Contacts of the helix formed by residues 23 - 38 (chain B) in PDB entry 2BEW
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 LEU 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASN* 1.3 72.3 - - - +
24B PHE* 1.3 64.2 + - - +
26B SER* 2.9 19.8 + - - +
27B VAL* 3.2 19.1 + - + +
165B PRO* 4.8 0.9 - - + -
167B SER* 3.7 28.7 - - - +
168B PRO* 3.9 7.4 - - + -
171B ALA* 3.9 16.6 - - + -
189B GLU* 4.4 11.9 - - + -
190B PRO* 4.5 14.4 - - + +
193B LEU* 3.6 43.5 - - + +
194B TYR* 3.3 24.7 + - + -
197B ALA 3.1 6.0 + - - +
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.4 21.1 - - - -
23B LEU* 1.3 76.5 - - - +
25B GLN* 1.3 80.3 + - + +
27B VAL* 3.3 5.2 + - - +
28B THR* 3.1 29.8 + - - -
54B PHE 3.6 20.2 - - - +
55B ARG* 3.7 44.2 - - + -
56B CYS* 3.8 9.6 - - - -
58B VAL* 6.2 0.4 - - + -
194B TYR* 3.2 46.4 + - + -
195B ARG* 3.7 34.3 - - + -
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Residues in contact with GLN 25 (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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20B LYS 4.3 3.5 - - - +
21B MET* 3.5 20.1 - - + +
22B ASN* 2.9 48.7 + - - +
24B PHE* 1.3 96.9 - - + +
26B SER* 1.3 59.6 + - - +
28B THR* 3.3 8.4 + - - -
29B SER* 2.9 28.9 + - - -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.9 10.4 - - - -
22B ASN 3.0 12.8 + - - -
23B LEU* 2.9 16.5 + - - -
25B GLN* 1.3 76.0 - - - +
27B VAL* 1.3 55.8 + - - +
29B SER* 3.3 2.9 + - - -
30B ALA* 2.9 27.9 + - - +
168B PRO* 3.3 41.6 + - - +
171B ALA* 3.7 9.5 - - - +
172B LYS* 3.6 13.4 - - - +
201B VAL* 4.3 8.3 - - - -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 3.2 25.4 + - + +
24B PHE 3.5 7.4 - - - +
25B GLN 3.2 0.2 - - - -
26B SER* 1.3 77.3 + - - +
28B THR* 1.3 65.9 + - - +
30B ALA* 3.2 2.8 + - - +
31B LEU* 2.9 34.1 + - + +
56B CYS* 3.9 16.8 - - + -
133B ARG* 3.6 26.9 - - - +
171B ALA* 4.7 7.6 - - + +
172B LYS* 5.6 0.9 - - - +
175B LEU* 3.9 14.8 - - + -
187B PHE* 4.8 0.9 - - + -
189B GLU* 3.7 24.7 - - + +
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Residues in contact with THR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.1 16.6 + - - -
25B GLN* 3.3 10.7 + - - -
27B VAL* 1.3 76.9 - - - +
29B SER* 1.3 53.9 + - - +
31B LEU* 3.3 3.6 + - - +
32B ASP* 2.8 37.7 + - + +
55B ARG 3.6 5.2 + - - -
56B CYS* 2.7 30.6 + - - +
58B VAL* 3.6 24.9 - - + +
60B LEU* 4.1 14.8 - - + +
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.8 23.9 - - - +
25B GLN 2.9 17.7 + - - -
26B SER 3.5 5.2 - - - -
27B VAL 3.1 0.2 - - - -
28B THR* 1.3 79.0 - - - +
30B ALA* 1.3 57.1 + - - +
32B ASP* 3.7 4.8 - - - +
33B ASN* 2.9 34.0 + - - +
172B LYS* 2.8 31.0 + - - +
203B ILE* 4.0 4.5 + - - -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 2.9 16.1 + - - +
27B VAL 3.6 4.5 - - - +
29B SER* 1.3 77.6 - - - +
31B LEU* 1.3 57.3 + - - +
33B ASN* 3.5 0.3 + - - +
34B SER* 2.9 32.8 + - - -
172B LYS* 4.0 35.1 - - + +
175B LEU* 3.8 22.9 - - + -
176B LEU* 3.6 11.6 - - + +
179B ILE* 5.0 0.9 - - + -
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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
----------------------------------------------------------
27B VAL* 2.9 33.4 + - + +
28B THR 3.7 0.4 - - - +
30B ALA* 1.3 72.6 - - - +
