Contacts of the strand formed by residues 52 - 58 (chain C) in PDB entry 2CKJ
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 THR 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C THR* 4.3 3.8 - - - +
49C GLY* 2.7 22.4 + - - -
50C ALA 3.4 1.6 - - - -
51C CYS* 1.4 77.9 - - - +
53C VAL* 1.3 74.9 + - - +
69C SER* 4.7 4.5 - - - -
70C ALA 3.9 7.4 - - - +
71C ASN* 4.5 2.8 - - - +
88C VAL 5.6 0.7 + - - -
118C PRO 5.4 0.2 - - - -
119C GLY* 4.0 16.7 + - - +
122C MET* 3.5 34.0 - - + +
123C SER* 4.2 10.3 - - - +
146C ASN* 4.1 0.7 + - - -
341C GLN* 3.1 30.7 + - + +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.2 12.1 - - + -
30C LEU* 4.6 11.7 - - + -
39C THR* 3.6 25.8 - - + +
52C THR* 1.3 80.9 - - - +
54C MET* 1.3 62.3 + - - +
55C LEU* 4.6 12.3 - - + -
69C SER* 3.4 7.6 - - - -
70C ALA* 3.1 37.2 + - + +
71C ASN 4.9 0.2 - - - -
72C ALA* 3.7 22.9 - - + -
85C VAL* 4.7 4.0 - - + -
86C THR 3.8 12.1 - - - +
87C THR* 4.7 6.3 - - - +
88C VAL 5.6 0.7 - - - +
122C MET* 4.4 8.2 - - + +
126C THR* 5.0 0.3 + - - -
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Residues in contact with MET 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 1.3 78.4 - - - +
55C LEU* 1.3 67.3 + - - +
56C SER* 3.3 26.3 + - - +
67C HIS* 3.6 19.3 - - + +
68C PHE 3.6 10.1 - - - +
84C ALA 3.5 1.7 - - - +
85C VAL* 3.5 3.5 - - - -
86C THR* 2.9 57.1 + - - +
122C MET* 3.9 10.7 - - + +
125C TYR* 4.1 21.3 - - + -
126C THR* 3.5 36.6 - - + +
129C ARG* 4.3 22.9 - - - +
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Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 4.9 2.2 - - + -
53C VAL* 4.6 9.2 - - + -
54C MET* 1.3 78.0 - - - +
56C SER* 1.3 59.6 + - - +
67C HIS* 3.6 1.2 - - - -
68C PHE* 2.9 68.4 + - + -
70C ALA* 4.1 19.7 - - + -
75C ALA* 6.0 4.7 - - + -
80C LEU* 4.0 33.2 - - + -
83C VAL* 4.5 13.2 - - + -
84C ALA 4.0 1.6 - - - -
85C VAL* 4.1 22.7 - - + -
345C VAL* 5.7 3.4 - - + -
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Residues in contact with SER 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C MET* 3.3 15.8 + - - +
55C LEU* 1.3 71.6 - - - +
57C LYS* 1.3 63.8 + - - +
66C VAL 3.1 5.6 - - - -
67C HIS* 2.8 37.9 + - - -
83C VAL* 3.6 1.9 - - - +
84C ALA* 3.1 39.2 + - - +
86C THR* 4.5 3.1 + - - -
129C ARG* 5.4 0.5 + - - -
212C PHE* 4.3 14.3 - - - -
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C SER* 1.3 77.4 - - - +
58C TYR* 1.3 70.9 + - - +
59C ASP* 3.4 9.9 + - - +
65C ILE* 3.7 1.9 - - - +
66C VAL* 2.8 48.7 + - + +
68C PHE* 4.4 20.9 - - + -
82C HIS 5.3 2.2 - - - +
83C VAL* 4.4 24.9 - - + +
212C PHE* 4.0 11.8 - - - -
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C LYS* 1.3 79.0 - - - +
59C ASP* 1.3 66.2 + - - +
60C ARG* 3.8 32.7 + - + +
63C ASN* 2.6 49.9 + - - +
64C LYS 3.7 12.1 - - - -
65C ILE* 4.5 7.0 - - + +
82C HIS 5.5 2.8 + - - -
212C PHE* 3.7 21.6 - - + -
216C LEU* 6.0 1.6 - - + -
217C LEU* 4.3 16.8 - - + +
220C LYS* 3.7 51.1 - - + -
224C ARG* 5.6 3.6 + - - -
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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