Contacts of the strand formed by residues 64 - 68 (chain N) in PDB entry 7K63
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 64 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55N TYR* 3.3 4.0 - - - -
56N GLN* 2.6 74.9 + - + +
58N LYS* 4.7 9.0 - - + +
62N SER 3.5 3.3 + - - +
63N PRO* 1.3 73.5 - - - +
65N THR* 1.3 64.9 + - - +
66N LEU* 4.2 16.0 - - + +
75N ASP 6.0 0.2 + - - -
76N GLY 5.8 1.0 + - - -
77N VAL* 4.8 12.9 - - - +
257N ASP 5.2 1.3 - - - -
259N TRP* 5.0 1.3 - - - -
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Residues in contact with THR 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N TRP 3.7 5.0 + - - -
55N TYR* 3.6 27.5 - - - -
63N PRO 4.4 0.2 + - - -
64N LYS* 1.3 82.0 + - - +
66N LEU* 1.3 66.2 + - - +
67N ILE 3.8 9.2 + - - -
68N TYR* 4.8 0.3 - - - +
74N ALA* 3.5 22.4 - - + +
77N VAL* 4.8 1.4 - - - +
255N THR* 3.6 18.5 - - + +
256N LEU 3.9 2.9 - - - -
257N ASP* 3.6 34.6 + - + +
259N TRP* 5.0 0.2 - - - +
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Residues in contact with LEU 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TRP* 2.8 13.0 + - + +
55N TYR 4.2 2.5 - - - +
56N GLN* 3.6 40.4 - - + +
64N LYS* 4.2 13.2 - - + +
65N THR* 1.3 79.7 - - - +
67N ILE* 1.3 70.9 + - + +
74N ALA* 2.8 27.5 + - - +
77N VAL* 3.4 32.9 - - + +
81N PHE* 3.7 28.0 - - + -
92N LEU* 4.9 6.1 - - + -
105N TYR* 3.6 25.4 - - + -
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Residues in contact with ILE 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53N SER* 3.2 6.3 - - - -
54N TRP* 2.9 42.1 + - + +
65N THR* 3.8 4.2 + - - -
66N LEU* 1.3 88.5 - - + +
68N TYR* 1.3 65.1 + - - +
70N ALA* 3.6 35.2 - - - +
71N THR 3.7 2.9 - - - +
72N SER 3.2 11.4 - - - +
73N LEU* 3.6 27.6 - - + -
81N PHE* 3.9 12.6 - - + +
83N GLY* 4.0 13.5 - - - +
92N LEU* 3.8 24.7 - - + -
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Residues in contact with TYR 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H LYS* 3.6 29.0 - - - -
109H HIS* 3.7 27.6 + + - -
112H SER* 4.2 13.3 + - - -
53N SER* 3.8 5.2 - - - -
65N THR* 4.8 0.7 - - - +
67N ILE* 1.3 75.3 - - - +
69N TYR* 1.3 67.3 + - + +
70N ALA 3.0 6.2 + - - +
72N SER* 2.8 59.9 + - - +
73N LEU 3.5 23.6 - - - -
74N ALA* 4.4 8.5 - - + -
253N ARG* 3.6 26.7 + - - +
254N SER* 4.9 3.1 - - - -
255N THR* 3.6 30.7 - - + -
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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