Contacts of the helix formed by residues 22 - 33 (chain C) in PDB entry 2BKU
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 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C GLY 3.3 1.0 - - - -
21C THR* 1.3 79.8 - - - +
23C LYS* 1.3 59.8 + - - +
25C THR* 3.7 0.5 - - - -
26C PHE* 2.9 31.9 + - - +
89C MET* 3.9 5.9 - - - +
122C ASN* 3.6 10.6 + - - -
151C ALA* 4.6 0.3 - - - +
220C GTP 3.2 36.4 + - - -
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.5 17.2 - - + +
16C VAL* 3.4 35.0 - - - +
17C GLY* 2.8 25.9 + - - +
18C ASP 3.1 10.1 + - - -
21C THR* 3.7 8.5 - - - +
22C GLY* 1.3 77.1 - - - +
24C THR* 1.3 62.5 + - - +
26C PHE* 3.4 2.7 + - - +
27C VAL* 3.1 28.1 + - - +
65C ASP* 3.5 12.6 - - - +
66C THR 3.1 26.9 - - - +
67C ALA 4.6 0.2 - - - -
68C GLY 4.2 0.2 - - - +
89C MET* 4.1 15.3 - - + -
220C GTP 2.8 44.7 + - - +
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Residues in contact with THR 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LYS* 1.3 73.2 - - - +
25C THR* 1.3 58.1 + - - +
27C VAL* 3.2 2.5 + - - +
28C LYS* 2.7 71.1 + - + +
36C GLU* 6.0 5.2 - - + -
40C VAL 5.6 2.9 - - - +
42C THR* 2.8 6.1 + - - +
46C GLU* 4.2 6.2 + - - +
65C ASP* 2.6 22.3 + - - +
220C GTP 3.1 13.6 + - - +
221C MG 2.1 31.1 - - - -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLY 3.7 5.4 - - - -
24C THR* 1.3 71.9 - - - +
26C PHE* 1.3 64.6 + - - +
28C LYS* 3.9 5.1 - - - +
29C ARG* 3.1 24.8 + - - +
34C GLU 4.8 0.3 - - - +
35C PHE* 3.6 38.1 - - + -
36C GLU* 3.9 22.9 + - - +
151C ALA* 4.0 5.6 - - + -
220C GTP 2.8 57.6 + - + -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 5.0 2.5 - - + -
22C GLY 2.9 19.4 + - - +
23C LYS 3.5 4.9 - - - +
24C THR 3.2 0.2 - - - -
25C THR* 1.3 78.2 - - - +
27C VAL* 1.3 67.8 + - + +
29C ARG* 3.5 3.7 + - - +
30C HIS* 3.2 42.9 + + - -
87C ILE* 4.4 13.7 - - + -
89C MET* 3.9 21.8 - - + -
120C CYS* 5.6 0.7 - - - -
122C ASN* 5.6 0.2 - - - +
149C ILE* 4.1 23.6 - - + -
150C SER 5.7 0.2 - - - -
151C ALA* 3.9 25.4 - - + -
157C PHE* 3.3 28.9 - + - -
160C PRO* 4.1 15.3 - - + -
161C PHE* 3.4 29.8 - + - -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.4 32.5 - - + -
23C LYS 3.1 7.2 + - - +
24C THR* 3.8 4.3 - - - +
26C PHE* 1.3 79.3 - - + +
28C LYS* 1.3 69.4 + - + +
30C HIS* 2.9 9.6 + - - +
31C LEU* 2.8 23.9 + - + +
48C HIS* 4.5 28.5 - - + -
50C LEU* 5.0 7.2 - - + -
63C VAL* 3.7 30.3 - - + -
65C ASP* 4.7 7.4 - - + +
161C PHE* 5.4 5.6 - - + -
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Residues in contact with LYS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C THR* 2.7 43.8 + - + +
25C THR* 3.9 5.2 - - - +
27C VAL* 1.3 72.8 - - + +
29C ARG* 1.3 54.2 + - - +
31C LEU* 3.1 15.1 + - + +
32C THR* 2.8 44.4 + - + +
34C GLU* 3.9 10.1 - - + +
36C GLU* 5.4 16.3 + - + +
46C GLU* 3.4 34.8 + - - -
48C HIS* 4.1 13.9 - - + +
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C THR 3.1 13.4 + - - +
26C PHE* 3.5 10.3 - - - +
28C LYS* 1.3 73.6 - - - +
30C HIS* 1.3 63.3 + - - +
33C GLY* 2.7 37.5 + - - +
34C GLU 3.5 18.1 + - - +
35C PHE* 4.0 10.4 - - + +
151C ALA 3.2 18.2 + - - +
152C LYS* 2.7 31.3 + - - +
153C SER 4.9 0.2 - - - -
154C ASN* 3.1 32.4 + - - +
157C PHE* 3.7 11.4 - - + -
567D GLN* 3.0 25.9 + - - +
570D GLN* 3.1 30.7 + - - +
574D SER* 5.2 0.2 + - - -
613D PHE* 3.3 25.5 - - - +
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 3.2 31.0 + + - +
27C VAL* 2.9 8.2 + - - +
29C ARG* 1.3 79.0 - - - +
31C LEU* 1.3 60.6 + - - +
33C GLY 4.8 0.3 + - - -
50C LEU* 3.6 23.3 - - + +
52C PHE* 3.6 31.6 - + - -
157C PHE* 3.1 75.5 + + - -
158C GLU* 4.1 3.8 - - + -
161C PHE* 3.6 16.3 - + - -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 2.8 16.1 + - + +
28C LYS* 3.1 15.0 + - + +
30C HIS* 1.3 79.1 - - - +
32C THR* 1.3 72.7 + - + +
48C HIS* 3.7 43.5 - - + +
49C PRO* 3.2 29.8 - - + +
50C LEU* 3.6 11.4 - - + -
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Residues in contact with THR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LYS* 2.8 24.3 + - + +
31C LEU* 1.3 96.4 - - + +
33C GLY* 1.3 58.1 + - - +
34C GLU* 3.2 34.8 + - - +
610D ASP* 4.3 4.0 - - - +
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ARG* 2.7 28.3 + - - -
30C HIS 4.8 0.4 + - - -
32C THR* 1.3 71.2 - - - +
34C GLU* 1.3 60.2 + - - +
35C PHE 3.8 1.4 + - - -
567D GLN* 3.7 22.2 - - - +
570D GLN* 4.0 17.7 + - - +
610D ASP* 3.6 14.4 - - - +
613D PHE* 5.8 0.5 - - - -
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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