Contacts of the strand formed by residues 37 - 44 (chain B) in PDB entry 1CKJ
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 GLU 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.8 6.7 - - + -
29B GLY 3.6 8.1 - - - +
30B THR* 4.8 3.4 - - - +
35B GLY 3.7 2.0 + - - +
36B GLU* 1.3 82.5 - - - +
38B VAL* 1.3 62.4 + - - +
72B ARG* 5.8 1.0 + - - -
86B GLU* 5.2 0.3 - - - -
87B LEU* 3.4 40.0 + - + +
143B LEU* 4.4 21.2 - - + +
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Residues in contact with VAL 38 (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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12B TYR* 3.8 21.3 - - + -
28B LEU* 4.1 2.3 - - - -
29B GLY* 3.0 42.2 + - - +
30B THR 4.1 0.2 - - - +
31B ASP* 4.5 0.9 - - + +
36B GLU* 3.9 28.9 - - + +
37B GLU* 1.3 79.0 - - - +
39B ALA* 1.3 60.8 + - - +
40B ILE* 4.2 4.0 - - + -
72B ARG* 4.5 9.0 - - + +
84B VAL* 3.6 25.8 - - + -
85B MET 3.7 11.4 - - - +
86B GLU* 5.1 1.6 - - - -
87B LEU* 3.8 18.0 - - - +
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Residues in contact with ALA 39 (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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18B ILE* 5.2 0.4 - - + -
26B ILE* 4.2 17.5 - - + -
27B TYR 3.8 4.0 - - - -
28B LEU* 5.2 0.4 - - - +
38B VAL* 1.3 75.6 - - - +
40B ILE* 1.3 62.6 + - - +
84B VAL* 3.4 2.6 - - - -
85B MET* 2.8 57.2 + - + +
86B GLU 4.4 0.9 - - - +
87B LEU* 4.0 24.7 - - + +
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Residues in contact with ILE 40 (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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8B VAL* 4.7 7.6 - - + -
12B TYR* 3.9 23.6 - - + -
13B ARG 4.4 2.0 - - - +
14B LEU* 3.9 27.1 - - + -
25B ASP 3.4 1.4 - - - +
26B ILE* 3.2 6.8 - - - -
27B TYR* 2.7 46.8 + - - +
29B GLY* 3.9 22.9 - - - -
38B VAL* 4.2 4.3 - - + -
39B ALA* 1.3 77.2 - - - +
41B LYS* 1.3 62.2 + - - +
42B LEU* 3.4 26.0 + - + -
82B VAL* 3.6 17.0 - - + -
83B MET 3.8 1.8 - - - -
84B VAL* 4.2 11.7 - - + -
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Residues in contact with LYS 41 (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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21B GLY* 4.4 3.2 - - - -
22B SER 4.2 9.7 - - - +
23B PHE* 3.5 26.0 - - - -
24B GLY* 4.3 16.8 - - - +
25B ASP 3.5 4.3 - - - +
26B ILE* 3.8 27.4 - - + -
39B ALA 4.1 0.2 + - - -
40B ILE* 1.3 72.7 - - - +
42B LEU* 1.3 74.5 + - - +
52B LEU* 4.0 14.4 - - + +
55B GLU* 2.6 35.2 + - - +
81B ASN 3.7 0.3 - - - +
82B VAL* 3.6 1.4 - - - -
83B MET* 2.9 58.4 + - + +
85B MET* 6.0 2.9 - - + -
154B ASP* 4.7 4.8 + - - -
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Residues in contact with LEU 42 (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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8B VAL* 5.2 6.7 - - + -
14B LEU* 4.5 18.4 - - + -
24B GLY* 3.5 24.1 - - - -
25B ASP* 3.2 16.1 + - + +
27B TYR* 4.1 27.4 - - + -
40B ILE* 3.4 22.4 - - + -
41B LYS* 1.3 90.3 - - - +
43B GLU* 1.3 60.7 + - - +
52B LEU* 5.1 0.7 - - - -
80B TYR* 3.9 42.6 - - + -
81B ASN 3.6 3.1 - - - +
82B VAL* 3.7 15.9 - - + -
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Residues in contact with GLU 43 (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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23B PHE* 3.7 20.8 - - + +
42B LEU* 1.3 76.2 - - - +
44B CYS* 1.3 72.6 + - - +
47B THR* 3.9 9.9 - - + +
49B HIS 4.2 1.9 - - - +
50B PRO* 3.4 19.9 - - - +
51B GLN 2.8 27.8 + - - -
52B LEU* 3.1 34.4 + - + +
53B HIS* 4.9 1.9 + - - -
80B TYR* 3.2 4.8 - - - -
81B ASN* 2.7 54.8 + - + +
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Residues in contact with CYS 44 (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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43B GLU* 1.3 78.6 - - - +
45B VAL* 1.3 65.4 + - - +
46B LYS* 3.9 24.5 - - - +
47B THR* 2.7 31.4 + - - +
50B PRO* 6.0 0.2 - - - +
79B ASP* 3.3 35.7 - - - -
80B TYR* 3.4 22.2 - - + -
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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