Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 2BBM
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 THR 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR* 3.1 15.2 + - - -
27A ILE* 1.3 77.1 - - - +
29A THR* 1.3 77.3 + - + +
30A LYS* 2.8 13.6 + - + +
31A GLU* 3.2 16.8 + - - +
32A LEU* 2.7 32.5 + - - +
52A ILE* 4.1 6.1 - - - -
61A GLY 4.5 4.0 - - - +
62A THR* 3.3 33.5 - - + +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 1.3 83.2 - - + +
30A LYS* 1.3 58.1 + - - +
32A LEU* 4.1 6.5 - - - -
33A GLY* 2.7 26.5 + - - -
45A GLU* 5.3 4.9 - - - +
48A LEU* 4.0 17.1 - - + +
49A GLN* 3.8 39.4 + - + +
52A ILE* 3.5 23.3 - - + +
61A GLY 5.6 0.9 - - - +
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASP* 4.7 13.5 - - - +
28A THR* 2.8 12.4 + - + -
29A THR* 1.3 80.5 + - - +
31A GLU* 1.3 61.0 + - + +
32A LEU 3.0 0.7 - - - -
33A GLY* 3.8 0.2 - - - -
34A THR* 2.7 47.0 + - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.6 27.6 - - + +
20A ASP* 2.4 14.0 - - - +
21A LYS* 4.6 1.8 - - + +
22A ASP* 2.9 22.9 - - - +
24A ASP* 3.3 2.4 - - - +
26A THR 2.4 24.3 - - - +
27A ILE* 4.3 2.0 - - - +
28A THR* 3.2 18.9 + - - +
30A LYS* 1.3 84.2 - - + +
32A LEU* 1.3 58.8 + - - +
34A THR* 2.8 17.7 + - - -
35A VAL* 3.1 22.6 - - - +
181A CA 1.9 31.3 - - - -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.7 5.1 - - - -
27A ILE* 4.1 22.4 - - + +
28A THR 2.7 21.9 + - - +
29A THR* 4.0 3.1 - - - +
31A GLU* 1.3 77.7 - - - +
33A GLY* 1.3 57.5 + - - +
35A VAL* 4.9 0.2 - - - -
36A MET* 2.6 65.8 + - + +
48A LEU* 3.8 30.1 - - + -
51A MET* 5.2 5.4 - - + -
52A ILE* 5.1 8.5 - - + -
14B ALA* 4.3 13.5 - - + -
17B PHE* 3.7 29.8 - - + -
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR 2.7 24.1 + - - -
32A LEU* 1.3 74.1 - - - +
34A THR* 1.3 64.2 + - - +
36A MET* 4.5 2.5 - - - -
37A ARG* 2.6 30.2 + - - +
42A ASN* 4.3 10.3 - - - +
48A LEU* 4.2 13.5 - - - -
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Residues in contact with THR 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.8 6.6 - - - +
30A LYS* 2.7 29.6 + - + +
31A GLU* 2.8 13.2 + - - -
33A GLY* 1.3 74.7 - - - +
35A VAL* 1.3 71.9 + - - +
37A ARG* 3.3 9.2 - - - +
38A SER* 3.0 20.0 + - - -
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.5 40.4 - - + +
21A LYS* 4.6 19.5 - - + +
31A GLU* 3.1 19.2 + - - +
34A THR* 1.3 81.3 + - - +
36A MET* 1.3 61.2 + - - +
38A SER* 2.6 33.4 + - - +
39A LEU* 3.0 26.1 + - + +
112A LEU* 6.5 0.9 - - + -
14B ALA* 5.2 4.0 - - + -
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Residues in contact with MET 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 2.6 55.0 + - + +
33A GLY* 4.0 2.5 - - - +
35A VAL* 1.3 75.5 - - - +
37A ARG* 1.3 50.9 + - - +
39A LEU* 4.0 9.9 - - + -
40A GLY* 2.7 34.4 + - - +
41A GLN 3.3 12.2 + - - +
42A ASN* 5.8 2.7 - - + +
43A PRO* 6.1 3.8 - - - -
48A LEU* 5.3 9.2 - - + -
51A MET* 5.5 4.7 - - + -
14B ALA* 3.5 34.2 - - + +
17B PHE 4.4 0.9 - - - -
18B LYS* 3.9 34.5 - - + +
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY 2.6 26.2 + - - +
34A THR* 3.3 7.9 - - - +
35A VAL 2.7 2.2 + - - -
36A MET* 1.3 69.4 - - - +
38A SER* 1.3 58.8 + - - +
39A LEU 2.9 10.0 + - - -
40A GLY 3.6 0.2 + - - -
41A GLN* 3.0 29.6 + - + -
42A ASN* 4.0 22.4 - - + +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR 3.0 12.2 + - - -
35A VAL* 2.6 18.1 + - - -
37A ARG* 1.3 72.6 - - - +
39A LEU* 1.3 62.0 + - - +
111A ASN* 4.3 25.7 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 3.5 22.0 - - + +
36A MET* 3.4 15.3 - - + +
37A ARG 2.9 1.6 + - - -
38A SER* 1.3 85.4 - - - +
40A GLY* 1.3 60.8 + - - +
91A VAL* 3.7 39.2 - - + +
108A VAL* 6.5 0.9 - - + -
112A LEU* 5.5 10.3 - - + -
11B VAL* 4.6 19.3 - - + -
14B ALA* 5.6 7.6 - - + -
15B ASN* 6.1 2.2 - - + +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 2.7 12.9 + - - -
39A LEU* 1.3 75.4 - - - +
41A GLN* 1.3 76.3 + - - +
43A PRO* 5.7 0.3 - - - +
18B LYS* 4.9 13.2 + - - -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 3.4 16.6 - - - +
37A ARG* 3.0 27.7 + - + +
40A GLY* 1.3 86.9 - - - +
42A ASN* 1.3 72.3 + - - +
43A PRO* 4.2 7.2 - - + +
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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