Contacts of the helix formed by residues 23 - 36 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C GLY 3.3 1.8 - - - -
22C SER* 1.3 78.7 - - - +
24C LYS* 1.3 63.7 + - - +
25C GLY 3.3 2.9 + - - -
26C THR* 3.5 11.3 + - - -
27C GLN* 3.1 27.0 + - - +
121C MET* 3.8 3.8 - - - -
131C ARG* 5.1 1.3 - - - -
1198C SO4 3.0 14.1 + - - -
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 3.7 30.7 - - + +
17C ILE* 3.8 4.9 - - - +
18C GLY 3.3 39.7 - - - +
22C SER* 3.5 9.7 - - - +
23C GLY* 1.3 77.8 - - - +
25C GLY* 1.3 58.8 + - - +
27C GLN* 3.3 1.8 + - - +
28C CYS* 2.9 34.1 + - - -
96C ASP* 2.7 32.9 + - - +
97C GLY* 4.5 7.0 - - - +
121C MET* 3.8 15.0 - - - -
1198C SO4 3.1 14.4 + - - +
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Residues in contact with GLY 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LYS* 1.3 81.1 - - - +
26C THR* 1.3 61.0 + - - +
28C CYS* 3.3 7.2 + - - +
29C GLU* 3.3 26.8 + - - +
39C HIS* 5.4 2.0 - - - -
96C ASP* 5.4 3.8 - - - -
1198C SO4 3.0 19.1 + - - -
1199C AMP 6.5 1.6 - - - -
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Residues in contact with THR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY* 3.5 12.6 + - - -
24C LYS 3.4 0.4 - - - -
25C GLY* 1.3 74.9 - - - +
27C GLN* 1.3 65.8 + - - +
29C GLU* 3.4 17.5 + - - +
30C LYS* 3.2 35.7 + - + +
182C PRO* 5.2 9.4 - - + -
1198C SO4 4.8 1.0 + - - -
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 5.2 1.3 - - + -
23C GLY* 3.1 19.4 + - - +
24C LYS* 3.3 6.9 + - - +
26C THR* 1.3 76.2 - - - +
28C CYS* 1.3 60.4 + - - +
30C LYS* 3.4 11.8 + - - +
31C LEU* 2.9 37.4 + - + +
121C MET* 4.0 8.1 - - + -
182C PRO* 2.7 44.6 + - - +
185C VAL* 3.8 16.4 - - + +
186C PHE* 3.2 22.3 - - - +
189C LEU* 3.1 34.1 - - + +
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Residues in contact with CYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.8 29.8 - - - -
24C LYS* 2.9 25.5 + - - +
25C GLY* 3.6 5.2 - - - +
26C THR 3.3 0.2 - - - -
27C GLN* 1.3 77.2 - - - +
29C GLU* 1.3 57.5 + - - +
31C LEU* 3.5 1.8 + - - +
32C VAL* 3.0 35.3 + - - +
39C HIS* 3.6 36.3 - - + +
94C LEU* 3.9 15.7 - - + +
96C ASP* 3.8 10.3 - - - +
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLY 3.3 14.1 + - - +
26C THR* 3.6 20.0 + - - +
27C GLN 3.3 0.4 - - - -
28C CYS* 1.3 76.5 - - + +
30C LYS* 1.3 60.1 + - + +
32C VAL* 3.4 6.8 + - - +
33C GLU* 3.0 28.4 + - - +
39C HIS* 5.8 1.3 - - + +
1199C AMP 3.7 31.8 + - - -
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 3.2 22.9 + - + +
27C GLN* 3.6 30.5 - - - +
29C GLU* 1.3 77.2 - - + +
31C LEU* 1.3 56.4 + - - +
33C GLU* 3.2 7.5 + - - +
34C LYS* 3.0 29.6 + - - +
182C PRO* 4.6 7.2 - - + +
183C GLU* 6.0 1.8 - - + +
186C PHE* 3.4 35.8 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.1 16.8 - - + -
27C GLN 2.9 22.5 + - - +
28C CYS 3.8 4.3 - - - +
30C LYS* 1.3 72.4 - - - +
32C VAL* 1.3 61.1 + - - +
35C TYR* 3.0 45.9 + - + +
36C GLY 3.8 0.2 + - - -
37C PHE* 3.9 7.6 - - + -
94C LEU* 4.1 26.0 - - + -
119C ILE* 5.0 1.1 - - + -
186C PHE* 3.8 17.9 - - + -
189C LEU* 4.1 27.6 - - + -
190C CYS* 4.4 1.6 - - - -
193C ILE* 3.3 34.1 - - + -
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C CYS 3.0 22.8 + - - +
29C GLU* 3.7 7.4 - - - +
31C LEU* 1.3 74.8 - - - +
33C GLU* 1.3 61.7 - - - +
36C GLY* 2.7 33.5 + - - +
37C PHE* 3.7 26.0 - - + +
39C HIS* 3.7 26.9 - - + +
94C LEU* 4.5 6.7 - - + -
1199C AMP 6.0 4.0 - - + +
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Residues in contact with GLU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLU 3.0 14.6 + - - +
30C LYS* 3.2 11.4 + - - +
32C VAL* 1.3 79.1 - - - +
34C LYS* 1.3 61.3 + - - +
36C GLY* 4.4 0.9 + - - -
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LYS 3.0 15.5 + - - +
33C GLU* 1.3 80.5 - - - +
35C TYR* 1.3 82.4 + - + +
186C PHE* 3.9 20.4 - - + -
190C CYS* 5.1 2.9 - - - -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 3.0 37.5 + - + +
34C LYS* 1.3 91.3 - - + +
36C GLY* 1.3 63.6 + - - +
37C PHE* 3.2 41.5 + + + -
91C ARG* 3.6 16.8 - - - +
190C CYS* 3.4 29.9 + - - +
193C ILE* 3.8 16.6 - - + -
194C ASP* 2.6 37.2 + - - -
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 2.7 28.5 + - - -
33C GLU 4.4 0.8 + - - -
34C LYS 3.6 1.4 - - - -
35C TYR* 1.3 72.9 - - - +
37C PHE* 1.3 65.7 + - - +
38C THR* 3.7 1.4 + - - -
90C THR* 5.4 0.2 - - - -
91C ARG* 3.7 17.7 + - - +
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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