Contacts of the helix formed by residues 23 - 36 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E GLY 3.1 2.9 + - - -
22E SER* 1.3 78.6 - - - +
24E LYS* 1.3 64.2 + - - +
25E GLY 3.4 2.4 + - - -
26E THR* 3.5 11.8 + - - -
27E GLN* 3.1 31.6 + - - +
121E MET* 4.7 1.3 - - - -
131E ARG* 5.0 1.3 - - - -
1198E SO4 2.9 14.3 + - - -
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Residues in contact with LYS 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 3.7 25.3 - - + +
17E ILE* 3.9 3.4 - - - +
18E GLY 3.4 39.5 - - - +
22E SER* 3.5 13.1 + - - +
23E GLY* 1.3 76.8 - - - +
25E GLY* 1.3 58.4 + - - +
27E GLN* 3.8 1.1 - - - +
28E CYS* 2.9 44.2 + - - -
96E ASP* 2.5 34.5 + - - +
97E GLY* 4.3 7.8 - - - +
121E MET* 4.1 13.9 - - + -
1198E SO4 3.1 11.3 + - - +
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Residues in contact with GLY 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY 3.4 0.2 - - - -
24E LYS* 1.3 75.8 - - - +
26E THR* 1.3 60.1 + - - +
28E CYS* 3.4 7.7 + - - +
29E GLU* 3.3 29.1 + - - +
39E HIS* 5.5 2.2 - - - -
96E ASP* 5.4 4.0 - - - -
1198E SO4 2.8 22.1 + - - -
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Residues in contact with THR 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY* 3.5 17.7 + - - -
25E GLY* 1.3 71.2 - - - +
27E GLN* 1.3 66.9 + - - +
29E GLU* 3.2 23.7 + - - +
30E LYS* 3.2 32.7 + - - +
182E PRO* 6.4 1.3 - - - -
1198E SO4 5.1 1.3 + - - -
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Residues in contact with GLN 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 5.2 2.5 - - + -
22E SER 5.9 0.2 - - - +
23E GLY* 3.1 23.2 + - - +
24E LYS* 3.8 6.1 - - - +
25E GLY 3.3 0.2 - - - -
26E THR* 1.3 79.2 + - - +
28E CYS* 1.3 56.2 + - - +
30E LYS* 3.3 11.5 + - - +
31E LEU* 2.9 34.2 + - - +
121E MET* 4.5 5.6 - - - -
182E PRO* 2.9 43.0 + - - +
185E VAL* 3.7 22.2 - - + +
186E PHE* 3.4 21.5 - - - +
189E LEU* 3.2 28.2 - - + +
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Residues in contact with CYS 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ILE* 3.9 32.1 - - - -
24E LYS* 2.9 30.0 + - - +
25E GLY* 3.6 7.0 - - - +
26E THR 3.3 0.2 - - - -
27E GLN* 1.3 76.4 - - - +
29E GLU* 1.3 55.7 + - + +
31E LEU* 3.4 2.7 + - - +
32E VAL* 3.0 34.9 + - - +
39E HIS* 3.7 25.1 - - + +
94E LEU* 4.0 15.9 - - + +
96E ASP* 4.0 15.7 - - - -
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Residues in contact with GLU 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E GLY 3.5 19.9 - - - +
26E THR* 3.2 23.8 + - - +
28E CYS* 1.3 72.9 - - + +
30E LYS* 1.3 62.7 + - + +
32E VAL* 3.4 6.7 + - - +
33E GLU* 2.9 29.7 + - - +
39E HIS* 6.0 1.6 - - + +
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Residues in contact with LYS 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E THR* 3.2 16.5 + - - +
27E GLN* 3.3 22.6 + - - +
29E GLU* 1.3 80.4 - - + +
31E LEU* 1.3 57.0 + - - +
33E GLU* 3.4 7.1 + - - +
34E LYS* 2.9 30.3 + - - +
182E PRO* 3.9 29.9 + - - +
183E GLU* 4.2 14.8 + - - +
186E PHE* 3.3 37.5 - - + +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 4.4 20.0 - - + -
27E GLN 2.9 20.5 + - - +
28E CYS 3.7 4.5 - - - +
29E GLU 3.3 0.2 - - - -
30E LYS* 1.3 72.3 - - - +
32E VAL* 1.3 57.7 + - - +
35E TYR* 2.7 59.0 + - + +
37E PHE* 4.7 5.8 - - + -
94E LEU* 3.7 29.8 - - + -
119E ILE* 5.1 0.7 - - + -
186E PHE* 3.8 15.7 - - + -
189E LEU* 4.4 19.5 - - + -
190E CYS* 4.6 1.3 - - - -
193E ILE* 3.3 34.3 - - + -
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Residues in contact with VAL 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E CYS 3.0 22.2 + - - +
29E GLU* 3.7 6.5 - - - +
31E LEU* 1.3 73.8 - - - +
33E GLU* 1.3 63.3 + - - +
36E GLY* 2.8 30.1 + - - -
37E PHE* 3.6 35.4 - - + +
39E HIS* 3.7 26.2 - - + +
94E LEU* 4.7 3.6 - - + -
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Residues in contact with GLU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU 2.9 18.3 + - - +
30E LYS* 3.6 8.5 - - - +
32E VAL* 1.3 79.1 - - - +
34E LYS* 1.3 60.7 + - - +
36E GLY* 4.6 0.7 + - - -
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Residues in contact with LYS 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS 2.9 17.8 + - - +
31E LEU 3.9 2.2 - - - +
33E GLU* 1.3 80.0 - - - +
35E TYR* 1.3 95.2 + - + +
186E PHE* 4.0 15.9 - - + -
190E CYS* 3.4 26.9 - - - -
194E ASP* 5.7 2.2 - - - -
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Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E LEU* 2.7 55.9 + - + +
34E LYS* 1.3 100.5 - - + +
36E GLY* 1.3 60.9 + - - +
37E PHE* 3.4 33.4 - + + -
91E ARG* 3.5 18.2 - - - +
190E CYS* 3.3 26.3 + - - +
193E ILE* 3.6 18.1 - - + +
194E ASP* 2.7 28.9 + - - -
197E PHE* 4.5 14.1 - + - -
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Residues in contact with GLY 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 2.8 19.0 + - - -
33E GLU 4.6 0.8 + - - -
34E LYS 3.7 1.0 - - - -
35E TYR* 1.3 77.5 - - - +
37E PHE* 1.3 65.8 + - - +
90E THR* 3.3 14.4 + - - -
91E ARG* 4.0 7.0 + - - +
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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