Contacts of the helix formed by residues 44 - 51 (chain B) in PDB entry 5JKC
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 TYR 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 3.4 22.8 - - + +
160A ARG* 3.1 27.2 + - - -
163A TYR* 4.4 16.4 - + + -
241A SER* 2.9 36.6 - - - -
242A PRO 4.8 7.9 + - - -
42B LYS* 5.7 2.5 - - - +
43B LEU* 1.3 71.3 - - - +
45B GLU* 1.3 82.2 + - + +
46B GLU 3.0 1.0 + - - -
47B CYS* 2.9 17.2 + - - +
58B LEU* 4.4 5.6 - - + +
61B SER* 3.0 18.1 + - - +
62B TRP* 3.8 42.8 - + + +
65B HIS* 3.4 36.1 - + - -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 6.1 0.5 - - - +
160A ARG* 4.1 8.4 + - - +
239A ASN* 3.5 27.4 - - - +
240A SER* 3.4 19.7 + - - -
241A SER* 3.0 34.5 + - - +
43B LEU 3.6 3.6 + - - -
44B TYR* 1.3 91.9 + - + +
46B GLU* 1.3 70.9 + - + +
48B ILE* 3.0 41.5 + - - +
49B PRO* 4.4 0.7 - - - +
65B HIS* 3.3 13.9 - - + +
210B TRP* 5.8 0.9 - - - -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 6.2 0.2 - - - +
44B TYR 3.0 1.2 + - - -
45B GLU* 1.3 88.0 - - + +
47B CYS* 1.3 55.8 + - - +
48B ILE 3.3 0.4 - - - -
49B PRO* 3.1 7.6 - - - +
50B TRP* 3.5 3.5 - - - -
65B HIS* 3.3 18.4 + - + +
88B LYS* 3.6 35.4 + - + +
91B ILE* 3.9 17.9 - - + -
92B GLN* 2.9 38.0 + - + -
95B CYS* 3.5 11.9 - - - -
210B TRP* 2.9 35.6 + - - +
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Residues in contact with CYS 47 (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 LEU* 3.2 17.3 - - + +
44B TYR 2.9 9.5 + - - +
46B GLU* 1.3 74.9 - - - +
48B ILE* 1.3 62.6 + - - +
49B PRO* 3.2 4.3 - - - -
50B TRP* 3.2 19.4 + - - -
61B SER* 3.7 40.8 - - - -
64B ALA* 4.6 3.4 - - - -
65B HIS* 4.1 0.9 - - - -
95B CYS* 2.0 54.5 - - + -
98B GLU* 6.2 0.2 - - - -
99B CYS* 3.9 12.6 - - - -
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Residues in contact with ILE 48 (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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240A SER* 3.1 29.8 - - - +
241A SER* 5.5 1.3 - - - +
43B LEU* 3.1 29.2 - - + +
44B TYR 4.0 0.4 + - - -
45B GLU 3.0 25.3 + - - +
47B CYS* 1.3 76.6 - - - +
49B PRO* 1.3 69.1 - - + +
50B TRP 3.0 1.6 + - - -
51B LYS* 3.0 37.7 + - + +
213B PRO* 4.1 20.8 - - + +
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Residues in contact with PRO 49 (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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45B GLU 4.4 0.4 - - - +
46B GLU 3.1 14.6 - - - +
47B CYS 3.2 2.5 - - - -
48B ILE* 1.3 94.4 - - + +
50B TRP* 1.3 68.0 + - + +
51B LYS 3.4 0.7 + - - -
52B ASP* 4.1 14.9 - - - +
210B TRP* 3.5 23.3 - - + +
211B PHE* 3.3 59.1 - - + +
213B PRO* 4.1 19.6 - - + +
217B ASN* 5.2 1.0 + - - +
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Residues in contact with TRP 50 (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 LEU* 3.9 2.9 - - + -
46B GLU 3.5 21.8 - - - -
47B CYS* 3.2 19.4 + - - +
48B ILE 3.0 1.2 + - - -
49B PRO* 1.3 83.2 - - + +
51B LYS* 1.3 63.6 + - - +
52B ASP* 3.2 4.0 - - - -
53B ASN 3.1 24.3 + - - +
54B ALA* 3.3 6.0 - - + +
95B CYS* 3.7 14.8 - - + -
96B PHE* 3.8 26.5 - + - -
99B CYS* 3.6 25.1 - - + +
100B SER* 3.9 20.0 - - - +
101B PRO* 4.1 6.7 - - + -
209B LYS 3.1 28.3 - - - -
210B TRP* 4.1 10.8 - + - -
211B PHE* 3.8 23.1 - + - -
217B ASN* 4.5 3.1 - - - +
302B CL 3.1 28.5 - - + +
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Residues in contact with LYS 51 (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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38B SER 4.6 0.2 - - - +
39B PRO* 3.3 2.3 - - - +
40B GLU* 2.8 46.3 + - - +
41B ASP* 2.8 30.9 + - - +
42B LYS* 4.1 8.1 - - - +
43B LEU* 3.6 27.2 - - + +
48B ILE* 3.0 37.3 + - + +
49B PRO 3.4 0.6 - - - -
50B TRP* 1.3 77.3 - - - +
52B ASP* 1.3 69.9 + - - +
53B ASN 3.3 0.5 + - - -
54B ALA* 4.7 0.6 + - - -
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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