Contacts of the helix formed by residues 73 - 83 (chain B) in PDB entry 3MDL
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 GLU 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLY* 3.1 38.9 + - - +
64B PHE 4.7 3.3 - - - +
65B TYR* 3.8 26.5 - - + +
71B THR 3.7 0.6 + - - -
72B PRO* 1.3 74.8 - - - +
74B PHE* 1.3 66.2 + - - +
75B LEU* 3.4 4.3 - - + +
76B THR* 3.1 8.4 + - - +
77B ARG* 3.0 19.2 + - - +
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Residues in contact with PHE 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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72B PRO 4.0 0.4 + - - -
73B GLU* 1.3 73.1 - - - +
75B LEU* 1.3 64.0 + - - +
77B ARG* 3.1 36.7 + - + +
78B ILE* 3.4 34.2 + - + +
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Residues in contact with LEU 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 GLU* 3.4 3.5 - - + +
74B PHE* 1.3 80.6 - - - +
76B THR* 1.3 58.1 + - - +
78B ILE* 3.5 10.2 + - - +
79B LYS* 3.1 46.6 + - - +
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Residues in contact with THR 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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62B THR 5.1 0.7 - - - +
63B GLY* 2.7 37.9 + - - +
64B PHE* 3.7 24.9 - - + -
72B PRO* 4.3 1.8 - - + -
73B GLU* 3.1 15.3 + - - +
75B LEU* 1.3 76.6 - - - +
77B ARG* 1.3 58.5 + - - +
79B LYS* 3.2 12.9 + - + +
80B LEU* 2.8 45.2 + - + +
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Residues in contact with ARG 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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71B THR* 4.7 8.5 - - - +
72B PRO* 3.4 45.8 + - + +
73B GLU 3.0 15.5 + - - +
74B PHE* 3.1 26.6 + - + +
76B THR* 1.3 75.7 - - - +
78B ILE* 1.3 58.9 + - + +
80B LEU* 3.4 7.3 + - - +
81B LEU* 3.0 27.9 + - - +
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Residues in contact with ILE 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 PHE* 3.4 43.4 + - + +
75B LEU* 3.9 8.1 - - - +
76B THR 3.3 0.4 - - - -
77B ARG* 1.3 74.4 - - + +
79B LYS* 1.3 65.7 + - - +
81B LEU* 3.2 8.0 + - + +
82B LEU* 3.0 44.9 + - + +
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Residues in contact with LYS 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 LEU* 3.1 32.3 + - - +
76B THR* 3.5 15.9 + - + +
78B ILE* 1.3 77.1 - - - +
80B LEU* 1.3 57.0 + - + +
82B LEU* 3.3 4.8 + - - +
83B LYS* 2.9 32.1 + - - +
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Residues in contact with LEU 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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64B PHE* 3.9 31.2 - - + -
72B PRO* 4.8 6.5 - - + -
76B THR* 2.8 33.1 + - + +
77B ARG* 3.8 5.4 - - - +
79B LYS* 1.3 74.9 - - + +
81B LEU* 1.3 61.4 + - - +
83B LYS* 3.8 20.8 + - + +
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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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77B ARG 3.0 17.4 + - - +
78B ILE* 3.2 10.3 + - + +
80B LEU* 1.3 78.7 - - - +
82B LEU* 1.3 66.0 + - + +
83B LYS 3.8 2.4 + - - +
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Residues in contact with LEU 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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78B ILE* 3.0 38.4 + - + +
79B LYS* 4.2 3.8 - - - +
81B LEU* 1.3 84.1 - - + +
83B LYS* 1.3 64.3 + - - +
84B PRO* 3.2 10.2 - - - +
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Residues in contact with LYS 83 (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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79B LYS 2.9 18.5 + - - +
80B LEU* 4.0 19.4 - - + +
81B LEU 3.4 3.1 - - - +
82B LEU* 1.3 75.4 - - - +
84B PRO* 1.3 78.8 - - + +
85B THR* 3.8 3.3 + - - +
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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