Contacts of the helix formed by residues 79 - 88 (chain B) in PDB entry 1D4W
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 LYS 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TRP* 3.8 8.5 - - - +
77B PHE* 3.6 4.9 - - - +
78B ARG* 1.3 79.7 - - + +
80B ILE* 1.3 61.3 + - - +
81B LYS* 4.2 7.9 - - + +
82B ASN* 2.8 37.9 + - - +
83B LEU 3.3 7.4 + - - -
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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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4B VAL* 3.7 24.5 - - + -
31B LEU* 3.8 28.3 - - + -
41B TYR* 4.6 5.8 - - + -
56B VAL* 3.9 29.2 - - + -
64B TRP* 3.5 39.1 - - + +
79B LYS* 1.3 73.7 - - + +
81B LYS* 1.3 59.8 + - + +
83B LEU* 3.1 10.5 + - + +
84B ILE* 2.9 39.3 + - + +
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Residues in contact with LYS 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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4B VAL* 5.0 10.3 - - + -
79B LYS* 3.1 6.6 - - + +
80B ILE* 1.3 82.7 - - - +
82B ASN* 1.3 67.8 + - - +
84B ILE* 3.9 10.2 - - - +
85B SER* 2.9 29.8 + - - +
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Residues in contact with ASN 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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77B PHE* 3.8 16.5 - - + -
78B ARG* 4.0 12.1 - - - +
79B LYS* 2.8 42.1 + - - +
81B LYS* 1.3 82.5 - - - +
83B LEU* 1.3 59.4 + - - +
85B SER* 3.3 5.4 + - - -
86B ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 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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43B LEU* 4.4 11.2 - - + -
56B VAL* 3.8 40.2 - - + -
64B TRP* 4.2 3.6 - - + +
65B SER* 3.8 11.7 - - - +
66B ALA* 3.8 22.4 - - + +
77B PHE* 3.6 30.4 - - + -
79B LYS 3.3 2.6 + - - -
80B ILE* 3.1 15.3 + - + +
82B ASN* 1.3 74.5 - - - +
84B ILE* 1.3 75.2 + - + +
86B ALA* 3.2 1.4 + - - +
87B PHE* 3.1 50.8 + - + -
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Residues in contact with ILE 84 (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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4B VAL* 3.7 30.1 - - + -
6B VAL* 4.4 13.0 - - + -
29B TYR* 4.2 9.6 - - + +
31B LEU* 5.0 8.1 - - + -
43B LEU* 4.9 9.9 - - + -
80B ILE* 2.9 30.9 + - + +
81B LYS* 4.0 7.4 - - - +
82B ASN 3.2 0.2 - - - -
83B LEU* 1.3 88.6 - - + +
85B SER* 1.3 63.3 - - - +
87B PHE 3.3 0.7 + - - -
88B GLN* 3.3 36.8 + - - +
98B LEU* 3.8 22.9 - - + +
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Residues in contact with SER 85 (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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81B LYS* 2.9 18.4 + - - +
82B ASN* 3.9 5.3 - - - -
84B ILE* 1.3 77.8 - - - +
86B ALA* 1.3 64.1 + - - +
88B GLN* 3.1 35.7 + - - +
89B LYS* 3.9 9.7 + - - +
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Residues in contact with ALA 86 (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 ARG* 4.8 8.3 - - - +
77B PHE* 3.5 28.5 - - + -
82B ASN 2.9 14.7 + - - +
83B LEU 3.2 9.6 + - - +
85B SER* 1.3 76.3 - - - +
87B PHE* 1.3 59.8 + - + +
88B GLN 3.2 0.2 - - - -
89B LYS* 3.2 27.4 + - - +
92B GLN* 3.4 18.2 - - - +
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Residues in contact with PHE 87 (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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43B LEU* 4.8 5.6 - - + -
66B ALA* 4.8 6.3 - - + -
75B ARG* 4.1 14.1 - - + -
77B PHE* 4.4 13.2 - + - -
83B LEU* 3.1 51.3 + - + +
84B ILE 3.3 1.5 + - - -
85B SER 3.2 0.2 - - - -
86B ALA* 1.3 74.2 - - + +
88B GLN* 1.3 60.6 + - - +
89B LYS 3.2 3.4 + - - +
92B GLN* 3.5 37.9 - - + +
94B ILE* 3.7 36.2 - - + +
97B PRO* 3.6 6.8 - - - +
98B LEU* 3.0 39.7 + - + +
284D VAL* 3.9 25.4 - - + -
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Residues in contact with GLN 88 (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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29B TYR* 3.2 21.4 + - - -
84B ILE* 3.3 24.9 + - - +
85B SER* 3.1 23.8 + - - +
87B PHE* 1.3 77.0 - - - +
89B LYS* 1.3 62.4 + - + +
90B PRO* 4.1 1.7 - - - +
97B PRO* 4.0 8.9 - - - +
98B LEU* 3.5 29.1 - - + +
99B GLN* 5.5 1.4 - - - +
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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