Contacts of the helix formed by residues 82 - 86 (chain B) in PDB entry 4JDL
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 ASN 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 4.0 30.1 - - - +
79B ARG* 2.9 34.2 + - - +
81B ASP* 1.3 79.0 + - + +
83B PRO* 1.3 62.1 - - - +
84B LYS* 3.0 31.1 - - - +
85B VAL* 2.7 39.7 + - - +
92B GLN* 4.7 3.4 - - - +
93B CYS* 4.0 19.7 + - - +
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Residues in contact with PRO 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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79B ARG 4.0 11.1 - - - +
80B PHE 4.3 0.9 - - - +
81B ASP 4.1 0.2 - - - -
82B ASN* 1.3 80.3 - - - +
84B LYS* 1.3 52.4 + - - +
85B VAL* 3.0 6.9 - - + +
86B TYR* 2.8 12.4 + - + -
87B LYS* 2.4 51.4 + - + +
90B ILE* 3.8 24.7 - - + -
93B CYS* 3.0 30.1 - - + -
107B ARG* 3.3 29.6 - - - +
109B VAL* 5.6 1.1 - - + -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 3.1 37.6 + - - +
84A LYS* 6.3 0.9 - - + -
92A GLN* 5.4 9.0 - - - +
82B ASN* 3.0 26.4 - - - +
83B PRO* 1.3 78.3 - - - +
85B VAL* 1.3 63.9 + - - +
86B TYR* 3.1 3.1 + - - +
87B LYS 3.2 25.4 + - - +
88B ASN* 4.7 12.4 + - - +
89B PHE 5.0 1.5 - - - +
90B ILE* 3.0 33.8 - - + +
91B ARG 5.5 1.1 - - - -
92B GLN 6.0 0.2 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 5.6 3.6 + - - -
82A ASN* 4.2 7.1 - - - +
85A VAL* 4.0 32.6 - - + +
76B LEU* 3.4 35.4 - - + +
79B ARG* 3.2 37.7 - - + +
82B ASN* 2.7 27.1 + - + +
83B PRO* 3.0 1.3 - - + +
84B LYS* 1.3 79.3 - - - +
86B TYR* 1.3 71.1 + - + +
195B SER 5.5 0.5 - - - +
198B ARG* 5.5 2.9 + - - -
199B SER* 5.8 0.5 + - - -
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Residues in contact with TYR 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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76B LEU* 5.5 1.1 - - + -
77B VAL* 3.7 38.9 - - + +
79B ARG 5.7 2.0 - - - -
83B PRO* 2.8 9.9 + - + -
84B LYS* 4.1 4.5 + - - +
85B VAL* 1.3 93.4 - - + +
87B LYS* 1.3 89.9 + - + +
88B ASN* 3.3 3.6 + - - -
134B ILE* 4.8 3.1 - - - +
136B PHE* 4.8 11.3 - - - -
152B THR* 4.3 11.6 + - - +
166B GLU* 5.6 0.2 + - - -
192B ASN* 3.5 18.1 - - + +
193B LEU* 3.5 30.9 - - + +
195B SER* 3.8 22.5 - - - +
196B LEU* 3.8 35.2 - - + -
198B ARG* 6.0 0.2 - - - +
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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