Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 5EBX
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 SER 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ARG* 4.1 2.1 - - - +
3A CYS* 3.7 7.1 - - - -
21A GLU* 3.1 19.8 + - - +
22A SER* 1.3 83.8 + - - +
24A CYS* 1.3 66.3 + - - +
42A GLY 2.9 36.1 + - - -
43A CYS* 3.5 15.8 + - - +
54A CYS* 4.9 1.6 - - - -
55A CYS 3.1 14.4 - - - -
56A GLU* 4.2 9.6 - - - -
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Residues in contact with CYS 24 (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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1A ARG* 3.5 20.9 - - - -
2A ILE 3.8 2.9 - - - -
3A CYS* 2.0 51.4 - - - -
23A SER* 1.3 71.8 - - - +
25A TYR* 1.3 58.8 + - - +
40A GLY 3.4 2.5 - - - -
42A GLY 3.2 7.4 - - - +
54A CYS* 3.5 4.5 - - - +
55A CYS* 2.9 28.0 + - - -
57A SER 4.1 0.9 - - - -
60A CYS* 3.6 22.2 - - - -
61A ASN* 3.5 19.1 - - - -
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Residues in contact with TYR 25 (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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24A CYS* 1.3 74.9 - - - +
26A ASN* 1.3 63.3 + - - +
27A LYS* 3.7 27.2 - - + -
38A GLU* 2.8 42.5 + - - +
39A ARG* 3.2 17.0 + - - -
40A GLY* 3.0 27.8 + - - -
41A CYS 3.2 21.5 - - - -
42A GLY 3.2 22.4 + - - +
44A PRO* 3.5 30.3 - - + -
52A LEU* 4.2 2.5 - - + -
53A SER 3.4 9.4 - - - +
54A CYS* 4.1 7.0 - - - -
61A ASN* 2.6 27.9 + - - -
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Residues in contact with ASN 26 (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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25A TYR* 1.3 77.0 - - - +
27A LYS* 1.3 64.5 + - - +
28A GLN* 4.7 4.9 - - - +
37A ILE* 3.7 32.2 - - - +
38A GLU 3.3 4.7 - - - -
39A ARG* 3.9 3.8 - - - +
51A LYS 3.9 0.9 - - - +
52A LEU* 3.7 1.6 - - - -
53A SER* 2.9 43.1 + - - +
61A ASN* 3.3 28.2 + - + +
62A ASN* 3.6 14.5 + - - -
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Residues in contact with LYS 27 (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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25A TYR* 3.7 19.7 - - + -
26A ASN* 1.3 77.0 - - - +
28A GLN* 1.3 62.8 - - - +
29A TRP* 4.0 24.8 - - + -
37A ILE* 3.2 5.2 - - - -
38A GLU* 2.7 62.9 + - + +
44A PRO* 4.4 14.5 - - - +
47A LYS* 4.2 20.3 - - - +
50A ILE* 4.1 24.0 - - + -
51A LYS 3.2 6.5 - - - +
52A LEU* 4.3 12.6 - - + -
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Residues in contact with GLN 28 (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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26A ASN* 4.7 5.9 - - - +
27A LYS* 1.3 77.6 - - - +
29A TRP* 1.3 68.4 + - - +
30A SER* 5.8 1.0 + - - -
35A THR* 4.0 23.5 - - + +
36A ILE 3.1 11.4 - - - +
37A ILE* 4.2 17.0 - - + +
50A ILE* 3.8 0.7 - - - -
51A LYS* 3.0 73.2 + - + +
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Residues in contact with TRP 29 (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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27A LYS* 4.0 26.9 - - + -
28A GLN* 1.3 88.2 - - - +
30A SER* 1.3 77.4 - - - +
31A ASP* 3.4 11.7 + - + -
35A THR* 3.6 1.7 - - - +
36A ILE* 2.7 80.8 + - + +
38A GLU* 3.7 31.9 - - + -
49A GLY 4.2 10.1 - - - +
50A ILE* 4.1 23.1 - - + -
51A LYS* 5.7 3.1 - - - +
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Residues in contact with SER 30 (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 GLN* 5.8 0.7 + - - -
29A TRP* 1.3 85.3 - - - +
31A ASP* 1.3 64.3 + - - +
34A GLY 3.2 13.9 - - - -
35A THR* 3.7 15.9 + - - +
51A LYS* 5.7 2.9 + - - -
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Residues in contact with ASP 31 (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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29A TRP* 3.4 11.2 + - + -
30A SER* 1.3 77.3 - - - +
32A PHE* 1.3 78.9 + - + +
33A ARG* 3.1 32.4 + - - +
34A GLY* 3.1 15.5 + - - +
36A ILE* 3.2 29.1 - - - +
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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