Contacts of the strand formed by residues 38 - 43 (chain A) in PDB entry 1E8O
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 LEU 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.4 35.2 - - + -
30A LYS 3.6 7.0 - - - +
31A TYR* 4.2 6.7 - - + -
37A ASN* 1.3 78.7 - - - +
39A CYS* 1.3 71.5 + - - +
40A VAL* 4.9 0.2 - - + -
52A LYS* 3.9 2.8 - - - +
53A THR* 2.8 32.5 + - - +
58A ASP* 4.9 2.2 - - + -
59A VAL* 4.2 18.4 - - + +
62A ILE* 3.2 33.9 - - + -
91B MET* 3.5 20.4 - - + -
94B LEU* 4.1 23.9 - - + +
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Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.0 1.7 - - - +
29A LEU* 3.7 3.3 - - - -
30A LYS* 3.3 44.4 + - + +
37A ASN* 5.9 0.9 - - - +
38A LEU* 1.3 85.2 - - - +
40A VAL* 1.3 66.6 + - - +
41A LYS* 4.1 5.6 + - - +
50A VAL* 4.8 8.5 - - - -
51A TYR 3.3 9.0 - - - -
52A LYS* 3.6 39.9 - - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TRP* 4.6 3.4 - - + -
10A PHE* 4.0 26.5 - - + -
27A VAL* 4.0 19.1 - - + -
28A VAL 3.7 10.1 - - - +
29A LEU* 4.4 8.7 - - + -
39A CYS* 1.3 76.7 - - - +
41A LYS* 1.3 63.5 + - - +
42A VAL* 4.8 0.2 - - + -
50A VAL* 3.5 2.6 - - - +
51A TYR* 2.7 41.3 + - + +
62A ILE* 3.4 46.7 - - + -
65A PHE* 4.9 9.6 - - + -
66A HIS* 5.3 2.7 - - + -
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.9 0.2 - - - -
26A ARG 4.1 0.3 - - - +
27A VAL* 3.5 4.2 - - - +
28A VAL* 3.1 53.4 + - + +
39A CYS* 5.2 5.4 - - - +
40A VAL* 1.3 78.2 - - - +
42A VAL* 1.3 65.6 + - - +
43A THR* 3.6 21.7 + - + +
48A CYS* 3.6 18.9 - - - -
49A LEU 3.0 15.5 - - - +
50A VAL* 3.7 15.5 - - + -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.2 10.5 - - + -
14A ALA* 4.0 35.9 - - + +
17A LEU* 4.5 14.2 - - + +
18A TYR* 5.6 4.0 - - + -
25A ALA* 5.1 4.5 - - + -
26A ARG 3.5 15.0 - - - +
27A VAL* 3.6 20.6 - - + -
41A LYS* 1.3 78.8 - - - +
43A THR* 1.3 67.8 + - - +
47A VAL 4.0 0.3 - - - +
48A CYS* 3.5 1.2 - - - -
49A LEU* 2.8 44.1 + - + +
65A PHE* 4.4 6.1 - - + -
69A LEU* 5.3 3.8 - - + -
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Residues in contact with THR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.8 2.4 - - - +
25A ALA* 3.3 7.3 - - - +
26A ARG* 3.0 54.8 + - - +
28A VAL* 6.4 0.7 - - + -
41A LYS* 3.6 18.2 - - + -
42A VAL* 1.3 74.8 - - - +
44A ASP* 1.3 61.8 + - - +
45A ASP* 3.7 13.9 + - - -
47A VAL 3.2 9.2 - - - +
48A CYS* 3.3 31.0 - - + -
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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