Contacts of the helix formed by residues 83 - 91 (chain A) in PDB entry 4W56
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ASN* 2.9 10.3 + - - +
82A ALA* 1.3 82.1 - - + +
84A LEU* 1.3 67.8 + - + +
86A PRO* 3.8 5.8 - - - +
87A VAL* 3.7 18.4 - - - +
118A LEU* 4.7 11.8 - - + +
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Residues in contact with LEU 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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78A ILE* 3.9 35.9 - - + +
81A ASN* 3.1 28.8 + - + +
83A LYS* 1.3 80.3 - - + +
85A LYS* 1.3 66.2 + - - +
87A VAL* 3.1 6.1 + - - +
88A TYR* 2.9 22.5 + - - +
103A VAL* 4.3 13.2 - - + -
108A GLU* 4.3 13.7 - - + +
111A VAL* 4.1 15.9 - - + -
118A LEU* 3.9 24.7 - - + -
200A 3GY 3.8 23.9 - - + -
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Residues in contact with LYS 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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78A ILE* 3.5 12.3 + - - +
79A LEU* 3.2 41.3 - - + +
81A ASN 2.9 16.3 + - - +
82A ALA* 5.1 1.3 - - - -
84A LEU* 1.3 76.7 - - - +
86A PRO* 1.3 65.4 - - + +
88A TYR* 3.2 6.4 + - - +
89A ASP* 2.6 60.7 + - - +
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Residues in contact with PRO 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* 3.2 25.8 - - - +
83A LYS 3.8 7.4 - - - +
84A LEU 3.6 1.6 - - - -
85A LYS* 1.3 94.3 - - + +
87A VAL* 1.3 64.7 + - + +
89A ASP* 3.5 7.5 + - + +
90A SER* 3.2 22.3 + - - -
122A GLN* 4.8 13.8 - - - -
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Residues in contact with VAL 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 LYS 3.7 18.6 - - - +
84A LEU 3.1 3.7 + - - +
86A PRO* 1.3 74.2 - - + +
88A TYR* 1.3 66.3 + - - +
90A SER* 2.6 25.2 + - - +
91A LEU* 3.3 10.9 - - + +
118A LEU* 3.8 39.9 - - + +
121A LEU* 4.0 5.8 - - + -
122A GLN* 4.0 29.2 - - - +
200A 3GY 3.5 29.8 - - + -
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Residues in contact with TYR 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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75A VAL* 4.5 12.8 - - + +
78A ILE* 3.5 27.8 - - + -
79A LEU* 4.1 23.6 - - + -
84A LEU 2.9 16.6 + - - +
85A LYS 3.6 2.7 - - - +
87A VAL* 1.3 76.7 - - - +
89A ASP* 1.3 74.5 + - - +
91A LEU* 3.0 16.6 + - - +
96A ARG* 3.1 69.5 + - + +
99A ALA* 4.2 11.4 - - + -
100A ILE* 3.6 25.6 - - + +
200A 3GY 3.6 9.1 - - + -
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Residues in contact with ASP 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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79A LEU* 4.6 4.0 - - - +
85A LYS* 2.6 56.9 + - - +
86A PRO* 3.9 7.4 - - + +
88A TYR* 1.3 87.4 - - - +
90A SER* 1.3 60.1 + - - +
96A ARG* 3.0 25.0 + - - +
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Residues in contact with SER 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 PRO 3.2 12.5 + - - -
87A VAL* 2.6 24.7 + - - -
89A ASP* 1.3 77.3 - - - +
91A LEU* 1.3 64.7 + - - +
121A LEU 4.6 1.0 + - - -
122A GLN* 4.1 26.4 + - - -
124A LYS* 2.8 27.8 + - - -
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Residues in contact with LEU 91 (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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87A VAL* 3.3 13.9 - - + +
88A TYR* 3.0 12.6 + - - +
89A ASP 4.0 0.3 - - - +
90A SER* 1.3 84.9 - - - +
92A ASP* 1.3 68.5 - - - +
95A ARG* 3.8 31.2 - - + +
96A ARG* 3.0 33.9 + - + +
99A ALA* 4.3 1.8 - - + -
121A LEU* 4.5 12.1 - - + +
124A LYS* 4.4 1.3 - - - +
126A TRP* 3.8 33.7 - - + -
153A PHE* 4.2 5.8 - - + -
200A 3GY 3.8 29.8 - - + -
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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