Contacts of the strand formed by residues 65 - 72 (chain B) in PDB entry 1O9T
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 MET 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 4.9 17.7 - - + -
60B VAL* 3.9 6.0 - - + +
61B CYS* 3.1 7.0 - - - +
62B LYS* 2.8 55.8 + - + +
63B THR 3.2 1.9 - - - +
64B GLY* 1.3 78.2 - - - +
66B VAL* 1.3 61.3 + - - +
67B LEU* 5.2 16.4 - - + -
100B PHE* 3.9 3.4 - - - -
106B ASN* 3.3 18.8 - - + +
108B LEU* 4.7 23.1 - - + -
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Residues in contact with VAL 66 (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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34B ILE* 5.9 0.2 - - + -
38B ILE* 4.1 7.2 - - + -
59B THR* 3.6 25.8 - - + -
60B VAL 3.4 3.1 - - - +
61B CYS* 4.2 6.1 - - + -
65B MET* 1.3 72.8 - - - +
67B LEU* 1.3 60.8 + - - +
68B LEU* 4.1 1.3 + - - +
84B VAL* 3.8 25.8 - - + -
88B ILE* 4.0 15.3 - - + -
100B PHE* 3.5 34.1 - - + -
105B CYS* 4.8 1.8 - - - -
106B ASN 2.6 13.4 + - - +
107B VAL* 3.4 5.8 - - + +
108B LEU* 2.7 35.2 + - - +
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Residues in contact with LEU 67 (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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60A VAL* 6.1 4.3 - - + -
62A LYS* 5.1 6.3 - - + -
65A MET* 4.8 18.4 - - + -
67A LEU* 6.6 0.2 - - + -
59B THR* 3.3 8.1 - - - +
60B VAL* 2.7 52.7 + - + +
65B MET* 4.2 15.2 - - + +
66B VAL* 1.3 73.2 - - - +
68B LEU* 1.3 67.7 + - - +
69B CYS* 3.4 29.9 + - - -
108B LEU* 3.3 25.8 - - + +
110B ALA* 4.1 12.8 - - + -
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Residues in contact with LEU 68 (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 ILE* 5.1 1.1 - - + -
39B SER* 6.1 0.2 - - - -
42B VAL* 4.1 11.7 - - + -
57B CYS* 4.2 13.7 - - + -
58B GLU 3.9 6.5 - - - +
59B THR* 4.6 10.8 - - + +
66B VAL* 4.1 2.6 - - + -
67B LEU* 1.3 72.0 - - - +
69B CYS* 1.3 75.4 + - - +
80B TYR* 3.6 37.0 - - + -
84B VAL* 4.0 26.5 - - + -
107B VAL* 5.7 0.7 - - + -
108B LEU 2.9 12.8 + - - +
109B VAL* 4.2 14.8 - - + -
110B ALA* 2.8 31.4 + - - +
111B LEU* 3.4 16.8 + - + -
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Residues in contact with CYS 69 (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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62A LYS* 3.4 31.4 - - - -
259A ASP* 3.4 19.5 - - + +
260A ALA* 4.5 6.7 - - - -
57B CYS* 3.2 8.3 - - - +
58B GLU* 3.0 41.0 + - + +
60B VAL* 5.4 4.0 - - - -
67B LEU* 3.4 33.7 - - - -
68B LEU* 1.3 76.6 - - - +
70B GLY* 1.3 59.0 + - - +
110B ALA 4.5 5.2 - - - -
111B LEU* 3.8 4.9 - - - -
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Residues in contact with GLY 70 (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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62A LYS* 5.2 1.2 - - - +
259A ASP* 3.0 22.5 + - - +
56B ALA 3.3 9.9 - - - -
57B CYS* 3.8 1.8 - - - -
69B CYS* 1.3 79.5 - - - +
71B GLU* 1.3 58.7 + - - -
110B ALA 4.5 2.0 + - - +
111B LEU* 3.3 13.0 - - - +
112B GLU* 3.0 32.6 + - - +
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Residues in contact with GLU 71 (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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259A ASP* 3.1 15.3 + - - +
54B LYS 4.1 0.9 - - - +
56B ALA* 2.8 28.5 + - - +
70B GLY* 1.3 72.8 - - - +
72B ILE* 1.3 63.3 + - - +
73B THR* 4.3 2.9 + - - -
112B GLU* 3.6 20.4 - - + +
114B GLN* 2.8 43.7 + - - +
1397B ATP 2.9 37.9 + - + +
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Residues in contact with ILE 72 (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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42B VAL* 4.3 5.4 - - + -
46B HIS* 3.2 26.5 - - + +
54B LYS 3.1 8.1 - - - +
55B VAL* 3.4 18.4 - - + -
56B ALA 3.3 24.9 - - - +
57B CYS* 4.4 5.8 - - + -
71B GLU* 1.3 81.4 - - - +
73B THR* 1.3 61.4 + - - +
74B SER 3.6 0.2 - - - -
80B TYR* 3.0 31.0 - - + +
111B LEU* 3.3 24.9 - - + -
112B GLU 3.0 5.5 + - - -
113B GLN* 3.2 8.7 - - + +
114B GLN* 3.2 20.7 + - - -
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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