Contacts of the helix formed by residues 69 - 75 (chain C) in PDB entry 2OKD
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 ARG 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 4.5 12.9 + - - -
25C GLN* 3.9 22.0 - - - +
29C ALA* 5.0 6.5 - - - +
31C GLY 4.8 4.9 + - - -
33C ASP* 3.0 32.5 + - - -
67C ALA 3.7 2.2 + - - -
68C PRO* 1.3 72.3 - - - +
70C SER* 1.3 67.0 + - - +
71C GLY* 4.7 3.4 - - - +
72C LEU* 3.4 24.0 + - + +
73C SER* 3.0 22.5 + - - -
77C ILE 5.0 0.2 - - - +
79C ILE* 5.5 0.2 - - - +
111C ARG* 3.4 45.1 - - + +
112C ILE 5.1 1.4 + - - -
113C ALA* 4.3 19.6 - - - +
114C GLN* 3.7 28.6 + - - +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY* 4.7 1.8 - - - -
82A GLY 4.4 3.1 + - - -
83A VAL* 4.5 8.7 + - - +
95A ILE* 4.4 1.1 - - - +
202A EDO 2.7 38.3 + - - -
68C PRO 3.8 2.5 + - - -
69C ARG* 1.3 73.7 - - - +
71C GLY* 1.3 66.6 + - - +
73C SER* 3.2 7.4 + - - -
74C LEU* 3.0 34.5 + - - +
114C GLN* 5.3 1.9 + - - +
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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
----------------------------------------------------------
69C ARG* 3.4 3.4 - - - +
70C SER* 1.3 79.3 - - - +
72C LEU* 1.3 62.2 + - - +
74C LEU* 3.4 17.5 + - - +
75C LYS* 3.4 20.1 + - - +
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Residues in contact with LEU 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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69C ARG* 3.4 18.6 + - + +
70C SER 3.3 0.6 - - - -
71C GLY* 1.3 73.4 - - - +
73C SER* 1.3 62.4 + - - +
75C LYS* 3.2 17.4 + - + +
76C GLY 3.2 5.7 + - - -
77C ILE* 2.8 47.9 + - + +
96C LEU* 5.1 1.6 - - + -
104C PHE* 3.6 38.1 - - + -
111C ARG 3.9 22.0 - - - +
112C ILE* 3.9 22.2 - - + +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 3.0 31.8 + - - +
80A GLY 4.4 0.7 - - - -
81A GLY* 3.5 35.2 + - - -
95A ILE* 4.0 8.7 - - - +
68C PRO* 3.5 8.3 - - - +
69C ARG 3.0 14.7 + - - -
70C SER 3.2 9.1 + - - -
72C LEU* 1.3 75.6 - - - +
74C LEU* 1.3 59.3 + - - +
75C LYS 3.1 0.7 - - - -
76C GLY 3.0 7.4 + - - -
77C ILE 3.4 16.7 + - - +
78C ASP* 4.8 1.7 + - - -
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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
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47A ARG* 4.5 10.9 - - - +
49A LEU* 4.0 29.8 - - + +
95A ILE* 3.7 28.3 - - + -
70C SER* 3.0 25.1 + - - +
71C GLY* 3.7 11.9 - - - +
72C LEU 3.3 0.2 - - - -
73C SER* 1.3 75.4 - - - +
75C LYS* 1.3 59.9 + - + +
76C GLY 3.3 1.1 + - - -
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Residues in contact with LYS 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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47A ARG* 5.1 0.2 - - - -
71C GLY 3.4 13.2 + - - +
72C LEU* 3.2 27.1 + - + +
73C SER 3.1 0.6 - - - -
74C LEU* 1.3 78.3 - - + +
76C GLY* 1.3 58.1 + - - +
77C ILE* 4.6 8.5 - - + +
100C GLY* 3.9 14.4 - - - -
104C PHE* 4.9 11.4 - - + -
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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