83C LEU* 2.9 21.5 + - + +
84C GLN 4.2 1.3 - - - +
86C ALA* 1.3 79.7 - - + +
88C ARG* 1.3 73.0 + - + +
89C ASN 3.2 3.1 + - - -
90C ASP 3.4 14.4 + - - +
93C LEU* 3.9 28.1 - - + +
94C ASN* 3.9 4.8 + - - +
97C LEU* 3.8 30.7 - - + +
102C ILE* 4.2 17.3 - - + -
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Residues in contact with ARG 88 (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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84C GLN* 2.9 55.5 + - + +
87C VAL* 1.3 85.5 - - + +
89C ASN* 1.3 60.7 + - - +
90C ASP 3.4 6.5 + - - +
94C ASN* 3.2 33.5 + - - +
97C LEU* 3.2 18.3 + - - -
98C GLY 4.1 8.7 + - - -
100C VAL* 2.4 32.1 + - - +
101C THR* 4.6 3.2 - - - +
102C ILE* 5.1 4.7 - - - +
108C LEU* 3.3 37.7 - - + +
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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