Contacts of the helix formed by residues 73 - 82 (chain B) in PDB entry 3COQ
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B PHE* 3.6 1.9 - - - -
72B PHE* 1.3 93.0 - - + +
74B ARG* 1.3 68.7 + - - +
75B GLU* 4.1 18.8 - - + +
76B ASP* 2.9 40.8 + - - +
77B LEU 3.4 6.1 + - - -
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Residues in contact with ARG 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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69B LEU* 3.7 27.7 - - + +
72B PHE 3.7 0.8 + - - -
73B PRO* 1.3 72.4 - - - +
75B GLU* 1.3 57.5 + - - +
77B LEU* 2.6 47.9 + - - +
78B ASP* 3.2 31.9 + - - +
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Residues in contact with GLU 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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73B PRO* 4.1 17.1 - - + +
74B ARG* 1.3 78.2 - - - +
76B ASP* 1.3 78.1 + - - +
78B ASP* 3.5 19.5 + - - +
79B MET* 3.5 29.9 + - + +
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Residues in contact with ASP 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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68B PHE* 3.8 15.7 - - + -
72B PHE* 4.3 3.7 - - + +
73B PRO* 2.9 40.3 + - + +
74B ARG 2.8 1.4 + - - -
75B GLU* 1.3 85.8 - - - +
77B LEU* 1.3 69.8 + - - +
79B MET* 2.9 32.5 + - - +
80B ILE* 3.2 13.7 + - - +
92B LEU* 4.5 20.8 - - + +
96B LEU 5.5 1.7 - - - +
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Residues in contact with LEU 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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64A LEU* 4.4 11.9 - - + -
65B GLU* 4.2 29.6 - - + +
68B PHE* 3.3 44.8 - - + -
69B LEU* 4.2 10.1 - - + -
74B ARG* 2.6 37.0 + - - +
76B ASP* 1.3 70.7 - - - +
78B ASP* 1.3 59.3 + - - +
80B ILE* 3.2 1.7 + - + +
81B LEU* 2.9 57.9 + - + +
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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 ARG* 3.2 45.8 + - - +
75B GLU* 3.6 14.5 - - - +
76B ASP 3.0 0.8 - - - -
77B LEU* 1.3 77.4 - - - +
79B MET* 1.3 68.3 + - + +
81B LEU* 3.8 12.3 + - - +
82B LYS* 3.4 34.3 + - - +
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Residues in contact with MET 79 (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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75B GLU* 3.7 25.1 - - + +
76B ASP* 2.9 29.6 + - - +
78B ASP* 1.3 77.9 - - + +
80B ILE* 1.3 71.5 + - + +
82B LYS* 2.9 19.0 + - - +
83B MET* 3.1 20.2 + - - +
92B LEU* 4.7 13.5 - - + -
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Residues in contact with ILE 80 (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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63A ARG* 3.3 20.0 - - + +
64A LEU* 4.9 10.5 - - + +
67A LEU* 4.1 26.5 - - + -
68B PHE* 4.4 11.9 - - + -
76B ASP 3.2 17.5 - - - +
77B LEU 3.2 3.5 + - - +
79B MET* 1.3 76.5 - - + +
81B LEU* 1.3 60.0 + - - +
82B LYS 2.8 0.2 - - - -
83B MET* 2.8 32.6 + - + +
89B ILE* 4.5 15.7 - - + -
92B LEU* 3.1 47.6 - - + -
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Residues in contact with LEU 81 (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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60A ARG* 3.3 59.1 + - + +
63A ARG* 2.7 31.5 + - - +
64A LEU* 4.6 10.1 - - + -
61B LEU* 4.2 7.9 - - + -
65B GLU* 3.6 24.2 - - - +
77B LEU* 2.9 39.9 + - + +
78B ASP* 4.0 13.5 - - - +
79B MET 3.2 0.2 - - - -
80B ILE* 1.3 80.2 - - - +
82B LYS* 1.3 58.0 + - - +
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Residues in contact with LYS 82 (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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60A ARG* 6.3 1.1 - - - +
63A ARG* 3.8 8.1 + - - +
78B ASP* 3.4 26.6 + - - +
79B MET* 2.9 13.2 + - - +
80B ILE 2.8 1.4 - - - -
81B LEU* 1.3 81.3 - - + +
83B MET* 1.3 60.8 + - - -
84B ASP* 3.5 2.3 + - - +
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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