Contacts of the helix formed by residues 70 - 78 (chain B) in PDB entry 2O2C
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 PRO 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B ASP 3.5 8.3 - - - +
69B GLU* 1.4 92.0 - - + +
71B ILE* 1.3 65.7 + - - +
72B LYS* 4.1 19.5 - - + -
73B LYS* 3.1 34.1 + - + +
74B HIS* 4.0 5.2 + - - -
107B HIS* 4.8 4.7 - - + +
523B GLY* 5.4 6.5 - - - -
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU 3.7 0.4 + - - -
70B PRO* 1.3 72.2 - - - +
72B LYS* 1.3 63.1 + - - +
74B HIS* 3.0 27.3 + - + +
75B PHE* 3.4 11.9 - - + -
104B SER 4.1 0.2 - - - +
105B LYS 3.8 7.9 - - - +
106B SER* 3.4 31.2 - - - +
107B HIS* 3.7 30.5 - - + +
488B MET* 3.7 28.5 - - + -
523B GLY* 3.7 30.1 - - - +
524B ARG 3.8 5.2 - - - +
525B PRO* 3.8 19.7 - - + -
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PRO* 4.1 19.3 - - + -
71B ILE* 1.3 78.3 - - - +
73B LYS* 1.3 64.6 + - - +
75B PHE* 3.2 14.5 + - - +
76B GLU* 3.2 39.4 + - - +
488B MET* 4.4 14.9 + - + +
489B ILE* 3.2 46.5 + - + +
495B GLU* 5.7 2.0 + - - -
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 2.5 40.8 - - + +
70B PRO* 3.1 25.6 + - + +
71B ILE 3.1 0.8 + - - -
72B LYS* 1.3 80.9 - - - +
74B HIS* 1.3 60.3 + - - +
76B GLU* 2.8 36.6 + - - +
77B THR* 3.0 35.8 + - - +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TYR* 4.9 5.1 + - + -
69B GLU* 4.1 34.9 + - + +
70B PRO 4.1 8.7 + - - -
71B ILE* 3.0 15.6 + - - +
73B LYS* 1.3 76.2 - - - +
75B PHE* 1.3 57.3 + - - +
78B ASP* 3.1 30.8 + - - +
81B ARG* 3.7 26.8 - - - +
106B SER 3.7 22.0 - - - -
107B HIS* 4.1 6.6 - - - -
108B ILE 4.0 16.2 + - - -
109B ASN* 4.0 24.5 - - + +
112B ILE* 6.0 0.4 - - - +
7002B GOL 3.2 23.4 + - - +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.4 18.2 - - + -
72B LYS* 3.2 9.3 + - - +
74B HIS* 1.3 76.2 - - - +
76B GLU* 1.3 62.7 + - + +
77B THR 3.4 0.2 - - - -
78B ASP 3.1 19.9 - - - +
79B SER* 4.1 4.5 + - - -
81B ARG* 3.9 14.4 - - + +
82B GLY 4.6 0.4 - - - -
104B SER* 3.4 43.5 - - - -
105B LYS* 4.2 0.9 - - + -
488B MET* 3.1 34.1 - - + -
591C ASP* 3.8 13.7 - - + -
592C SER* 3.4 34.4 + - - +
593C SER* 3.7 23.3 - - - -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS* 3.2 28.9 + - + +
73B LYS* 2.8 36.6 + - - +
75B PHE* 1.3 79.8 - - - +
77B THR* 1.3 60.2 + - - +
78B ASP 5.0 0.3 - - - -
79B SER* 5.1 1.4 + - - -
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 5.1 1.0 + - - -
73B LYS* 3.0 22.3 + - - +
76B GLU* 1.3 78.3 - - - +
78B ASP* 1.3 58.5 + - + +
79B SER 4.0 2.0 + - - -
7002B GOL 3.6 25.3 + - - +
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B HIS 3.1 8.0 + - - +
75B PHE* 3.1 15.7 - - - +
77B THR* 1.3 75.2 - - + +
79B SER* 1.3 62.0 + - - +
80B GLU* 3.0 22.2 + - - +
81B ARG* 3.3 29.8 + - + +
84B ARG* 3.0 28.9 + - - +
85B TYR* 4.6 0.3 - - - -
7002B GOL 2.9 35.7 + - - +
592C SER* 4.6 1.2 + - - -
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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