Contacts of the strand formed by residues 75 - 81 (chain B) in PDB entry 3KTC
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 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B SER 2.9 9.2 + - - +
49B TYR* 3.1 38.7 - - + +
50B VAL* 2.9 26.2 + - - +
69B LEU* 4.9 3.1 - - - -
74B LEU* 1.3 78.1 - - - +
76B ALA* 1.3 63.3 + - - +
118B LEU 5.8 1.8 - - - +
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Residues in contact with ALA 76 (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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49B TYR* 4.4 2.5 - - - -
50B VAL 3.3 6.7 - - - +
52B LEU* 3.5 25.6 - - + -
69B LEU* 4.5 6.7 - - + +
75B LYS* 1.3 75.1 - - - +
77B ILE* 1.3 59.3 + - - +
78B GLY 4.4 0.4 - - - +
79B ILE* 4.4 3.8 - - + -
118B LEU* 4.0 34.7 + - + +
119B GLY 4.2 3.5 - - - +
120B ALA* 3.2 26.8 + - + -
121B ASN* 4.3 0.5 + - - +
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Residues in contact with ILE 77 (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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49B TYR* 3.8 23.1 - - + -
50B VAL 2.9 17.9 + - - +
51B ASP* 4.2 2.2 - - + +
75B LYS 3.5 2.4 + - - -
76B ALA* 1.3 73.5 - - - +
78B GLY* 1.3 60.5 + - - +
120B ALA* 3.8 0.4 - - - -
121B ASN* 2.9 63.4 + - - +
122B TYR* 3.5 25.5 + - + +
266B VAL* 4.0 16.8 - - + -
268B GLN* 3.8 30.7 - - - +
343B EDO 3.8 18.4 - - - +
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Residues in contact with GLY 78 (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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50B VAL 3.9 2.1 + - - +
51B ASP* 3.3 9.3 - - - -
52B LEU* 3.0 22.7 + - - +
76B ALA* 3.5 0.6 - - - +
77B ILE* 1.3 84.2 + - - +
79B ILE* 1.3 71.5 + - - +
120B ALA* 4.1 2.7 - - - -
122B TYR* 3.2 26.7 - - - -
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Residues in contact with ILE 79 (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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52B LEU* 3.3 20.6 - - + +
54B TYR* 3.6 28.9 - - + -
56B PHE* 5.4 1.8 - - + -
76B ALA* 4.4 3.6 - - + -
78B GLY* 1.3 85.4 - - - +
80B THR* 1.3 59.3 + - - +
81B PRO* 3.3 6.1 - - - +
111B SER* 4.0 19.7 - - - +
114B ILE* 3.9 16.4 - - + -
115B VAL* 3.6 28.9 - - + +
118B LEU* 3.9 26.7 - - + -
120B ALA* 4.5 2.9 - - + -
122B TYR 3.2 5.1 + - - -
123B VAL* 3.5 3.1 - - - -
124B LYS* 2.8 28.9 + - - +
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Residues in contact with THR 80 (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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14B TRP* 4.0 3.2 - - - -
51B ASP* 2.6 24.9 + - - -
52B LEU 2.9 10.6 + - - -
53B PRO* 3.2 8.0 - - - +
54B TYR 2.9 21.8 + - - -
79B ILE* 1.3 72.7 - - - +
81B PRO* 1.3 73.1 - - - +
82B GLU* 3.3 2.1 + - - +
84B TYR* 4.0 10.3 - - + +
124B LYS* 2.9 41.3 + - - +
126B TRP* 5.2 2.2 - - + -
337B UNL 3.7 21.5 - - - +
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Residues in contact with PRO 81 (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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54B TYR 3.3 9.2 - - - +
79B ILE 3.3 11.2 - - - +
80B THR* 1.3 86.2 - - - +
82B GLU* 1.3 57.2 + - - +
83B ILE* 2.9 25.0 + - + +
84B TYR* 3.7 7.4 - - - -
107B LEU* 4.2 9.9 - - + -
108B MSE 3.8 29.8 - - + -
111B SER* 3.5 26.5 - - - +
123B VAL* 3.6 13.7 - - + -
124B LYS 3.4 13.4 - - - +
125B VAL* 5.3 3.8 - - + -
126B TRP 5.2 1.0 + - - +
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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