Contacts of the helix formed by residues 70 - 85 (chain C) in PDB entry 1OJ7
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 ALA 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.0 29.5 + - + +
68C ASN 3.1 4.9 + - - +
69C PRO* 1.3 73.0 - - - +
71C TYR* 1.3 66.4 + - - +
72C GLU* 4.0 14.4 - - - +
73C THR* 3.1 6.0 + - - +
74C LEU* 3.0 24.3 + - - +
153C SER* 3.5 7.9 - - - +
155C LYS* 4.0 21.8 - - + -
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Residues in contact with TYR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO 3.9 0.6 + - - -
70C ALA* 1.3 71.3 - - - +
72C GLU* 1.3 68.0 + - + +
74C LEU* 3.3 6.2 + - - +
75C MET* 2.9 64.9 + - + +
103C PHE* 3.8 18.6 - + - -
115C ASP* 2.4 33.4 + - - -
116C PRO* 3.8 5.9 - - + +
117C TRP* 3.7 34.8 - + + -
152C ILE* 4.0 8.4 - - + +
153C SER 2.8 19.0 + - - +
154C ARG* 3.7 39.7 + - + -
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Residues in contact with GLU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 3.1 0.2 + - - -
71C TYR* 1.3 96.5 + - + +
73C THR* 1.3 62.0 + - - +
75C MET* 3.7 10.0 + - - +
76C ASN* 3.8 16.0 + - - +
154C ARG* 3.5 5.7 + - - +
155C LYS* 3.0 48.2 + - - +
156C THR* 3.0 43.7 + - + +
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 3.4 23.5 - - + -
63C GLY 5.2 0.2 - - - +
64C GLY* 3.6 27.1 - - - +
65C ILE* 4.6 3.6 - - + +
66C GLU* 2.4 29.9 + - - +
70C ALA* 3.1 8.6 + - - +
72C GLU* 1.3 76.0 - - - +
74C LEU* 1.3 65.6 + - + +
76C ASN* 3.1 28.5 + - - +
155C LYS* 4.4 6.8 + - - -
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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
----------------------------------------------------------
62C PHE* 5.1 0.7 - - + -
65C ILE* 3.8 29.8 - - + -
69C PRO* 4.2 4.0 - - + -
70C ALA 3.0 22.4 + - - +
71C TYR 3.8 3.1 - - - +
73C THR* 1.3 77.4 - - + +
75C MET* 1.3 57.3 + - - +
77C ALA* 3.0 9.0 + - - +
78C VAL* 3.0 29.0 + - - +
100C GLY* 3.6 39.3 - - - +
103C PHE* 3.7 31.6 - - + -
104C ILE* 3.8 9.9 - - + +
152C ILE* 3.8 22.7 - - + -
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Residues in contact with MET 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TYR* 2.9 50.4 + - + +
72C GLU* 4.0 7.9 - - - +
73C THR 3.2 0.4 - - - -
74C LEU* 1.3 74.5 - - - +
76C ASN* 1.3 65.7 + - - +
78C VAL* 3.7 25.7 - - + +
79C LYS* 3.0 24.9 + - + +
82C ARG* 4.5 7.4 - - - +
103C PHE* 4.1 4.9 - - - -
116C PRO* 3.5 41.5 - - + -
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Residues in contact with ASN 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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62C PHE* 3.9 16.1 - - + -
72C GLU 3.8 16.3 + - - +
73C THR* 3.1 15.9 + - - +
75C MET* 1.3 78.2 - - - +
77C ALA* 1.3 62.8 + - - +
79C LYS* 3.5 9.7 + - - +
80C LEU* 3.2 21.7 + - - +
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Residues in contact with ALA 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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33C LEU* 4.6 6.0 - - + +
62C PHE* 3.7 33.6 - - + -
73C THR 3.7 0.6 + - - -
74C LEU 3.0 10.6 + - - +
76C ASN* 1.3 78.0 - - - +
78C VAL* 1.3 57.8 + - - +
80C LEU* 3.2 5.9 + - - +
81C VAL* 2.9 33.7 + - - +
104C ILE* 3.4 29.2 - - + -
