Contacts of the strand formed by residues 69 - 76 (chain B) in PDB entry 5I0X
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 THR 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B TYR 3.8 0.8 + - - -
68B LEU* 1.3 75.6 + - - +
70B ILE* 1.3 63.7 + - - +
71B SER* 4.2 1.3 - - - -
86B THR* 5.3 9.2 - - + -
115B HIS 3.4 3.8 - - - +
116B ILE* 3.5 1.4 - - - -
117B GLU* 2.9 63.3 + - - +
118B PRO 5.0 0.2 + - - -
121B LYS* 4.5 9.0 - - - +
122B ALA* 4.0 18.9 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.3 2.9 - - + -
49B ILE* 3.5 32.8 - - + -
68B LEU* 4.0 13.4 + - + -
69B THR* 1.3 81.2 - - - +
71B SER* 1.3 70.6 + - - +
86B THR* 3.3 9.2 - - - +
87B PHE* 3.0 51.8 + - + +
98B TYR* 3.6 33.6 - - + -
114B TYR* 4.1 18.2 - - + -
115B HIS 3.3 6.5 - - - +
116B ILE* 4.2 9.9 - - + -
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B THR* 4.2 1.3 - - - -
70B ILE* 1.3 78.1 - - - +
72B TYR* 1.3 61.8 + - - +
85B GLY 3.4 13.5 - - - -
86B THR* 3.8 12.6 - - - +
87B PHE* 5.8 0.4 - - - -
114B TYR* 3.4 4.5 - - - -
115B HIS* 2.8 53.3 + - - +
117B GLU* 5.3 4.9 + - - -
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.1 1.8 - - + -
71B SER* 1.3 76.5 - - - +
73B THR* 1.3 63.4 + - - +
74B LEU* 3.9 23.3 - - + -
83B GLN* 2.6 40.5 + - - -
84B GLU* 3.2 9.2 + - - +
85B GLY* 2.8 73.5 + - - +
86B THR 3.7 4.5 - - - -
87B PHE* 3.6 26.7 - + + -
100B ALA* 4.9 0.7 - - + -
102B ILE* 3.1 30.1 - - + +
112B VAL* 4.1 8.1 - - + -
113B THR 3.1 9.4 - - - +
114B TYR* 4.0 17.3 - - + -
115B HIS* 4.1 1.8 - - - -
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 1.3 71.2 - - - +
74B LEU* 1.3 61.4 + - - +
75B VAL* 4.2 9.8 - - + +
82B LYS* 3.8 23.3 - - + -
83B GLN 3.4 3.1 - - - -
84B GLU* 2.7 33.9 + - - +
111B LYS 3.8 1.4 - - - +
112B VAL* 3.4 2.4 - - - -
113B THR* 2.9 39.9 + - - +
115B HIS* 2.8 26.9 + - - -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 5.2 5.8 - - + -
72B TYR* 3.9 13.4 - - + -
73B THR* 1.3 73.2 - - - +
75B VAL* 1.3 61.6 + - - +
82B LYS* 3.2 4.2 - - - +
83B GLN* 2.7 52.0 + - + +
102B ILE* 3.9 16.4 - - + -
103B LYS 4.9 1.6 - - - +
104B MET* 3.7 27.4 - - - -
105B MET* 3.4 16.9 - - + +
110B TYR* 3.5 25.1 - - + -
111B LYS 3.7 2.2 - - - +
112B VAL* 3.8 23.1 - - + -
147B PHE* 4.3 11.9 - - + -
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Residues in contact with VAL 75 (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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73B THR* 4.2 11.7 - - + +
74B LEU* 1.3 80.0 - - - +
76B ASN* 1.3 66.5 + - - +
77B ASN* 3.3 26.8 + - - +
80B GLY* 4.1 12.3 - - - +
81B GLU 3.2 8.3 - - - +
82B LYS* 4.0 20.6 - - + -
110B TYR* 3.2 9.4 - - - -
111B LYS* 2.9 43.8 + - + +
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Residues in contact with ASN 76 (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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75B VAL* 1.3 70.9 - - - +
77B ASN* 1.3 52.0 + - - +
78B ASP* 2.9 21.7 + - - +
79B THR* 3.2 22.5 + - - +
80B GLY* 2.7 35.5 + - - -
81B GLU 2.9 11.7 + - - +
105B MET* 3.0 28.6 + - + +
106B GLY 3.5 0.6 + - - -
107B VAL 3.0 21.6 + - - -
108B GLY* 3.6 5.9 - - - -
109B ASN 3.9 1.2 - - - +
110B TYR* 3.5 33.7 + - + +
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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