Contacts of the strand formed by residues 78 - 83 (chain J) in PDB entry 3KC3
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 VAL 78 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69J VAL* 3.6 2.6 - - - -
70J LEU* 2.7 45.3 + - + +
71J GLY 2.9 17.3 + - - +
77J LYS* 1.3 79.3 - - - +
79J LEU* 1.3 60.4 - - - +
91J ALA* 4.2 5.6 - - + -
92J LEU 3.3 22.9 - - - +
93J LYS* 4.0 18.8 - - + -
138J MET* 4.1 9.2 - - + -
500J MK2 3.6 47.8 - - + +
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J VAL* 4.7 7.9 - - + -
66J THR 3.4 24.5 - - - +
67J SER* 4.1 13.9 - - - +
68J GLN 3.5 10.8 - - - +
69J VAL* 4.0 21.1 - - + -
70J LEU* 4.4 2.9 - - - -
77J LYS* 4.5 17.7 - - + +
78J VAL* 1.3 85.0 - - - +
80J GLN* 1.3 63.7 + - - +
81J ILE* 4.4 1.6 - - + -
91J ALA* 3.8 3.5 - - - -
92J LEU* 2.9 49.1 + - + +
94J MET* 6.0 4.7 - - - -
45K GLN* 6.3 1.6 - - + -
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Residues in contact with GLN 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66J THR* 3.1 27.0 + - - +
68J GLN* 3.1 45.5 + - + +
70J LEU* 3.8 28.1 - - + +
79J LEU* 1.3 73.7 - - - +
81J ILE* 1.3 70.1 + - - +
82J PHE* 3.2 40.5 - - - -
89J LYS* 3.8 28.9 - - - +
90J PHE 3.8 5.3 - - - +
140J CYS* 4.7 5.4 - - - -
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Residues in contact with ILE 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J ILE* 4.9 0.7 - - + -
63J TYR* 3.4 35.2 - - + -
64J LYS 3.1 12.3 - - - +
65J VAL* 3.7 25.1 - - + -
79J LEU 4.0 1.1 - - - +
80J GLN* 1.3 84.5 + - - +
82J PHE* 1.3 71.1 + - - +
89J LYS* 3.6 1.9 - - - -
90J PHE* 2.8 54.5 + - + +
91J ALA 4.3 0.2 - - - +
92J LEU* 3.7 31.0 - - + +
137J VAL* 4.1 19.1 - - + -
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Residues in contact with PHE 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J TYR* 3.5 7.0 - - - -
64J LYS* 2.8 54.8 + - + +
66J THR* 3.4 28.7 - - + -
68J GLN* 5.3 1.6 - - - -
80J GLN* 3.2 33.4 - - - -
81J ILE* 1.3 82.4 - - - +
83J ASN* 1.3 67.6 - - - +
87J GLN* 4.1 33.0 - - + +
88J GLU 3.0 10.8 - - - +
89J LYS* 4.4 12.6 - - + -
90J PHE 4.7 0.4 - - - +
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Residues in contact with ASN 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J ASP* 3.7 11.4 + - - +
63J TYR* 3.9 23.4 - - + -
64J LYS* 5.7 0.2 - - - -
82J PHE* 1.3 74.2 - - - +
84J LYS* 1.3 67.2 + - - +
85J ARG* 3.2 40.9 - - - +
86J THR* 2.5 43.8 + - - +
87J GLN* 3.0 32.1 + - - -
88J GLU 2.8 12.1 + - - +
90J PHE* 4.5 9.6 - - + -
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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