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Residues in contact with VAL 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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74C LEU 3.0 19.0 + - - +
75C MET* 3.3 25.3 + - + +
77C ALA* 1.3 74.1 - - - +
79C LYS* 1.3 62.8 + - - +
81C VAL* 3.2 7.7 + - - +
82C ARG* 3.0 57.8 + - - +
103C PHE* 4.6 2.0 - - + -
104C ILE* 4.0 20.9 - - - +
107C ALA* 3.6 25.8 - - + -
108C ALA* 4.0 13.0 - - - +
116C PRO* 5.5 0.2 - - + -
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Residues in contact with LYS 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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75C MET* 3.0 17.9 + - + +
76C ASN* 3.6 10.3 - - - +
78C VAL* 1.3 79.0 - - - +
80C LEU* 1.3 61.8 + - - +
82C ARG* 3.4 9.5 + - - +
83C GLU* 3.0 56.9 + - + +
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Residues in contact with LEU 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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33C LEU* 4.0 29.2 - - + -
60C LEU* 4.6 12.6 - - + -
61C GLU 4.5 7.4 - - - +
62C PHE* 4.5 19.5 - - + -
76C ASN 3.2 11.1 + - - +
77C ALA 3.4 6.5 - - - +
79C LYS* 1.3 78.9 - - - +
81C VAL* 1.3 57.1 + - - +
83C GLU* 3.4 8.7 + - - +
84C GLN* 3.0 62.4 + - + +
86C VAL* 5.0 0.7 - - + -
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Residues in contact with VAL 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 25.4 - - + -
77C ALA 2.9 17.7 + - - +
78C VAL* 3.2 9.4 + - - +
80C LEU* 1.3 76.0 - - - +
82C ARG* 1.3 58.3 + - - +
85C LYS* 3.1 23.2 + - - -
86C VAL* 3.1 31.0 + - + +
89C LEU* 4.1 5.4 - - + -
104C ILE* 3.9 15.7 - - + -
108C ALA* 3.6 11.4 - - + -
131C ILE* 3.2 33.9 - - + -
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Residues in contact with ARG 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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75C MET* 4.5 11.1 - - - +
78C VAL* 3.0 36.8 + - + +
79C LYS* 3.8 7.7 - - - +
81C VAL* 1.3 76.5 - - - +
83C GLU* 1.3 66.2 + - + +
85C LYS* 3.5 15.9 + - - +
107C ALA 3.1 24.6 + - - -
108C ALA* 3.4 22.6 + - + +
110C TYR* 3.2 22.2 + - - +
111C PRO 4.4 1.0 + - - -
112C GLU* 3.8 47.2 + - - +
114C ILE 5.5 0.8 + - - -
116C PRO* 5.0 7.5 - - - +
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Residues in contact with GLU 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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79C LYS* 3.0 51.6 + - + +
80C LEU* 4.0 7.7 - - - +
82C ARG* 1.3 79.4 - - + +
84C GLN* 1.3 77.5 + - - +
85C LYS* 3.6 6.9 + - - +
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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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31C ARG* 3.0 25.9 + - - -
60C LEU* 3.7 26.3 - - + +
80C LEU* 3.0 41.2 + - + +
83C GLU* 1.3 90.9 + - + +
85C LYS* 1.3 71.0 + - - +
86C VAL* 4.3 3.8 - - + -
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Residues in contact with LYS 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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31C ARG* 3.7 12.8 + - - +
81C VAL 3.1 9.1 + - - -
82C ARG 3.5 11.9 + - - +
83C GLU 3.4 6.1 - - - +
84C GLN* 1.3 82.1 - - - +
86C VAL* 1.3 65.5 + - - +
87C THR* 3.6 13.6 + - + +
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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