Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 1CK2
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 GLY 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE 3.8 1.2 - - - +
45A ALA* 2.8 53.5 + - - +
77A LEU* 3.6 20.3 - - - +
78A GLY* 4.7 7.0 - - - -
81A VAL* 5.2 5.2 - - - -
86A ARG 3.0 7.4 + - - -
87A VAL* 1.3 65.9 - - - +
89A VAL* 1.3 59.3 + - - -
90A VAL* 3.9 6.3 - - - -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.6 2.8 - - - +
26A GLY* 2.9 35.4 + - - +
27A TYR* 3.3 37.9 - - + +
30A THR* 4.2 6.2 - - + +
43A ILE 3.4 12.8 - - - +
44A ILE* 4.2 11.0 - - + +
46A ALA* 4.4 11.2 - - + +
48A THR* 5.5 1.6 - - + +
56A LEU* 3.5 31.9 - - + -
87A VAL* 2.9 22.9 + - + +
88A GLY* 1.3 71.1 - - - +
90A VAL* 1.3 63.0 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.2 8.5 - - + -
18A ILE* 4.8 1.6 - - + -
23A TYR* 4.9 0.4 - - + -
24A THR 3.4 13.7 - - - +
25A LEU* 3.7 20.9 - - + -
30A THR* 4.5 2.9 + - - -
42A ILE* 3.5 1.0 - - - +
43A ILE* 2.8 35.8 + - + +
77A LEU* 3.5 27.6 - - + -
81A VAL* 3.8 17.0 - - + -
88A GLY 3.8 5.8 - - - +
89A VAL* 1.3 78.5 - - - +
91A SER* 1.3 80.5 + - - +
92A ILE* 4.2 16.4 - - + -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.2 3.3 - - - -
24A THR* 2.8 49.6 + - - +
30A THR* 2.6 24.3 + - - -
34A LEU* 3.9 9.0 - - - -
39A SER* 5.2 1.8 - - - -
41A LEU* 3.2 12.3 - - - -
42A ILE* 3.3 17.0 - - - +
43A ILE 4.6 0.4 - - - +
90A VAL* 1.3 81.9 + - - +
92A ILE* 1.3 68.1 + - - +
93A LEU* 4.3 1.3 - - - -
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Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.2 28.3 - - + -
17A VAL* 4.2 16.4 - - + -
18A ILE* 4.4 4.7 - - + -
22A LYS 3.5 10.8 - - - +
23A TYR* 3.5 25.4 - - + -
39A SER* 3.9 1.8 - - - -
40A LYS* 2.9 24.4 + - - +
41A LEU* 2.8 38.1 + - + +
90A VAL* 4.2 7.0 - - + -
91A SER* 1.3 77.0 - - - +
93A LEU* 1.3 64.5 + - - +
94A GLU 4.3 0.4 - - - +
95A ALA* 4.0 11.7 - - - +
100A ILE* 4.9 4.5 - - + -
101A LEU* 3.5 26.0 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.8 23.3 + - + +
23A TYR 3.9 22.4 - - - +
24A THR* 4.2 12.1 - - + -
33A SER* 4.4 26.5 - - - +
36A GLN* 6.2 1.1 - - + -
38A LYS* 2.7 41.4 + - + +
39A SER* 4.1 11.4 - - - +
40A LYS* 4.3 8.2 - - - +
91A SER* 3.9 5.4 - - - +
92A ILE* 1.3 77.5 - - - +
94A GLU* 1.3 73.0 + - - +
95A ALA 4.2 0.4 - - - -
101A LEU* 5.0 4.5 - - - +
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY* 3.2 1.2 - - - -
22A LYS* 2.6 77.1 + - + +
38A LYS* 2.6 35.5 + - - +
92A ILE* 4.3 2.0 - - - -
93A LEU* 1.3 93.7 - - - +
95A ALA* 1.3 57.4 + - - +
96A GLY* 2.9 14.5 + - - +
101A LEU* 5.1 1.8 - - - -
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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