32B ASP* 1.3 60.8 + - - +
34B SER* 3.2 5.7 + - - -
35B LEU* 3.0 33.8 + - - +
43B ILE* 3.9 10.3 - - + -
56B CYS 3.9 18.4 - - - +
57B THR* 4.0 18.6 - - + -
60B LEU* 3.7 16.8 - - + -
94B ILE* 3.8 40.2 - - + -
133B ARG* 4.0 16.8 - - - +
175B LEU* 4.3 2.9 - - + -
179B ILE* 4.2 9.4 - - + -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 2.8 22.1 + - + +
29B SER* 3.7 7.2 - - - +
31B LEU* 1.3 72.8 - - - +
33B ASN* 1.3 65.9 + - - +
34B SER 3.2 0.2 + - - -
35B LEU 3.4 0.2 + - - -
36B ALA* 3.0 21.7 + - - +
60B LEU* 3.8 17.9 - - + +
63B LYS* 3.0 29.7 + - - +
64B TYR* 2.6 36.8 + - - -
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 2.9 24.1 + - - +
30B ALA 3.7 4.5 - - - +
32B ASP* 1.3 78.1 + - - +
34B SER* 1.3 61.9 + - - +
36B ALA* 3.5 7.1 + - - +
37B LYS* 3.3 27.6 + - - +
172B LYS* 2.8 29.2 + - - -
176B LEU* 4.4 4.5 - - + -
203B ILE 3.3 15.8 + - - -
204B GLU* 4.6 3.4 + - - +
205B PRO* 3.1 37.8 - - + +
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Residues in contact with SER 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.9 15.8 + - - -
31B LEU* 3.5 9.0 - - - -
32B ASP 3.2 0.2 - - - -
33B ASN* 1.3 75.0 - - - +
35B LEU* 1.3 72.4 + - - +
37B LYS* 3.4 9.0 + - - +
38B ASP* 3.0 31.3 + - - +
41B ALA* 4.8 2.2 - - - -
94B ILE* 4.5 2.2 - - - -
176B LEU* 3.2 16.6 - - - +
179B ILE* 3.4 32.3 - - - +
180B GLU* 5.3 0.2 + - - -
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Residues in contact with LEU 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 3.0 22.5 + - - +
34B SER* 1.3 76.9 - - - +
36B ALA* 1.3 62.6 + - - +
37B LYS 3.5 0.2 + - - -
38B ASP 3.5 5.7 + - - +
39B PRO* 4.5 0.7 - - - +
41B ALA* 3.6 36.8 - - + +
43B ILE* 3.8 24.9 - - + -
60B LEU* 5.8 0.7 - - + -
64B TYR* 3.8 38.8 - - + -
68B ARG* 3.2 42.8 + - + +
69B VAL* 4.0 19.5 - - + -
94B ILE* 4.2 8.1 - - + -
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Residues in contact with ALA 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 ASP* 3.0 13.9 + - - +
33B ASN* 3.7 8.1 - - - +
34B SER 3.2 0.4 - - - -
35B LEU* 1.3 81.0 - - - +
37B LYS* 1.3 58.7 + - + +
38B ASP 5.2 0.3 - - - -
39B PRO* 5.3 1.2 - - - +
64B TYR* 3.3 24.8 + - + +
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Residues in contact with LYS 37 (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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33B ASN 3.3 18.8 + - - +
34B SER* 3.9 10.8 - - - +
36B ALA* 1.3 79.0 - - + +
38B ASP* 1.3 65.4 + - + +
39B PRO* 3.6 9.7 - - - +
176B LEU* 4.7 2.9 - - - -
180B GLU* 3.1 34.1 + - - +
205B PRO* 4.5 25.4 - - + -
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Residues in contact with ASP 38 (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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34B SER* 3.0 15.6 + - - +
35B LEU 3.5 2.8 - - - +
37B LYS* 1.3 83.9 - - + +
39B PRO* 1.3 63.2 - - - +
40B THR* 2.9 29.8 + - - +
41B ALA* 3.1 9.9 + - + +
68B ARG* 2.9 20.3 + - - -
92B THR* 2.7 31.7 + - - +
179B ILE* 5.6 1.4 - - - +
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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
------------------------------------------------------------
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