Contacts of the strand formed by residues 78 - 85 (chain B) in PDB entry 5C14
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 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B LYS* 4.6 2.7 - - - -
51B ASP* 4.2 10.1 - - - -
76B ASP 4.5 0.9 - - - -
77B SER* 1.3 81.9 + - - +
79B THR* 1.3 62.2 + - - -
80B TYR* 4.0 6.1 - - - -
96B TYR 3.7 3.5 - - - +
97B GLN* 2.7 28.7 + - - +
98B LEU* 3.4 13.7 - - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR 3.1 6.2 - - - +
50B LYS* 3.1 3.0 - - - +
51B ASP* 2.6 58.8 + - - -
52B ASP* 4.7 13.3 + - - +
78B GLY* 1.3 69.9 - - - -
80B TYR* 1.3 63.8 + - - +
81B LYS* 5.8 4.0 - - + +
95B GLU* 6.3 2.7 - - + -
96B TYR 4.0 7.4 - - - +
97B GLN* 4.7 7.1 + - - +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 4.1 17.0 - - + -
18B TRP* 4.8 5.6 - + + -
28B LEU* 3.6 26.9 - - + +
49B TYR 3.1 13.0 - - - -
50B LYS* 3.5 19.1 - - + +
55B PHE* 3.4 31.5 - + - -
67B TYR* 5.9 1.6 - + - -
69B ILE* 5.1 6.9 - - + +
76B ASP* 2.8 31.4 + - - +
78B GLY 3.7 8.1 - - - -
79B THR* 1.3 78.3 - - - +
81B LYS* 1.3 62.8 + - - +
94B ALA 4.3 0.5 - - - +
95B GLU* 4.3 0.7 - - - -
96B TYR* 3.0 43.2 + - + +
98B LEU* 3.2 42.8 - - + -
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Residues in contact with LYS 81 (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 MET* 3.4 14.7 - - - +
47B LEU 3.7 0.7 - - - +
48B PHE* 3.7 0.5 - - - -
49B TYR* 3.0 71.2 + - + +
52B ASP* 3.3 27.2 + - - +
79B THR* 5.8 3.6 - - + +
80B TYR* 1.3 77.5 - - - +
82B CYS* 1.3 60.4 + - - +
83B THR* 5.2 3.8 - - + -
92B THR* 4.7 16.0 - - + +
93B THR* 3.7 7.9 - - - +
94B ALA 4.2 11.0 - - - +
95B GLU* 5.9 0.2 - - - -
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Residues in contact with CYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 4.3 1.0 - - - +
12B MET* 3.5 16.0 - - + +
30B CYS* 2.0 49.6 - - - -
46B MET* 3.9 13.2 - - - -
47B LEU 3.3 9.6 - - - +
48B PHE* 4.7 4.3 - - + -
81B LYS* 1.3 69.8 - - - +
83B THR* 1.3 76.6 + - - +
84B VAL 4.1 0.5 + - - -
91B LYS 4.3 0.3 - - - +
92B THR* 3.6 2.8 + - - +
93B THR* 2.4 60.0 + - + +
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Residues in contact with THR 83 (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 GLN 3.5 1.3 - - - +
46B MET* 3.5 2.3 - - - -
47B LEU* 2.8 64.8 + - - +
49B TYR* 4.0 24.7 - - + +
81B LYS* 5.2 4.0 - - + -
82B CYS* 1.3 77.7 - - - +
84B VAL* 1.3 61.1 + - - +
85B ILE* 5.2 4.4 - - - +
90B GLU* 5.1 8.5 - - + -
91B LYS 4.2 1.1 - - - -
92B THR* 2.9 27.8 - - + +
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Residues in contact with VAL 84 (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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7B ILE* 4.0 9.1 - - + +
10B VAL* 3.5 43.3 - - + -
30B CYS* 5.0 2.0 - - - -
32B ALA* 4.8 13.7 - - + -
34B VAL* 6.0 1.3 - - + -
44B HIS* 4.5 15.3 - - + -
45B GLN 3.1 8.7 - - - +
46B MET* 4.2 23.3 - - + -
82B CYS* 4.9 0.9 - - - -
83B THR* 1.3 74.3 - - - +
85B ILE* 1.3 74.4 + - - +
86B VAL* 4.9 4.3 - - + -
90B GLU* 3.6 3.8 - - - +
91B LYS 3.5 20.7 + - - +
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Residues in contact with ILE 85 (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 GLN 6.2 0.2 - - - -
44B HIS* 3.4 4.2 - - - -
45B GLN* 2.7 67.8 + - + +
47B LEU* 5.7 6.5 - - + -
83B THR* 5.2 7.4 - - - +
84B VAL* 1.3 82.7 - - - +
86B VAL* 1.3 87.6 + - - +
87B ASN* 4.9 3.8 - - - +
88B ASN* 5.2 1.3 - - - -
89B LYS 3.5 9.9 - - - +
90B GLU* 3.7 20.6 - - + +
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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