Contacts of the helix formed by residues 23 - 36 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D GLY 3.3 1.6 - - - -
22D SER* 1.3 79.2 - - - +
24D LYS* 1.3 60.9 + - - +
25D GLY 3.6 1.1 - - - -
26D THR* 3.8 15.8 - - - +
27D GLN* 3.0 33.7 + - - +
121D MET* 4.3 0.9 - - - -
131D ARG* 3.6 13.4 - - - +
1197D SO4 2.8 16.2 + - - -
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Residues in contact with LYS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.9 25.4 - - + +
17D ILE 4.0 5.6 - - - -
18D GLY* 3.5 38.4 + - - +
22D SER* 3.4 8.9 - - - +
23D GLY* 1.3 75.3 - - - +
25D GLY* 1.3 58.2 + - - +
27D GLN* 2.9 3.3 + - - +
28D CYS* 2.8 37.4 + - - -
96D ASP* 2.7 40.3 + - - +
97D GLY* 3.1 24.0 - - - +
121D MET* 3.7 12.3 - - + -
1197D SO4 3.0 11.6 + - - +
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LYS* 1.3 79.8 - - - +
26D THR* 1.3 61.9 + - - +
28D CYS* 3.4 14.4 + - - +
29D GLU* 3.4 22.1 + - - +
39D HIS* 5.3 2.8 - - - -
96D ASP* 5.3 3.1 - - - -
1197D SO4 2.9 17.5 + - - -
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLY* 3.8 26.2 + - - +
25D GLY* 1.3 73.2 - - - +
27D GLN* 1.3 68.3 + - - +
29D GLU* 3.5 17.6 + - - +
30D LYS* 3.4 18.2 + - - +
131D ARG* 5.6 4.3 - - - +
182D PRO* 5.0 9.0 - - - +
1197D SO4 4.2 6.3 + - - +
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Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 5.4 0.2 - - + -
23D GLY 3.0 22.1 + - - +
24D LYS 2.9 4.5 + - - +
26D THR* 1.3 80.1 + - - +
28D CYS* 1.3 59.9 + - - +
30D LYS* 3.2 7.3 + - - +
31D LEU* 3.0 32.8 + - + +
121D MET* 3.7 13.9 - - + -
182D PRO* 2.9 41.6 + - - +
185D VAL* 3.7 12.6 - - + +
186D PHE* 3.4 22.0 - - - +
189D LEU* 3.1 34.6 - - + +
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Residues in contact with CYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 3.8 31.2 - - - -
24D LYS* 2.8 24.3 + - - +
25D GLY* 3.8 4.7 - - - +
27D GLN* 1.3 72.0 - - - +
29D GLU* 1.3 52.8 + - - +
31D LEU* 3.2 10.3 + - - +
32D VAL* 2.8 40.3 + - - +
39D HIS* 3.2 29.4 - - + +
94D LEU* 4.1 7.1 - - + +
96D ASP* 3.7 22.7 - - - -
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLY 3.4 13.9 + - - +
26D THR* 3.6 20.7 - - - +
27D GLN 3.3 0.4 - - - -
28D CYS* 1.3 76.4 - - + +
30D LYS* 1.3 58.5 + - - +
32D VAL* 3.4 8.4 + - - +
33D GLU* 3.1 35.5 + - + +
39D HIS* 5.5 4.5 - - + +
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Residues in contact with LYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR 3.4 8.9 + - - +
27D GLN* 3.2 11.8 + - - +
29D GLU* 1.3 77.8 - - - +
31D LEU* 1.3 57.1 + - - +
33D GLU* 3.5 5.5 + - - +
34D LYS* 2.9 32.4 + - - +
186D PHE* 3.5 30.0 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D ILE* 4.6 13.7 - - + -
27D GLN 3.0 19.5 + - - +
28D CYS* 3.2 15.0 + - - +
30D LYS* 1.3 74.6 - - - +
32D VAL* 1.3 60.1 + - - +
34D LYS* 4.4 2.2 - - + +
35D TYR* 3.0 33.8 + - + +
36D GLY 4.0 0.7 + - - -
37D PHE* 4.2 9.0 - - + -
94D LEU* 4.3 20.6 - - + -
119D ILE* 4.7 1.6 - - + -
186D PHE* 3.8 21.3 - - + -
189D LEU* 4.4 23.1 - - + -
190D CYS* 4.8 5.6 - - - -
193D ILE* 3.3 35.4 - - + -
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D CYS 2.8 21.2 + - - +
29D GLU* 3.6 9.4 - - - +
31D LEU* 1.3 77.0 - - - +
33D GLU* 1.3 63.2 + - + +
36D GLY* 2.8 32.2 + - - -
37D PHE* 4.2 21.8 - - - +
39D HIS* 3.7 34.5 - - + +
94D LEU* 4.9 4.7 - - + -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.1 18.3 + - + +
30D LYS* 4.0 5.2 - - - +
32D VAL* 1.3 81.1 - - + +
34D LYS* 1.3 58.7 + - - +
35D TYR 3.6 0.2 - - - -
36D GLY 4.6 1.0 + - - -
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS 2.9 19.7 + - - +
31D LEU* 4.4 2.7 - - + +
32D VAL 3.2 0.2 - - - -
33D GLU* 1.3 78.6 - - - +
35D TYR* 1.3 60.7 + - - +
36D GLY 4.0 0.2 - - - -
186D PHE* 3.5 22.9 - - + -
190D CYS* 5.8 2.0 - - - -
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Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 3.0 12.0 + - + +
34D LYS* 1.3 78.5 - - - +
36D GLY* 1.3 66.0 + - - +
37D PHE* 3.1 35.8 + - + -
91D ARG* 4.0 12.8 - - - +
193D ILE* 5.6 6.1 - - + -
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Residues in contact with GLY 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D VAL* 2.8 17.8 + - - -
33D GLU 4.6 1.0 - - - -
35D TYR* 1.3 77.1 - - - +
37D PHE* 1.3 63.0 - - - +
38D THR* 3.9 0.9 + - - -
90D THR* 5.6 0.5 - - - -
91D ARG* 3.9 23.1 + - - +
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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