Contacts of the helix formed by residues 25 - 38 (chain B) in PDB entry 2B4M
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 SER 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.5 18.2 - - - +
22B ASP* 2.5 24.0 + - - -
23B PRO 3.2 2.9 - - - +
24B GLY* 1.3 80.2 - - - +
26B GLY* 1.3 62.9 + - - +
27B ILE* 3.7 1.4 - - - +
28B MET* 3.1 26.3 + - - +
29B SER* 3.3 14.4 + - - -
178B TRP* 4.2 12.6 - - - -
310B PBE 3.1 19.3 - - - -
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 4.3 0.4 + - - -
25B SER* 1.3 72.0 - - - +
27B ILE* 1.3 57.3 + - - +
28B MET 3.2 0.5 + - - -
29B SER* 3.2 8.4 + - - -
30B LEU* 3.0 38.0 + - - +
229B THR* 3.7 26.6 - - - +
230B HIS* 5.9 1.2 - - - -
310B PBE 2.9 14.6 + - - -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 3.4 38.8 - - + -
25B SER* 3.7 2.2 - - - +
26B GLY* 1.3 75.4 - - - +
28B MET* 1.3 57.3 + - + +
29B SER 3.5 0.2 - - - -
30B LEU* 3.7 9.1 - - - +
31B THR* 2.7 39.5 + - - +
70B THR* 4.1 18.4 - - - +
71B GLY 3.4 26.2 - - - +
72B TRP* 3.8 19.3 - - + -
93B TYR* 4.5 9.4 - - + -
253B MET* 3.8 20.0 - - + -
254B GLY 4.3 2.7 - - - +
310B PBE 3.2 19.3 + - - +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 4.0 7.4 - - - -
21B ILE* 3.4 33.0 - - + +
22B ASP 3.2 11.2 - - - +
23B PRO* 3.9 11.4 - - + +
25B SER* 3.1 27.8 + - - +
27B ILE* 1.3 77.7 - - - +
29B SER* 1.3 59.4 + - - +
31B THR* 3.5 3.3 + - - -
32B ASP* 3.1 26.7 + - - +
45B LEU* 3.7 38.7 - - + +
46B ILE 4.1 1.8 - - - +
47B SER* 3.1 32.5 - - - +
70B THR* 4.5 7.9 - - - -
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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
----------------------------------------------------------
23B PRO 5.3 2.0 + - - -
24B GLY 5.9 0.5 - - - -
25B SER 3.3 9.2 + - - -
26B GLY* 3.2 10.6 + - - -
28B MET* 1.3 73.6 - - - +
30B LEU* 1.3 60.7 + - - +
32B ASP* 3.1 11.3 + - - +
33B LYS* 3.0 27.0 + - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY 3.0 24.3 + - - +
27B ILE* 3.7 5.4 - - - +
29B SER* 1.3 78.6 - - - +
31B THR* 1.3 54.4 + - - +
33B LYS* 3.3 20.3 + - - +
34B ALA* 2.9 25.1 + - - +
92B SER 3.7 24.5 - - - +
93B TYR* 3.6 34.0 - - + +
228B ASN* 4.3 24.0 - - + +
229B THR* 4.9 1.1 - - - -
253B MET* 3.8 33.4 - - + -
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Residues in contact with THR 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.9 1.8 - - + -
27B ILE* 2.7 23.2 + - - +
28B MET* 3.7 6.7 - - - -
29B SER 3.2 0.2 - - - -
30B LEU* 1.3 73.2 - - - +
32B ASP* 1.3 61.3 + - - +
34B ALA* 3.0 3.1 + - + +
35B MET* 2.8 46.3 + - + +
45B LEU* 3.9 31.4 - - + -
70B THR* 3.6 18.2 - - + +
93B TYR* 3.1 27.2 + - - +
255B LEU* 4.3 8.7 - - + -
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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 MET 3.1 15.3 + - - +
29B SER* 3.1 13.9 - - - +
31B THR* 1.3 74.5 - - - +
33B LYS* 1.3 63.8 + - - +
35B MET* 3.5 19.4 + - - +
36B LYS* 2.7 58.0 + - - +
45B LEU* 4.8 4.4 - - - +
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER 3.0 11.8 + - - +
30B LEU* 3.4 21.6 - - - +
32B ASP* 1.3 75.0 - - - +
34B ALA* 1.3 50.7 + - - +
36B LYS* 3.2 12.5 + - + +
37B ASP* 2.7 59.2 + - - +
92B SER* 3.6 22.9 + - - +
231B LYS* 5.4 10.1 - - - +
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Residues in contact with ALA 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 LEU 2.9 14.6 + - - +
31B THR* 3.0 9.4 + - + +
33B LYS* 1.3 74.8 - - - +
35B MET* 1.3 57.1 + - + +
37B ASP 2.8 19.8 + - - -
38B TYR* 3.0 26.1 + - + +
40B LEU* 5.1 2.0 - - + -
92B SER* 3.7 23.3 - - - +
93B TYR* 3.9 24.7 - - + +
255B LEU* 5.7 2.7 - - + -
267B ILE* 5.1 4.7 - - + -
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Residues in contact with MET 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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18B ILE* 4.1 22.2 - - + -
31B THR* 2.8 28.6 + - + +
32B ASP* 3.9 19.5 - - - +
34B ALA* 1.3 72.0 - - + +
36B LYS* 1.3 59.7 + - + +
39B ASP* 3.4 2.4 + - - -
40B LEU* 2.7 55.7 + - + +
41B ASN* 4.2 8.4 + - - +
43B TRP* 4.9 14.1 - - - +
44B THR 5.0 0.2 - - - -
45B LEU* 3.7 45.8 - - + +
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Residues in contact with LYS 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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236A LYS* 2.7 31.2 + - - -
32B ASP* 2.7 55.1 + - - +
33B LYS* 3.4 13.7 - - + +
34B ALA 3.0 0.4 - - - -
35B MET* 1.3 79.2 - - + +
37B ASP* 1.3 54.7 + - - +
38B TYR 3.6 0.2 + - - -
39B ASP* 3.7 4.9 + - - +
41B ASN* 4.4 22.1 - - - +
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 6.0 1.4 - - - +
236A LYS* 3.2 39.0 - - + +
33B LYS* 2.7 46.3 + - - +
34B ALA 2.8 6.3 + - - +
36B LYS* 1.3 75.8 - - - +
38B TYR* 1.3 63.2 + - + +
39B ASP* 3.4 1.5 - - - +
90B LYS* 3.7 21.0 + - + +
92B SER* 3.1 27.7 + - - +
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA* 3.0 25.6 + - - +
37B ASP* 1.3 79.0 - - - +
39B ASP* 1.3 72.2 + - - +
40B LEU* 3.5 18.6 - - + +
88B ASP* 2.4 24.7 + - - -
89B PRO* 3.2 10.9 - - + +
90B LYS* 2.9 45.8 + - + +
92B SER* 3.2 23.1 - - - -
267B ILE* 3.6 37.9 - - + +
268B GLU* 4.1 30.1 - - + -
271B LYS* 3.3 26.6 - - + +
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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