Contacts of the strand formed by residues 34 - 41 (chain A) in PDB entry 2E9U
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 ALA 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.2 8.5 - - + -
26A ALA 3.3 7.2 - - - +
27A VAL* 4.3 9.6 - - + +
32A GLU 3.5 3.5 + - - +
33A GLU* 1.3 76.2 - - - +
35A VAL* 1.3 69.7 + - - +
71A TYR* 5.4 0.9 + - - -
86A TYR* 3.6 34.2 + - + +
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Residues in contact with VAL 35 (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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9A TRP* 3.6 39.0 - - + -
25A LEU* 3.6 3.5 - - - +
26A ALA* 2.7 48.2 + - + +
33A GLU* 4.6 9.4 - - + +
34A ALA* 1.3 81.6 - - - +
36A ALA* 1.3 58.2 + - - +
37A VAL* 4.5 2.0 - - + -
71A TYR* 3.8 28.0 - - + +
83A PHE* 4.3 17.9 - - + -
84A LEU 3.7 8.3 - - - +
86A TYR* 3.6 10.8 - - - +
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Residues in contact with ALA 36 (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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15A LEU* 3.9 11.7 - - + -
23A VAL* 4.4 5.2 - - + -
24A GLN 3.6 4.7 - - - -
35A VAL* 1.3 74.1 - - - +
37A VAL* 1.3 60.1 - - - +
38A LYS 4.1 0.2 - - - -
82A LEU 3.5 0.7 - - - +
83A PHE* 3.6 1.7 - - - -
84A LEU* 2.6 48.7 + - + +
85A GLU 3.7 2.7 - - - +
86A TYR* 3.8 2.5 - - - +
1001A A25 3.3 42.6 - - + +
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Residues in contact with VAL 37 (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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11A LEU* 5.9 5.8 - - + -
23A VAL* 3.4 4.9 - - - -
24A GLN* 2.7 46.8 + - + +
26A ALA* 3.4 31.9 - - + -
35A VAL* 4.5 1.1 - - + +
36A ALA* 1.3 76.3 - - - +
38A LYS* 1.3 63.6 + - - +
39A ILE* 3.6 26.2 + - + +
81A TYR* 4.3 17.9 - - + -
82A LEU 3.4 7.6 - - - +
83A PHE* 4.3 23.8 - - + -
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Residues in contact with LYS 38 (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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20A TYR* 3.8 39.8 - - + +
22A GLU 4.0 2.2 - - - -
23A VAL* 4.3 12.3 - - + -
36A ALA 4.1 0.6 + - - -
37A VAL* 1.3 70.5 - - - +
39A ILE* 1.3 65.1 + - - +
40A VAL* 3.7 8.8 + - + +
52A ILE* 5.7 0.9 - - + -
55A GLU* 2.6 41.3 + - - +
80A GLN 3.4 7.3 - - - +
81A TYR* 3.7 1.6 - - - -
82A LEU* 2.8 52.7 + - + +
84A LEU* 4.0 15.9 - - + +
148A ASP* 3.4 21.8 + - - +
150A GLY* 5.0 0.8 - - - -
1001A A25 5.6 5.6 - - + -
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Residues in contact with ILE 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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11A LEU* 5.8 6.1 - - + -
20A TYR* 3.9 2.6 - - - +
21A GLY* 3.8 7.3 + - - -
22A GLU* 2.8 61.4 + - + +
24A GLN* 4.4 9.0 - - + -
37A VAL* 3.6 21.8 - - + +
38A LYS* 1.3 73.0 - - - +
40A VAL* 1.3 62.6 + - - +
41A ASP* 4.2 2.1 + - + +
79A ILE* 4.1 21.5 - - + -
80A GLN 3.8 1.3 - - - +
81A TYR* 3.5 36.3 - - + -
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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
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20A TYR* 3.9 21.8 - - + +
38A LYS* 4.6 9.0 - - + +
39A ILE* 1.3 76.3 - - - +
41A ASP* 1.3 70.7 + - - +
42A MET* 3.4 4.3 + - + +
48A CYS* 5.3 4.3 - - - -
52A ILE* 3.5 35.7 - - + -
79A ILE* 4.0 0.6 - - - -
80A GLN* 3.1 50.6 + - + +
82A LEU* 4.4 4.0 - - + -
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Residues in contact with ASP 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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20A TYR 4.0 9.1 + - - +
21A GLY* 6.4 0.2 - - - -
39A ILE* 4.2 2.7 + - + +
40A VAL* 1.3 76.3 - - - +
42A MET* 1.3 54.2 + - - +
43A LYS* 2.6 71.9 + - + +
48A CYS* 4.6 1.6 - - - -
78A ASN* 3.4 18.2 - - - +
79A ILE* 3.5 19.6 - - + +
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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