Contacts of the helix formed by residues 73 - 82 (chain B) in PDB entry 1D7K
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 SER 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ASN* 3.0 20.5 + - - -
72B ASP* 1.3 82.1 - - - +
74B LYS* 1.3 66.8 + - - +
75B ALA 4.4 0.4 - - - -
76B ILE* 3.0 23.2 + - - +
77B VAL* 3.3 10.6 + - - +
284B PHE* 4.6 0.3 - - - -
391B VAL* 4.5 5.9 - - - +
405B ILE* 4.3 11.3 - - - +
407B TYR* 3.1 28.7 + - - -
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Residues in contact with LYS 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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8B GLU* 6.4 2.0 - - + -
9B PHE* 4.8 11.7 - - + -
72B ASP 3.4 3.2 + - - +
73B SER* 1.3 73.8 - - - +
75B ALA* 1.3 64.1 + - - +
76B ILE 3.2 0.7 + - - -
77B VAL* 3.4 1.6 + - - +
78B LYS* 3.3 33.1 + - - +
97B LEU* 4.7 14.5 - - + +
100B SER* 5.1 4.3 - - - -
101B LEU* 3.9 39.6 - - + +
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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
----------------------------------------------------------
9B PHE* 3.7 44.9 - - + +
45B LEU* 4.2 2.3 - - + +
73B SER 3.3 0.4 - - - -
74B LYS* 1.3 81.5 - - - +
76B ILE* 1.3 56.0 + - - +
78B LYS* 4.2 0.9 - - - +
79B THR* 2.9 30.7 + - - -
407B TYR* 3.6 37.2 + - + -
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ALA* 5.4 0.4 - - + -
45B LEU* 3.7 16.2 - - + -
48B ILE* 3.5 27.7 - - + +
66B TYR* 4.2 17.9 - - + +
71B ASN* 4.2 15.3 - - - +
73B SER* 3.0 23.8 + - - +
75B ALA* 1.3 73.6 - - - +
77B VAL* 1.4 68.2 + - - +
78B LYS 3.1 2.0 - - - -
79B THR* 3.4 4.5 + - - -
80B LEU* 2.9 29.4 + - + +
280B VAL* 3.8 22.2 - - + -
284B PHE* 3.9 15.5 - - + -
407B TYR* 3.8 14.8 - - + -
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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
----------------------------------------------------------
66B TYR* 4.4 16.8 - - + -
68B VAL* 4.7 9.4 - - + -
71B ASN 4.9 0.4 - - - +
72B ASP 4.7 4.0 - - - +
73B SER 3.3 10.5 + - - +
74B LYS* 3.4 2.9 + - - +
76B ILE* 1.4 77.3 - - - +
78B LYS* 1.3 51.7 + - - +
80B LEU* 3.3 1.0 + - - -
81B ALA* 2.6 31.3 + - + +
87B PHE* 3.4 33.1 - - + -
97B LEU* 4.5 18.8 - - + -
98B VAL* 4.2 17.0 - - + -
101B LEU* 3.7 28.3 - - + -
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Residues in contact with LYS 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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7B GLU* 3.3 33.2 + - - +
9B PHE* 3.1 40.6 - - + -
74B LYS* 3.3 22.1 + - - +
75B ALA 4.2 0.7 - - - +
77B VAL* 1.3 78.4 - - - +
79B THR* 1.3 64.4 + - - +
80B LEU 3.2 0.7 - - - -
81B ALA* 4.1 8.2 - - + +
82B ALA* 3.1 23.5 + - + +
101B LEU* 4.4 28.2 - - + +
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Residues in contact with THR 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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9B PHE* 5.5 2.6 - - - -
45B LEU* 3.7 30.1 - - + +
48B ILE* 5.0 10.3 - - + -
49B LEU* 3.5 33.6 - - + +
75B ALA 2.9 18.8 + - - -
76B ILE* 3.8 4.5 - - - -
78B LYS* 1.3 80.2 - - - +
80B LEU* 1.3 63.2 + - + +
82B ALA* 3.5 10.9 + - - +
83B THR* 3.7 11.1 + - - -
409B MET* 4.6 5.3 - - + +
417B MET* 4.4 14.1 - - - +
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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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48B ILE* 4.0 25.8 - - + +
49B LEU* 6.3 1.6 - - + -
52B HIS* 5.3 1.1 - - + -
66B TYR* 3.7 43.3 - - + -
76B ILE* 2.9 27.2 + - + +
77B VAL 3.7 3.4 - - - +
79B THR* 1.3 76.5 - - + +
81B ALA* 1.3 60.3 + - - +
83B THR* 2.8 37.0 + - + +
84B GLY 3.4 2.6 + - - -
85B THR* 3.5 27.2 + - + +
87B PHE* 4.1 6.3 - - + -
279B TYR* 4.0 28.3 - - + -
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Residues in contact with ALA 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 VAL* 2.6 22.8 + - + +
78B LYS* 4.2 8.3 - - + +
79B THR 3.5 0.2 - - - -
80B LEU* 1.3 70.2 - - - +
82B ALA* 1.3 58.2 + - - +
83B THR 2.9 6.6 + - - -
84B GLY* 3.5 1.2 + - - -
87B PHE* 3.5 12.2 - - + -
101B LEU* 4.9 7.2 - - + +
103B VAL* 3.5 31.6 - - + -
107B ARG* 3.3 22.1 + - - +
421B GLN 4.8 2.1 - - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 3.1 19.1 + - + +
79B THR 4.0 5.2 - - - +
80B LEU 3.2 0.8 - - - -
81B ALA* 1.3 73.9 - - - +
83B THR* 1.3 55.7 + - - +
84B GLY 3.6 0.2 - - - -
417B MET* 4.5 12.4 - - + +
420B PHE* 3.7 3.5 - - - +
421B GLN* 3.0 61.0 + - + +
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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