Contacts of the strand formed by residues 39 - 45 (chain B) in PDB entry 4I0A
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B HIS* 6.0 0.9 - - - +
38B GLU* 1.3 92.0 + - + +
40B LEU* 1.3 59.0 + - - +
41B TYR* 3.8 3.1 + - - -
72B GLY 3.4 0.7 - - - +
83B ARG* 2.8 48.2 + - - -
97B GLU* 2.8 34.9 + - + +
98B ILE 3.3 8.3 - - - +
99B SER* 4.0 15.0 - - - +
100B TYR* 3.3 10.9 - - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.3 2.2 - - + -
39B THR* 1.3 75.2 - - - +
41B TYR* 1.3 65.2 + - - +
70B PHE* 3.7 26.0 - - + -
71B ILE 3.4 17.7 - - - +
72B GLY 4.1 0.2 - - - -
73B GLU* 3.7 31.2 - - + -
76B LEU* 5.5 1.8 - - + -
97B GLU* 3.3 4.9 - - - +
98B ILE* 2.7 47.8 + - + +
100B TYR* 3.6 13.1 - - + -
103B PHE* 3.7 41.3 - - + -
117B LEU* 4.0 9.0 - - + -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 5.5 1.1 - - - -
24B TYR* 4.5 13.7 - + - -
30B LEU* 4.0 19.4 + - + -
31B ILE* 3.7 31.3 - - + +
39B THR* 3.8 7.3 + - - -
40B LEU* 1.3 77.0 - - - +
42B TYR* 1.3 62.6 + - - +
70B PHE* 3.3 11.4 - - - -
71B ILE* 2.7 50.9 + - + +
72B GLY* 4.4 0.4 - - - -
83B ARG* 3.5 24.0 + - - -
95B VAL* 3.7 24.2 - - + -
96B ALA 3.1 9.4 - - - +
97B GLU* 3.1 38.9 + - + -
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Residues in contact with TYR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.3 43.0 - - + +
15B PHE* 3.7 22.4 - + + -
16B LEU* 3.8 21.5 - - + -
41B TYR* 1.3 76.4 - - - +
43B ILE* 1.3 81.2 + - - +
44B VAL* 3.3 6.9 + - + -
67B GLN* 6.2 0.4 - - + -
68B GLY* 3.3 39.0 + - - -
69B ASP 3.6 4.0 - - - -
70B PHE* 3.8 32.1 - + + -
95B VAL* 3.5 3.1 - - - -
96B ALA* 2.7 42.7 + - + -
120B GLN* 5.3 0.2 - - - -
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Residues in contact with ILE 43 (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 TYR* 1.3 78.7 - - - +
44B VAL* 1.3 58.7 + - - +
45B LYS 3.5 23.1 - - - +
46B GLY 3.5 17.0 - - - +
48B VAL* 3.7 34.1 - - + +
65B LEU* 3.8 16.6 - - + +
66B ASN 3.6 18.6 - - - +
67B GLN* 3.7 9.6 - - - +
68B GLY 2.8 28.1 + - - -
69B ASP 2.9 16.9 + - - +
71B ILE* 3.8 20.6 - - + -
93B CYS* 5.2 1.6 - - - -
94B GLU 3.8 3.8 - - - +
95B VAL* 4.6 9.2 - - + +
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Residues in contact with VAL 44 (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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16B LEU* 4.1 32.1 - - + -
21B ILE* 4.7 13.5 - - + -
42B TYR* 3.3 12.0 + - + +
43B ILE* 1.3 74.3 - - - +
45B LYS* 1.3 60.2 + - + +
67B GLN* 3.3 20.7 - - - +
94B GLU* 2.8 41.7 + - + +
96B ALA* 4.3 9.2 - - + +
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Residues in contact with LYS 45 (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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23B LYS* 4.9 14.4 - - - +
43B ILE* 3.5 8.6 - - - +
44B VAL* 1.3 81.7 - - + +
46B GLY* 1.3 64.3 + - - +
67B GLN* 4.2 11.2 - - - +
92B ALA* 4.0 18.9 + - - +
93B CYS* 3.3 19.6 + - - +
94B GLU* 2.9 58.5 + - + +
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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