Contacts of the helix formed by residues 73 - 82 (chain B) in PDB entry 4DKE
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 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 4.2 16.7 - - + +
72B PHE* 1.3 74.8 - - - +
74B ILE* 1.3 73.4 + - + +
75B ALA* 3.2 27.4 - - - +
76B ASN* 2.9 27.7 + - - +
77B VAL* 3.1 10.9 + - - +
167B ASN* 3.2 39.7 - - - +
170B ARG* 6.0 3.6 - - - +
171B VAL* 3.7 10.4 - - - +
1D NAG 6.3 1.2 - - - -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 1.3 81.4 - - + +
75B ALA* 1.3 66.9 + - + +
77B VAL* 2.8 13.7 - - + +
78B THR* 2.8 34.6 + - - +
170B ARG* 4.9 20.4 - - + +
171B VAL* 3.9 7.6 - - + +
174B LEU* 4.2 28.9 - - + -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ARG* 3.2 24.3 - - - +
74B ILE* 1.3 83.3 - - + +
76B ASN* 1.3 58.4 + - - +
78B THR* 3.5 7.8 + - - +
79B ARG* 3.0 49.8 + - - +
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Residues in contact with ASN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.9 4.7 - - - +
72B PHE* 3.7 16.8 - - + -
73B ARG* 2.9 36.6 + - - +
75B ALA* 1.3 78.6 - - - +
77B VAL* 1.3 57.2 + - - +
79B ARG* 3.0 15.9 - - - +
80B LEU* 2.9 34.9 + - + +
1D NAG 1.4 65.5 + - - +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 4.5 11.2 - - + -
73B ARG 3.1 3.9 + - - +
74B ILE* 2.8 30.9 + - - +
76B ASN* 1.3 75.5 - - - +
78B THR* 1.3 56.7 + - - +
80B LEU* 3.6 7.8 - - - +
81B GLN* 2.7 40.9 + - + +
90B LEU* 4.0 24.2 - - + -
171B VAL* 4.9 6.5 - - + -
174B LEU* 3.2 29.8 - - + -
175B LEU* 3.7 28.3 - - + -
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 2.8 23.7 + - - +
75B ALA* 3.6 8.2 - - - +
77B VAL* 1.3 74.0 - - - +
79B ARG* 1.3 64.6 + - - +
81B GLN* 3.9 9.6 + - - +
82B ARG* 3.1 45.2 + - + +
174B LEU* 5.4 2.8 - - - +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 3.0 39.3 + - - +
76B ASN* 3.0 29.8 + - - +
78B THR* 1.3 78.9 - - - +
80B LEU* 1.3 61.0 + - + +
82B ARG* 3.8 5.3 - - - +
83B ALA* 3.4 22.5 + - - +
1D NAG 3.0 39.8 + - - -
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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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72B PHE* 4.0 21.1 - - + -
76B ASN* 2.9 27.5 + - + +
77B VAL 3.8 1.6 - - - +
78B THR 3.1 0.2 - - - -
79B ARG* 1.3 83.9 - - + +
81B GLN* 1.3 61.1 + - - +
82B ARG 3.1 1.6 - - - -
83B ALA* 2.9 19.2 + - + -
84B GLN 3.0 9.0 + - - -
85B VAL* 3.1 29.5 + - + +
90B LEU* 3.4 32.8 - - + -
93B LEU* 4.3 14.4 - - + -
1D NAG 6.3 0.9 - - + -
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 2.7 34.5 + - + +
78B THR* 3.9 9.2 + - - +
80B LEU* 1.3 72.7 - - - +
82B ARG* 1.3 61.1 + - + +
83B ALA 3.1 0.2 - - - -
84B GLN* 3.0 19.4 + - - +
85B VAL 4.6 4.9 - - - +
87B GLU* 4.4 18.9 + - - +
90B LEU* 4.1 16.0 - - + +
174B LEU* 4.8 16.8 + - - +
175B LEU* 4.9 4.6 - - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.1 34.5 + - + +
79B ARG* 3.8 6.3 - - - +
81B GLN* 1.3 78.1 - - + +
83B ALA* 1.3 56.3 + - - +
84B GLN 3.4 2.5 - - - -
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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