Contacts of the helix formed by residues 80 - 90 (chain A) in PDB entry 1DKE
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 LEU 80 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 4.1 22.0 - - + +
68A ASN* 4.2 11.2 - - - +
69A ALA* 4.6 10.8 - - + -
76A MET* 2.8 21.9 + - + +
77A PRO 3.9 1.6 - - - -
79A ALA* 1.3 73.5 - - + +
81A SER* 1.3 56.4 + - - +
82A ALA 3.5 2.2 - - - -
83A LEU* 3.2 28.1 + - + +
84A SER* 2.8 28.2 + - - -
132A VAL* 3.9 34.8 - - + -
135A VAL* 3.7 27.4 - - + -
136A LEU* 4.2 10.5 - - + -
142A HEM 6.1 1.1 - - + -
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO 3.3 11.6 + - - -
78A ASN* 3.2 20.6 + - - -
79A ALA 3.5 1.0 + - - -
80A LEU* 1.3 75.1 - - - +
82A ALA* 1.3 57.7 + - - +
84A SER* 3.3 1.9 + - - -
85A ASP* 3.0 20.6 + - - -
139A LYS* 2.9 39.2 + - - +
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ALA 5.4 0.2 + - - -
80A LEU 3.5 0.8 - - - -
81A SER* 1.3 78.0 - - - +
83A LEU* 1.3 59.5 + - + +
85A ASP* 3.3 10.7 + - - +
86A LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ALA* 3.6 31.6 - - + -
80A LEU* 3.2 24.1 + - + +
82A ALA* 1.3 76.8 - - - +
84A SER* 1.3 68.1 + - - +
86A LEU* 4.3 19.1 - - + +
87A HIS* 3.0 38.8 + - + +
136A LEU* 3.7 14.1 - - + -
142A HEM 3.8 37.7 - - + -
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO 5.2 0.9 + - - -
80A LEU 2.8 15.5 + - - -
81A SER* 3.3 3.5 + - - -
83A LEU* 1.3 78.3 - - - +
85A ASP* 1.3 59.6 + - - +
88A ALA* 3.1 26.5 + - - +
135A VAL* 3.4 29.4 + - - +
136A LEU* 3.7 19.0 - - - +
138A SER* 4.0 2.0 + - - -
139A LYS* 2.9 39.0 + - - +
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Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 3.0 19.8 + - - +
82A ALA* 3.6 11.1 - - - +
83A LEU 3.2 0.2 - - - -
84A SER* 1.3 75.6 - - - +
86A LEU* 1.3 58.1 + - - +
88A ALA 3.2 1.2 + - - -
89A HIS* 2.8 53.2 + - + +
139A LYS* 2.8 31.4 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 2.9 17.2 + - - +
83A LEU* 4.0 15.9 - - + +
84A SER 3.4 0.4 - - - -
85A ASP* 1.3 75.0 - - - +
87A HIS* 1.3 59.5 + - + +
90A LYS* 3.0 47.6 + - + -
91A LEU* 3.3 39.1 + - + -
142A HEM 3.7 32.5 - - + -
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.0 36.5 + - + +
86A LEU* 1.3 78.9 - - + +
88A ALA* 1.3 61.2 + - - +
91A LEU* 3.8 19.1 - - + -
92A ARG* 2.8 31.2 + - - -
93A VAL* 4.4 7.0 - - + -
98A PHE* 4.1 18.2 - + + -
136A LEU* 3.9 19.5 - - + +
140A TYR* 3.7 12.7 - - + +
142A HEM 2.1 76.3 + + + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 3.1 19.9 + - - +
85A ASP 3.8 2.2 - - - +
87A HIS* 1.3 77.9 - - - +
89A HIS* 1.3 69.6 + - + +
92A ARG* 3.5 15.3 - - - +
139A LYS* 3.6 38.6 - - + +
140A TYR* 3.6 24.6 - - + +
37D TRP* 5.6 0.7 - - - +
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 2.8 47.5 + - + +
88A ALA* 1.3 90.6 + - + +
90A LYS* 1.3 71.1 + - + +
92A ARG* 3.4 22.5 + - - +
139A LYS* 4.3 15.2 - - + +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LEU* 3.0 32.3 + - + +
88A ALA 3.8 0.2 - - - -
89A HIS* 1.3 91.5 - - + +
91A LEU* 1.3 72.9 - - + +
92A ARG* 3.2 25.0 + - - +
40D ARG* 4.8 2.8 + - - +
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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