Contacts of the strand formed by residues 25 - 31 (chain B) in PDB entry 5E0T
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.3 5.9 - - - +
24B ASN* 1.3 93.6 - - + +
26B ALA* 1.3 65.4 + - - +
39B SER* 3.9 12.6 + - - -
70B VAL 3.2 7.4 - - - +
71B ASN* 4.8 2.9 - - + +
72B LEU* 4.4 1.3 - - - -
119B MET* 3.7 30.4 - - + +
121B LEU* 3.4 33.0 - - + +
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Residues in contact with ALA 26 (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 ILE* 4.2 2.0 - - + -
25B GLU* 1.3 80.0 - - - +
27B CYS* 1.3 60.9 + - - +
28B TRP* 3.9 0.8 - - - -
37B LEU* 3.9 28.9 - - + -
38B GLN 5.3 0.2 - - - +
39B SER* 4.1 16.8 - - - -
68B MET 3.6 1.2 - - - +
70B VAL* 2.9 34.1 + - - +
72B LEU* 4.1 16.2 - - + -
121B LEU* 3.6 7.4 - - - +
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Residues in contact with CYS 27 (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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26B ALA* 1.3 74.5 - - - +
28B TRP* 1.3 62.2 + - - +
29B ASP* 3.4 18.9 + - - +
36B ASN 4.2 1.6 - - - +
37B LEU* 4.1 13.5 - - - +
38B GLN 4.6 8.2 + - - +
39B SER* 5.6 0.2 - - - -
67B ALA* 3.5 39.3 - - - -
68B MET 3.2 7.2 - - - -
69B GLY* 4.4 4.9 - - - -
121B LEU* 4.2 6.2 - - + +
123B VAL* 4.2 28.5 - - + -
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Residues in contact with TRP 28 (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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12B LEU* 4.7 11.9 - - + -
15B VAL* 4.5 4.9 - - + -
16B LEU* 3.9 22.9 - - + -
19B LEU* 4.5 3.1 - - + -
26B ALA 3.9 3.6 - - - -
27B CYS* 1.3 69.9 - - - +
29B ASP* 1.3 62.3 + - - +
30B ILE* 3.6 8.8 + - + +
35B VAL* 3.5 28.5 - - + -
36B ASN 3.9 3.4 - - - -
37B LEU* 3.4 28.3 - - + +
50B LEU* 4.0 21.1 - - + -
52B LEU* 4.8 2.5 - - + -
66B LEU 3.5 4.0 - - - +
67B ALA* 3.5 0.3 - - - -
68B MET* 2.7 51.1 + - + +
70B VAL* 3.5 30.4 - - + +
72B LEU* 3.7 21.3 - - + +
75B MET* 3.8 29.8 - - + -
90B LEU* 5.7 7.0 - - + -
99B LEU* 6.5 0.2 - - + -
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Residues in contact with ASP 29 (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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27B CYS* 3.7 25.4 - - - +
28B TRP* 1.3 70.8 - - - +
30B ILE* 1.3 62.4 + - - +
31B SER* 5.3 0.6 + - - -
34B GLY 3.7 1.4 - - - +
35B VAL* 3.7 2.6 - - - +
36B ASN* 2.7 60.3 + - + +
38B GLN* 5.0 9.2 + - - +
66B LEU 3.6 3.3 - - - +
67B ALA* 3.9 9.4 - - - +
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Residues in contact with ILE 30 (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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2B PHE* 3.3 61.0 - - + -
28B TRP* 3.9 14.8 - - + +
29B ASP* 1.3 78.1 - - - +
31B SER* 1.3 66.8 + - - +
34B GLY 3.8 2.0 - - - +
35B VAL* 4.7 11.9 - - + -
60B TYR* 3.8 8.3 - - - +
62B CYS* 4.0 9.4 - - - -
65B ASN* 3.4 6.4 - - - +
66B LEU* 2.9 41.7 + - + +
68B MET* 3.4 26.5 - - + -
90B LEU* 6.1 0.7 - - + -
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Residues in contact with SER 31 (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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29B ASP 5.3 0.8 + - - -
30B ILE* 1.3 77.6 - - - +
32B SER* 1.3 63.0 + - - +
33B SER* 3.1 22.3 + - - -
34B GLY 3.2 10.6 + - - -
60B TYR* 2.7 30.5 + - - -
62B CYS* 3.7 10.7 - - - +
65B ASN* 3.4 25.8 - - - -
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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