Contacts of the strand formed by residues 63 - 71 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59L ILE* 2.8 33.4 + - + +
60L ILE* 3.3 26.5 - - - +
61L ASP 3.7 0.6 - - - -
62L ASP* 1.3 87.3 - - + +
64L LYS* 1.3 58.2 + - - +
65L VAL* 3.6 5.8 + - + +
81L ILE* 3.6 26.5 - - + -
82L PHE 3.0 18.4 - - - +
83L ASN* 3.6 24.6 + - + +
84L LYS* 4.3 4.5 - - - +
90L PHE* 4.2 13.0 - + - -
121L VAL* 4.0 6.8 - - - +
122L ASP* 2.8 21.2 + - - -
124L TYR* 3.0 30.5 - + - -
137L VAL* 3.8 25.1 - - + +
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Residues in contact with LYS 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J GLN* 5.4 8.3 - - - +
60L ILE* 6.0 0.2 - - - -
63L TYR* 1.3 69.5 - - - +
65L VAL* 1.3 66.6 + - - +
66L THR* 3.3 21.7 + - - +
81L ILE* 3.4 0.6 - - - -
82L PHE* 2.7 44.9 + - + +
83L ASN 5.6 0.2 - - - +
84L LYS* 4.4 20.7 - - + +
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Residues in contact with VAL 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J PHE* 3.6 43.1 - - + +
45J GLN* 4.6 12.5 + - - +
59L ILE* 5.0 11.2 - - + -
60L ILE* 4.9 12.1 - - + +
63L TYR* 3.6 12.9 + - + +
64L LYS* 1.3 77.0 - - - +
66L THR* 1.3 72.9 + - - +
79L LEU* 4.3 4.0 - - + -
81L ILE* 3.9 26.7 - - + -
92L LEU* 4.0 18.8 - - + -
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Residues in contact with THR 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J PHE* 4.1 3.4 - - - +
64L LYS* 4.2 15.3 - - - +
65L VAL* 1.3 90.8 - - - +
67L SER* 1.3 65.7 + - - +
68L GLN* 3.3 17.9 + - - +
79L LEU* 4.2 5.6 - - - +
80L GLN* 3.0 27.7 + - - +
82L PHE* 3.7 33.2 - - + -
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Residues in contact with SER 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J PHE* 3.3 33.0 + - - -
66L THR* 1.3 80.3 + - - +
68L GLN* 1.3 62.3 + - - +
69L VAL* 3.5 6.8 + - - +
79L LEU* 3.9 15.2 - - - +
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Residues in contact with GLN 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L THR* 3.3 10.4 + - - +
67L SER* 1.3 79.6 - - - +
69L VAL* 1.3 87.4 + - - +
70L LEU* 3.4 19.8 - - - +
79L LEU* 3.5 4.1 - - - -
80L GLN* 3.1 38.8 + - + +
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Residues in contact with VAL 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67L SER 3.5 7.8 + - - +
68L GLN* 1.3 94.7 + - - +
70L LEU* 1.3 63.2 + - - +
71L GLY 3.5 23.8 - - - +
72L LEU* 3.9 26.0 - - + -
77L LYS* 4.5 11.2 - - + -
78L VAL 3.3 16.8 - - - +
79L LEU* 4.3 9.4 - - + -
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Residues in contact with LEU 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLN* 3.4 20.2 - - - +
69L VAL* 1.3 75.3 - - - +
71L GLY* 1.3 59.8 + - - +
72L LEU* 5.6 2.5 - - - +
78L VAL* 2.8 30.0 + - + +
79L LEU 4.3 6.3 - - - +
80L GLN* 4.1 26.5 - - + +
91L ALA* 3.9 17.9 - - + -
140L CYS* 4.4 15.0 - - - -
142L ASP* 6.3 0.9 - - + -
500L MK2 3.4 61.4 - - + +
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Residues in contact with GLY 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L VAL* 3.5 3.8 - - - +
70L LEU* 1.3 82.3 - - - +
72L LEU* 1.3 66.0 + - - +
77L LYS 3.7 0.3 - - - -
78L VAL* 2.7 36.5 + - - +
500L MK2 3.8 25.8 - - - -
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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