Contacts of the strand formed by residues 26 - 37 (chain A) in PDB entry 2BUK
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 HIS 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASN* 3.2 35.1 + - + +
24A LEU 3.0 26.7 + - - -
25A GLU* 1.3 74.6 - - - +
27A LYS* 1.3 66.8 + - - +
28A ARG* 4.1 9.9 - - - +
57A ILE* 5.4 2.4 - - - +
68A VAL* 3.9 34.2 - - + +
191A VAL* 4.0 18.2 - - + +
192A TYR 3.5 5.8 - - - -
193A THR* 3.8 8.4 - - + +
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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 GLU* 3.8 37.7 - - + +
26A HIS* 1.3 77.0 - - - +
28A ARG* 1.3 60.5 + - - +
54A GLY 5.2 3.4 + - - -
55A ASP* 5.5 4.4 - - - +
56A ASP 4.1 11.8 + - - +
57A ILE* 3.0 22.9 - - - +
59A GLN 3.5 20.6 + - - +
60A ARG* 4.6 2.8 - - - +
61A SER* 4.7 4.2 - - - +
191A VAL* 3.4 0.5 - - - -
192A TYR* 2.8 50.7 + - + +
194A ASP* 2.7 36.5 + - + +
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Residues in contact with ARG 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 HIS 4.1 9.2 - - - +
27A LYS* 1.3 79.2 - - - +
29A PHE* 1.3 62.5 + - - +
57A ILE* 3.0 24.9 + - + +
58A ASN* 3.0 24.5 - - - +
71A LYS* 5.8 0.8 - - - +
189A GLU* 3.1 36.5 + - + -
190A ALA 3.3 4.0 - - - +
191A VAL* 3.8 30.1 - - + +
192A TYR* 4.1 1.8 - - - -
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Residues in contact with PHE 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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28A ARG* 1.3 75.9 - - - +
30A ALA* 1.3 69.2 + - - +
31A LEU* 3.7 29.8 - - + -
47A LEU 3.2 25.6 - - - -
50A GLY* 3.6 35.0 - - - -
51A ILE* 3.7 31.6 - - + -
58A ASN* 4.1 26.2 - - + -
188A TYR* 4.4 11.2 - + - -
189A GLU* 3.1 8.3 - - - +
190A ALA* 2.9 34.3 + - + +
192A TYR* 4.1 7.6 - - + -
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Residues in contact with ALA 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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29A PHE* 1.3 88.8 - - - +
31A LEU* 1.3 66.0 + - - +
58A ASN* 5.3 1.3 + - - +
188A TYR 3.4 6.7 - - - +
189A GLU* 4.6 5.6 - - + +
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Residues in contact with LEU 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 PHE* 3.7 17.9 - - + -
30A ALA* 1.3 79.8 - - - +
32A ILE* 1.3 74.7 + - - +
33A ASN* 4.3 8.1 - - + +
46A ASN 3.7 23.6 - - - +
47A LEU* 3.8 30.3 - - + +
50A GLY* 6.1 0.7 - - - +
186A SER* 4.7 2.0 - - - +
187A SER* 3.2 6.4 - - - -
188A TYR* 2.8 40.9 + - + +
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Residues in contact with ILE 32 (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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31A LEU* 1.3 80.8 - - - +
33A ASN* 1.3 64.7 + - - +
34A SER* 3.9 18.2 - - - +
186A SER 3.5 9.6 - - - +
187A SER* 4.6 10.3 - - - -
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Residues in contact with ASN 33 (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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31A LEU* 4.3 6.9 - - + +
32A ILE* 1.3 73.8 - - - +
34A SER* 1.3 61.7 + - - +
36A ASN* 3.3 32.6 + - - +
45A GLN* 3.2 33.7 + - - +
184A TRP* 4.0 6.5 - - - -
185A ASP* 3.5 1.9 - - - -
186A SER* 2.7 45.1 + - - +
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Residues in contact with SER 34 (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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32A ILE* 3.9 21.6 + - - +
33A ASN* 1.3 77.6 + - - +
35A GLY* 1.3 67.3 - - - +
36A ASN* 3.5 9.0 + - - +
185A ASP* 3.6 19.6 + - - +
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Residues in contact with GLY 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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34A SER* 1.3 74.6 - - - +
36A ASN* 1.3 61.7 + - - +
37A THR* 5.2 1.9 - - - +
183A LEU* 4.1 22.7 - - - +
184A TRP 3.7 1.0 + - - -
185A ASP* 2.9 17.7 + - - -
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Residues in contact with ASN 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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33A ASN* 3.3 47.8 + - - +
34A SER 4.1 3.2 + - - -
35A GLY* 1.3 81.8 + - - +
37A THR* 1.3 64.6 + - - +
45A GLN* 5.4 3.0 + - - +
183A LEU* 3.0 7.7 - - - -
184A TRP* 2.8 64.5 + - + +
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Residues in contact with THR 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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35A GLY 5.2 1.6 - - - +
36A ASN* 1.3 79.2 - - - +
38A ASN* 1.3 69.0 + - - +
39A ALA* 3.5 5.4 + - - +
43A THR* 5.7 1.9 + - - +
175A GLN* 4.2 0.2 - - - +
180A LEU 3.8 19.1 + - - +
181A VAL* 5.2 2.9 - - - +
182A GLY 3.3 5.2 - - - +
183A LEU* 3.9 15.9 - - + -
184A TRP* 3.4 13.5 + - - -
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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