Contacts of the helix formed by residues 23 - 36 (chain A) in PDB entry 2BWJ
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 GLY 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLY 3.3 2.0 - - - -
22A SER* 1.3 78.7 - - - +
24A LYS* 1.3 65.2 + - - +
25A GLY 3.3 2.5 - - - -
26A THR* 3.2 12.8 + - - -
27A GLN* 3.2 27.6 + - - +
121A MET* 3.8 5.2 - - - -
131A ARG* 5.3 0.7 - - - -
1199A SO4 3.1 14.6 + - - -
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Residues in contact with LYS 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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16A ILE* 3.6 29.6 - - + +
17A ILE 4.1 0.2 - - - -
18A GLY* 3.3 36.3 + - - +
22A SER* 3.5 9.9 - - - +
23A GLY* 1.3 78.1 - - - +
25A GLY* 1.3 63.6 + - - +
27A GLN* 3.2 3.3 + - - +
28A CYS* 3.0 32.1 + - - -
96A ASP* 2.8 33.1 + - - +
97A GLY* 4.4 7.8 - - - +
121A MET* 3.8 15.5 - - - -
1199A SO4 3.1 15.9 + - - +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 1.3 79.7 - - - +
26A THR* 1.3 62.6 + - - +
28A CYS* 3.3 15.6 + - - +
29A GLU* 3.4 21.4 + - - +
39A HIS* 5.1 2.2 - - - -
96A ASP* 5.0 6.1 - - - -
1199A SO4 3.0 18.6 + - - -
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Residues in contact with THR 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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23A GLY* 3.2 17.1 + - - -
25A GLY* 1.3 76.8 - - - +
27A GLN* 1.3 66.7 + - - +
29A GLU* 3.5 21.0 + - - +
30A LYS* 3.3 33.4 + - - +
182A PRO* 5.6 3.5 - - - +
1199A SO4 4.7 1.5 + - - +
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Residues in contact with GLN 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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16A ILE* 5.4 1.6 - - + -
23A GLY* 3.2 20.0 + - - +
24A LYS* 3.2 6.7 + - - +
26A THR* 1.3 80.8 + - - +
28A CYS* 1.3 57.1 + - - +
30A LYS* 3.4 15.4 + - - +
31A LEU* 2.9 34.8 + - + +
121A MET* 4.0 6.7 - - + -
182A PRO* 2.8 39.1 + - - +
185A VAL* 3.8 20.6 - - + +
186A PHE* 3.3 32.6 - - - +
189A LEU* 3.6 20.6 - - + +
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Residues in contact with CYS 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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16A ILE* 3.7 34.1 - - - -
24A LYS* 3.0 20.7 + - - +
25A GLY 3.6 7.0 - - - +
26A THR 3.3 0.2 - - - -
27A GLN* 1.3 77.4 - - - +
29A GLU* 1.3 55.8 + - - +
31A LEU* 3.7 2.1 - - - +
32A VAL* 2.9 35.3 + - - +
39A HIS* 3.5 36.3 - - + +
94A LEU* 3.8 17.6 - - + +
96A ASP* 4.0 6.3 - - - -
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Residues in contact with GLU 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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25A GLY 3.4 17.0 + - - +
26A THR* 3.7 23.1 - - - +
27A GLN 3.3 0.2 - - - -
28A CYS* 1.3 77.9 - - + +
30A LYS* 1.3 61.8 + - + +
32A VAL* 3.6 7.7 + - - +
33A GLU* 3.2 22.7 + - - +
39A HIS* 5.6 5.2 - - + +
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Residues in contact with LYS 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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26A THR* 3.3 24.1 + - - +
27A GLN* 3.4 25.7 + - - +
28A CYS 3.3 0.4 - - - -
29A GLU* 1.3 77.7 - - + +
31A LEU* 1.3 64.4 + - - +
33A GLU* 3.4 6.0 + - - +
34A LYS* 3.0 25.6 + - - +
182A PRO* 3.6 20.4 + - - +
183A GLU* 4.6 4.8 + - - +
186A PHE* 3.4 41.6 - - + +
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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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16A ILE* 4.6 9.6 - - + -
27A GLN 2.9 23.0 + - - +
28A CYS* 3.7 5.2 - - - +
30A LYS* 1.3 73.9 - - - +
32A VAL* 1.3 65.1 + - - +
35A TYR* 3.0 48.7 + - + +
37A PHE* 4.3 5.1 - - + -
94A LEU* 3.7 30.7 - - + -
119A ILE* 5.1 0.4 - - + -
186A PHE* 3.7 17.3 - - + -
189A LEU* 4.3 26.0 - - + -
190A CYS* 4.3 1.8 - - - -
193A ILE* 3.6 33.7 - - + -
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Residues in contact with VAL 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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28A CYS 2.9 22.7 + - - +
29A GLU* 3.7 8.7 - - - +
30A LYS 3.3 0.2 - - - -
31A LEU* 1.3 74.1 - - - +
33A GLU* 1.3 60.5 + - - +
36A GLY* 2.8 34.5 + - - -
37A PHE* 3.4 27.6 - - + +
39A HIS* 3.4 31.9 - - + +
94A LEU* 4.9 4.9 - - + -
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Residues in contact with GLU 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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29A GLU 3.2 14.8 + - - +
30A LYS* 3.7 7.2 - - - +
31A LEU 3.3 0.2 - - - -
32A VAL* 1.3 84.0 - - - +
34A LYS* 1.3 61.1 + - - +
36A GLY* 4.3 2.4 + - - -
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Residues in contact with LYS 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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30A LYS 3.0 17.5 + - - +
31A LEU 4.1 1.8 - - - +
33A GLU* 1.3 77.7 - - - +
35A TYR* 1.3 88.1 + - + +
186A PHE* 3.9 22.9 - - + -
190A CYS* 3.3 28.3 - - - -
194A ASP* 4.8 6.3 + - - -
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Residues in contact with TYR 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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31A LEU* 3.0 49.6 + - + +
34A LYS* 1.3 99.1 - - + +
36A GLY* 1.3 62.9 + - - +
37A PHE* 3.4 37.9 + + + -
91A ARG* 3.3 25.4 - - - +
190A CYS* 3.3 32.0 + - - +
193A ILE* 3.8 17.8 - - + +
194A ASP* 2.6 30.0 + - - -
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Residues in contact with GLY 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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32A VAL* 2.8 16.0 + - - -
33A GLU 4.3 2.1 + - - -
34A LYS 3.5 1.8 - - - -
35A TYR* 1.3 78.1 - - - +
37A PHE* 1.3 60.7 + - - +
90A THR* 3.4 4.5 + - - -
91A ARG* 3.1 32.8 + - - +
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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