Contacts of the strand formed by residues 63 - 69 (chain G) 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 TYR 63 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G ILE* 2.8 20.2 + - + +
60G ILE* 3.0 29.1 + - - +
62G ASP* 1.3 86.9 - - + +
64G LYS* 1.3 62.4 + - - +
65G VAL* 3.7 5.6 + - + +
81G ILE* 3.6 24.9 - - + -
82G PHE 3.3 5.6 - - - +
83G ASN* 3.7 29.3 + - + -
84G LYS* 3.8 3.4 - - - +
85G ARG* 5.4 2.0 - - - -
90G PHE* 4.1 18.9 - + - -
121G VAL* 3.7 13.0 - - - +
122G ASP* 3.1 21.8 + - - -
124G TYR* 3.2 38.6 - + - -
137G VAL* 4.0 20.7 - - + +
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G TYR* 1.3 71.6 - - - +
65G VAL* 1.3 69.8 + - - +
66G THR* 3.8 8.4 + - + -
81G ILE* 3.4 3.3 - - - +
82G PHE* 2.7 70.9 + - + +
84G LYS* 3.8 16.7 - - + +
87G GLN* 4.3 15.6 + - - -
44H PRO* 5.6 8.5 - - + -
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Residues in contact with VAL 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ILE* 4.5 18.6 - - + -
60G ILE* 4.8 6.0 - - + +
63G TYR* 3.7 11.0 + - + +
64G LYS* 1.3 77.7 - - - +
66G THR* 1.3 76.0 + - - +
79G LEU* 4.8 6.3 - - + -
81G ILE* 3.6 22.0 - - + -
92G LEU* 4.4 13.7 - - + -
44H PRO* 3.9 23.1 - - - +
45H GLN* 3.7 41.3 + - + +
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Residues in contact with THR 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LYS* 3.8 12.5 + - + -
65G VAL* 1.3 90.6 - - - +
67G SER* 1.3 61.2 + - - +
68G GLN* 3.1 22.1 + - - +
79G LEU* 4.1 10.0 - - - +
80G GLN* 3.0 24.1 + - - +
82G PHE* 3.5 34.5 - - + -
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Residues in contact with SER 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F HIS* 5.4 9.0 - - - +
66G THR* 1.3 74.5 - - - +
68G GLN* 1.3 60.4 + - - +
69G VAL* 2.9 14.9 + - - +
79G LEU* 3.5 15.3 - - - +
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Residues in contact with GLN 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G THR* 3.1 14.6 + - - +
67G SER* 1.3 73.8 - - - +
69G VAL* 1.3 71.8 + - - +
70G LEU* 5.8 0.9 - - + -
79G LEU* 3.4 1.7 - - - -
80G GLN* 2.6 52.3 + - + +
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Residues in contact with VAL 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G SER 2.9 11.6 + - - +
68G GLN* 1.3 87.9 + - - +
70G LEU* 1.3 67.6 + - - +
71G GLY* 3.6 9.4 - - - +
72G LEU* 3.3 49.1 - - + +
77G LYS* 5.4 0.9 - - + -
78G VAL 3.5 7.0 - - - +
79G LEU* 3.8 16.4 - - + -
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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