Contacts of the helix formed by residues 23 - 36 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLY 3.3 3.0 + - - -
22B SER* 1.3 77.9 - - - +
24B LYS* 1.3 64.0 + - - +
25B GLY 3.4 2.7 - - - -
26B THR* 3.5 9.0 + - - -
27B GLN* 3.1 27.2 + - - +
121B MET* 3.8 4.3 - - - -
131B ARG* 4.0 5.1 - - - +
1199B SO4 3.0 13.9 + - - -
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 3.7 28.9 - - + +
17B ILE* 3.8 4.7 - - - +
18B GLY* 3.5 34.1 - - - +
22B SER* 3.3 10.7 + - - +
23B GLY* 1.3 74.6 - - - +
25B GLY* 1.3 70.1 + - - +
27B GLN* 3.3 0.5 + - - +
28B CYS* 2.9 32.0 + - - -
96B ASP* 2.6 36.1 + - - +
97B GLY* 4.4 7.8 - - - +
121B MET* 3.9 14.1 - - - +
1199B SO4 3.1 14.3 + - - +
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 3.4 0.2 - - - -
24B LYS* 1.3 79.4 - - - +
26B THR* 1.3 62.9 + - - +
28B CYS* 3.4 6.4 + - - +
29B GLU* 3.3 28.2 + - - +
39B HIS* 5.1 2.3 - - - -
96B ASP* 5.2 4.5 - - - -
1199B SO4 3.0 20.7 + - - -
1201B AMP 5.4 0.9 - - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY* 3.5 10.4 + - - -
24B LYS 3.3 0.4 - - - -
25B GLY* 1.3 74.4 - - - +
27B GLN* 1.3 66.2 + - - +
29B GLU* 3.3 19.2 + - - +
30B LYS* 3.2 35.8 + - + +
182B PRO* 5.8 5.8 - - + -
1199B SO4 4.9 1.1 + - - -
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Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 5.5 0.9 - - + -
23B GLY 3.1 19.6 + - - +
24B LYS 3.9 2.9 - - - +
26B THR* 1.3 76.1 - - - +
28B CYS* 1.3 65.3 + - - +
30B LYS* 3.1 12.4 + - - +
31B LEU* 2.9 29.1 + - + +
121B MET* 3.7 22.7 - - + -
182B PRO* 3.0 41.0 + - - +
185B VAL* 3.7 9.2 - - - +
186B PHE* 3.3 34.3 - - - +
189B LEU* 3.5 19.3 - - + +
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Residues in contact with CYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.7 34.5 - - - -
24B LYS* 2.9 24.7 + - - +
25B GLY 3.6 3.8 - - - +
26B THR 3.4 0.2 - - - -
27B GLN* 1.3 74.8 - - - +
29B GLU* 1.3 56.2 + - - +
31B LEU* 3.2 4.2 + - - +
32B VAL* 2.8 34.6 + - - +
39B HIS* 3.4 26.5 - - + +
94B LEU* 3.9 14.5 - - + +
96B ASP* 3.8 17.0 - - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY 3.3 16.3 + - - +
26B THR* 3.3 19.8 + - - +
28B CYS* 1.3 77.0 - - - +
30B LYS* 1.3 58.4 + - + +
32B VAL* 3.3 8.8 + - - +
33B GLU* 2.9 29.7 + - - +
1201B AMP 3.3 46.2 + - - +
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Residues in contact with LYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 3.2 25.7 + - + +
27B GLN* 3.1 24.9 + - - +
29B GLU* 1.3 78.1 - - + +
31B LEU* 1.3 56.7 - - - +
33B GLU* 3.3 7.6 + - - +
34B LYS* 2.8 30.1 + - - +
182B PRO* 4.5 13.0 - - + +
183B GLU* 5.4 2.8 - - - +
186B PHE* 3.4 49.8 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 4.4 10.5 - - + -
27B GLN 2.9 19.0 + - - +
28B CYS* 3.5 8.5 - - - +
30B LYS* 1.3 74.7 - - - +
32B VAL* 1.3 57.3 + - - +
35B TYR* 2.7 56.8 + - + +
37B PHE* 4.2 5.3 - - + -
94B LEU* 4.1 29.2 - - + -
119B ILE* 5.0 1.3 - - + -
186B PHE* 3.8 16.6 - - + -
189B LEU* 4.2 26.0 - - + -
190B CYS* 4.5 1.1 - - - -
193B ILE* 3.4 33.9 - - + -
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B CYS 2.8 21.2 + - - +
29B GLU* 3.6 7.6 - - - +
31B LEU* 1.3 75.7 - - - +
33B GLU* 1.3 60.4 + - - +
36B GLY* 2.8 30.6 + - - -
37B PHE* 3.8 24.9 - - + +
39B HIS* 3.6 33.0 - - + +
94B LEU* 4.4 7.0 - - + -
1201B AMP 4.2 12.8 - - - +
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU 2.9 17.8 + - - +
30B LYS* 3.5 7.6 - - - +
32B VAL* 1.3 80.3 - - - +
34B LYS* 1.3 62.1 + - - +
36B GLY* 4.5 1.0 + - - -
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS 2.8 20.5 + - - +
31B LEU 4.0 1.8 - - - +
33B GLU* 1.3 76.7 - - - +
35B TYR* 1.3 96.7 + - + +
36B GLY 3.6 0.2 - - - -
186B PHE* 3.8 15.5 - - + -
190B CYS* 3.6 27.6 - - - -
194B ASP* 5.0 4.8 + - - -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 2.7 46.7 + - + +
34B LYS* 1.3 98.6 - - + +
36B GLY* 1.3 59.5 + - - +
37B PHE* 3.3 39.9 - + + -
91B ARG* 3.4 20.6 - - - +
190B CYS* 3.2 35.8 + - - +
193B ILE* 3.7 17.3 - - + -
194B ASP* 2.9 27.8 + - - -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B VAL* 2.8 17.6 + - - -
33B GLU 4.5 1.0 + - - -
34B LYS 3.6 1.4 - - - -
35B TYR* 1.3 77.9 - - - +
37B PHE* 1.3 65.8 + - - +
38B THR* 3.8 1.4 + - - -
90B THR* 5.4 0.5 - - - -
91B ARG* 3.7 28.4 + - - +
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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