Contacts of the strand formed by residues 40 - 45 (chain B) in PDB entry 1O7Z
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 GLU 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B CYS* 3.5 8.8 - - - +
10B THR* 2.7 35.2 + - + +
11B CYS* 2.7 48.4 + - + +
14B ILE* 5.9 3.8 - - + -
28B GLU 3.6 1.7 - - - +
29B ILE* 3.6 1.2 - - - -
30B ILE* 2.8 50.4 + - + +
36B CYS* 3.8 13.4 - - - +
38B ARG* 3.9 16.4 + - + +
39B VAL* 1.3 78.3 - - - +
41B ILE* 1.3 62.3 + - - +
42B ILE* 4.3 1.3 + - + -
56B PRO* 5.8 0.7 - - - -
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Residues in contact with ILE 41 (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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68A VAL* 5.9 3.6 - - + +
11B CYS* 4.4 1.0 - - - -
14B ILE* 5.9 0.6 - - - +
27B LEU* 3.6 29.2 - - + -
28B GLU 3.3 6.7 - - - +
29B ILE* 4.5 17.5 - - + -
39B VAL* 4.3 10.5 + - + -
40B GLU* 1.3 78.4 - - - +
42B ILE* 1.3 65.0 + - - +
53B CYS* 3.2 6.2 - - - +
54B LEU* 2.8 51.2 + - + +
56B PRO* 3.6 37.9 - - + -
61B ILE* 4.4 13.2 - - + -
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Residues in contact with ILE 42 (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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10B THR* 3.5 32.3 - - + +
11B CYS* 3.8 15.7 - - - -
26B LYS 3.9 0.5 - - - +
27B LEU* 3.5 4.5 - - - -
28B GLU* 2.9 59.9 + - + +
30B ILE* 5.0 10.5 - - + -
40B GLU* 5.0 2.2 - - + +
41B ILE* 1.3 81.2 - - - +
43B ALA* 1.3 72.9 + - - +
44B THR* 3.9 1.6 + - - +
51B LYS* 4.3 22.7 - - + +
52B ARG 3.5 7.4 - - - +
53B CYS* 4.1 5.6 - - - +
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Residues in contact with ALA 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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19B VAL* 4.3 5.4 - - + -
24B LEU* 3.4 21.8 - - + -
26B LYS 3.5 4.9 - - - -
27B LEU* 3.9 12.7 - - + +
41B ILE 4.3 0.2 - - - -
42B ILE* 1.3 74.3 - - - +
44B THR* 1.3 60.5 + - - +
45B MET* 4.0 16.0 + - + +
51B LYS* 3.2 6.1 - - - +
52B ARG 2.8 37.0 + - - +
54B LEU* 4.1 11.1 - - + +
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Residues in contact with THR 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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24B LEU* 3.7 1.6 - - - +
25B GLU* 2.7 39.0 + - + +
26B LYS* 2.8 38.2 + - + +
28B GLU* 4.3 3.5 + - - -
42B ILE* 4.6 1.6 + - - +
43B ALA* 1.3 73.7 - - - +
45B MET* 1.3 66.5 + - - +
50B GLU 4.0 4.0 - - - +
51B LYS* 2.8 41.1 + - + +
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Residues in contact with MET 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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19B VAL* 3.7 44.6 - - + -
23B SER* 3.1 23.8 - - - +
24B LEU* 4.7 0.9 - - - -
25B GLU* 3.8 6.2 - - - +
43B ALA* 4.3 8.7 - - + +
44B THR* 1.3 91.2 - - - +
46B LYS* 1.3 63.3 + - - +
47B LYS 3.3 14.6 + - - +
49B GLY* 5.9 0.9 + - - -
50B GLU* 3.0 40.3 + - + +
52B ARG* 3.8 39.7 - - + +
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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