Contacts of the helix formed by residues 23 - 36 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F GLY 3.2 2.4 + - - -
22F SER* 1.3 78.6 - - - +
24F LYS* 1.3 61.7 + - - +
25F GLY 3.4 2.7 - - - -
26F THR* 2.9 27.1 + - - -
27F GLN* 3.1 14.8 + - - +
121F MET* 3.9 4.7 - - - -
131F ARG* 4.9 2.2 - - - -
1199F SO4 2.9 14.3 + - - -
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Residues in contact with LYS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 3.7 29.6 - - + +
17F ILE* 3.9 1.8 - - - +
18F GLY 3.5 35.8 + - - +
22F SER* 3.5 9.0 - - - +
23F GLY* 1.3 74.3 - - - +
25F GLY* 1.3 61.6 + - - +
27F GLN* 3.3 1.6 + - - +
28F CYS* 2.9 37.2 + - - -
96F ASP* 2.8 34.6 + - - +
97F GLY* 4.5 9.0 - - - +
121F MET* 3.7 15.9 - - - -
1199F SO4 3.3 16.6 + - - +
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Residues in contact with GLY 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLY 3.4 0.2 - - - -
24F LYS* 1.3 79.2 - - - +
26F THR* 1.3 61.1 + - - +
28F CYS* 3.5 6.6 + - - +
29F GLU* 3.3 29.9 + - - +
39F HIS* 5.3 2.6 - - - -
96F ASP* 5.6 3.6 - - - -
1199F SO4 2.9 19.0 + - - -
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Residues in contact with THR 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F GLY* 2.9 22.8 + - - -
25F GLY* 1.3 74.1 - - - +
27F GLN* 1.3 70.8 + - - +
29F GLU* 3.2 18.9 + - - +
30F LYS* 3.2 33.8 + - - +
182F PRO* 5.2 6.2 - - - +
1199F SO4 5.5 0.6 + - - +
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Residues in contact with GLN 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 5.0 2.2 - - + -
23F GLY* 3.1 21.1 + - - +
24F LYS* 3.3 7.4 + - - +
26F THR* 1.3 79.1 + - - +
28F CYS* 1.3 55.4 + - - +
30F LYS* 3.2 13.3 + - - +
31F LEU* 2.9 35.0 + - - +
121F MET* 3.9 8.7 - - + -
182F PRO* 2.8 42.4 + - - +
185F VAL* 3.8 16.7 - - + +
186F PHE* 3.1 30.1 - - - +
189F LEU* 3.2 26.9 - - + +
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Residues in contact with CYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ILE* 3.8 32.5 - - - -
24F LYS* 2.9 26.0 + - - +
25F GLY* 3.8 5.4 - - - +
26F THR 3.2 0.2 - - - -
27F GLN* 1.3 72.7 - - - +
29F GLU* 1.3 65.5 + - - +
31F LEU* 3.5 2.3 + - - +
32F VAL* 3.0 30.7 + - - +
39F HIS* 3.5 36.8 - - + +
94F LEU* 3.9 15.4 - - + +
96F ASP* 4.1 9.0 - - - -
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Residues in contact with GLU 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLY 3.3 16.9 + - - +
26F THR* 3.2 18.8 + - - +
28F CYS* 1.3 79.4 - - - +
30F LYS* 1.3 57.8 + - + +
32F VAL* 3.4 7.5 + - - +
33F GLU* 3.0 28.2 + - - +
39F HIS* 5.2 0.4 + - - -
1202F AMP 3.7 30.5 + - - -
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Residues in contact with LYS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F THR* 3.3 18.6 - - - +
27F GLN* 3.2 22.9 + - - +
29F GLU* 1.3 75.6 - - + +
31F LEU* 1.3 61.3 + - - +
33F GLU* 3.4 6.8 + - - +
34F LYS* 2.9 30.5 + - - +
182F PRO* 4.2 19.7 + - - +
183F GLU* 4.4 20.6 + - - +
186F PHE* 3.5 41.4 - - + +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 4.4 9.9 - - + -
27F GLN 2.9 24.2 + - - +
28F CYS 3.8 4.3 - - - +
29F GLU 3.4 0.2 - - - -
30F LYS* 1.3 73.4 - - - +
32F VAL* 1.3 60.6 + - - +
35F TYR* 2.8 46.0 + - + +
37F PHE* 4.1 8.4 - - + -
94F LEU* 3.9 31.2 - - + -
119F ILE* 4.9 2.7 - - + -
186F PHE* 3.7 19.5 - - + -
189F LEU* 4.2 24.7 - - + -
190F CYS* 4.6 1.3 - - - -
193F ILE* 3.5 31.9 - - + -
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F CYS 3.0 21.7 + - - +
29F GLU* 3.5 7.9 - - - +
30F LYS 3.2 0.2 - - - -
31F LEU* 1.3 76.3 - - - +
33F GLU* 1.3 62.2 + - - +
36F GLY* 2.7 32.1 + - - -
37F PHE* 3.6 30.7 - - - +
39F HIS* 3.7 26.2 - - + +
94F LEU* 4.6 5.6 - - + -
1202F AMP 4.4 16.2 - - + +
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Residues in contact with GLU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F GLU 3.0 16.7 + - - +
30F LYS* 3.7 8.1 - - - +
32F VAL* 1.3 82.5 - - + +
34F LYS* 1.3 61.4 + - - +
36F GLY* 4.5 0.9 + - - -
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Residues in contact with LYS 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS 2.9 17.0 + - - +
31F LEU 4.0 1.6 - - - +
33F GLU* 1.3 81.1 - - - +
35F TYR* 1.3 94.6 + - + +
36F GLY 3.7 0.2 + - - -
91F ARG* 5.6 1.7 + - - -
186F PHE* 3.6 26.7 - - + -
190F CYS* 3.6 14.8 - - - -
194F ASP* 4.9 4.5 - - - -
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Residues in contact with TYR 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 2.8 50.2 + - + +
34F LYS* 1.3 103.0 - - + +
36F GLY* 1.3 59.7 + - - +
37F PHE* 3.4 38.6 - + + -
91F ARG* 3.5 32.1 + - - +
190F CYS* 3.2 28.8 + - - +
193F ILE* 3.7 18.9 - - + +
194F ASP* 2.8 28.6 + - - -
197F PHE* 5.6 2.7 - - + -
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Residues in contact with GLY 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F VAL* 2.7 24.3 + - - -
33F GLU 4.5 1.0 + - - -
34F LYS 3.5 2.2 + - - -
35F TYR* 1.3 73.2 - - - +
37F PHE* 1.3 64.2 + - - +
38F THR* 3.7 2.4 + - - -
91F ARG* 3.1 27.2 + - - +
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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