Contacts of the strand formed by residues 53 - 59 (chain B) in PDB entry 4JCQ
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 ILE 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ARG* 3.5 31.6 - - + +
24B VAL* 4.2 11.0 - - + -
42B LEU* 4.3 12.8 - - + +
45B LEU* 3.8 38.8 - - + -
51B ASP 4.0 0.9 - - - +
52B PRO* 1.3 73.7 - - - +
54B THR* 1.3 68.2 + - - +
55B ILE* 4.4 4.3 - - + -
77B ILE* 3.8 21.3 - - + -
79B PRO* 3.8 22.4 - - + -
80B THR 2.9 9.4 + - - +
81B VAL* 3.4 8.2 - - + +
82B LYS* 2.8 34.0 + - - +
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Residues in contact with THR 54 (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 THR 5.4 0.9 + - - -
22B ARG 3.0 10.6 + - - -
23B THR* 3.3 14.5 - - - +
24B VAL 2.9 24.9 + - - +
52B PRO* 5.5 1.4 + - - +
53B ILE* 1.3 75.1 + - - +
55B ILE* 1.3 64.2 + - - +
56B PHE* 3.9 22.7 - - + -
82B LYS* 3.4 17.5 - - + +
84B VAL* 4.0 21.5 - - + -
186B ARG* 5.6 1.9 + - - +
189B LEU* 4.2 20.4 - - + +
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Residues in contact with ILE 55 (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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24B VAL* 3.2 22.4 - - + +
26B ILE* 3.6 32.3 - - + -
38B VAL* 5.5 0.2 - - + -
42B LEU* 4.2 16.2 - - + -
53B ILE* 4.4 5.6 - - + -
54B THR* 1.3 77.2 - - - +
56B PHE* 1.3 59.8 + - - +
57B ILE* 3.7 15.7 + - + +
74B ILE* 3.9 25.6 - - + -
81B VAL* 3.6 26.9 - - + -
82B LYS 2.8 13.3 + - - +
83B VAL* 3.3 8.2 - - + +
84B VAL 2.7 32.2 + - - -
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Residues in contact with PHE 56 (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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43A LEU* 4.5 10.8 - - + -
73A MET* 3.9 26.5 - - + -
76A PHE* 3.8 31.0 - + - -
23B THR* 3.6 31.6 - - + -
24B VAL 3.0 6.9 + - - -
25B LEU* 3.6 18.1 - - + -
26B ILE* 2.8 27.7 + - - +
27B TYR* 3.6 15.4 - - + +
54B THR* 3.9 19.3 - - + -
55B ILE* 1.3 72.1 - - - +
57B ILE* 1.3 62.1 + - - +
84B VAL* 3.3 34.5 - - + +
86B THR* 4.5 5.4 - - + -
108B LEU* 4.5 7.0 - - + -
186B ARG* 5.3 2.7 - - - -
189B LEU* 5.3 0.2 - - + -
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Residues in contact with ILE 57 (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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26B ILE* 3.4 19.5 - - + +
30B ILE* 5.9 0.2 - - + -
55B ILE* 3.7 16.4 - - + +
56B PHE* 1.3 76.2 - - - +
58B ASN* 1.3 61.7 + - - +
59B SER* 4.2 17.7 - - - +
83B VAL* 3.9 20.2 - - + -
84B VAL 2.9 12.1 + - - +
85B GLY* 4.9 0.9 - - - -
86B THR* 2.9 29.4 + - - +
89B VAL* 3.6 18.7 - - + +
93B GLY* 4.4 13.7 - - - +
96B ILE* 4.0 15.5 - - + -
97B TYR* 3.8 35.4 - - + -
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Residues in contact with ASN 58 (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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32A GLN* 3.3 16.5 + - - +
35A ALA* 5.5 0.8 - - - +
65A GLU* 3.2 20.4 + - - +
66A ALA* 4.4 3.8 - - - +
69A THR* 2.6 31.5 + - - +
26B ILE 2.9 7.5 + - - -
27B TYR* 3.2 21.5 - - + -
28B GLY 2.9 23.9 + - - -
57B ILE* 1.3 71.4 - - - +
59B SER* 1.3 59.2 + - - +
86B THR* 3.1 18.2 + - + +
87B GLY* 3.9 0.6 - - - -
88B TRP* 3.1 22.1 - - - -
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Residues in contact with SER 59 (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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26B ILE 4.4 2.7 - - - -
28B GLY 2.7 22.9 + - - -
30B ILE* 3.3 23.8 - - - +
57B ILE* 4.0 15.7 - - - +
58B ASN* 1.3 74.7 + - - +
60B GLN* 1.3 60.9 + - - +
61B GLY 3.1 15.6 + - - -
88B TRP* 2.8 19.3 + - - +
89B VAL* 3.4 1.4 - - - -
90B ALA 2.9 25.5 + - - +
93B GLY* 4.5 4.8 - - - -
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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