Contacts of the helix formed by residues 18 - 31 (chain A) in PDB entry 5BOU
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A THR* 4.1 7.9 - - + -
11A THR 3.5 7.0 - - - -
12A PHE* 3.5 55.9 - - + +
16A GLY 3.9 1.5 + - - +
17A LYS* 1.3 69.3 - - - +
19A GLY* 1.3 65.6 + - - +
20A GLN 3.4 2.2 - - - -
21A ILE* 3.1 43.2 + - + +
22A ASP* 3.2 17.1 + - - +
79B LEU* 4.2 22.4 - - + -
128B ARG* 3.9 29.8 - - - +
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Residues in contact with GLY 19 (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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10A THR* 5.1 0.2 - - - +
11A THR 4.0 7.1 + - - +
13A SER* 5.5 2.1 + - - -
17A LYS* 3.6 7.6 + - - -
18A LEU* 1.3 72.5 - - - +
20A GLN* 1.3 57.3 + - - +
22A ASP* 3.1 10.8 + - - +
23A TYR* 2.9 53.1 + - - -
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Residues in contact with GLN 20 (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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9A LEU* 3.6 25.9 + - + +
10A THR* 3.3 24.5 - - + +
18A LEU 3.4 1.0 - - - -
19A GLY* 1.3 75.5 - - - +
21A ILE* 1.3 56.9 + - - +
23A TYR* 3.9 26.1 - - - +
24A ALA* 3.0 27.4 + - - +
128A ARG* 4.3 10.7 - - + +
129A PRO* 3.8 21.5 - - + +
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Residues in contact with ILE 21 (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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10A THR* 4.3 6.0 - - + +
18A LEU* 3.1 41.7 + - + +
20A GLN* 1.3 75.0 - - - +
22A ASP* 1.3 67.8 + - - +
24A ALA* 3.2 8.0 + - - +
25A LEU* 3.0 35.2 + - + +
122A THR* 3.3 37.2 - - + +
129A PRO* 4.3 4.5 - - + -
152A PRO* 4.7 2.5 - - + -
153A SER* 3.9 37.7 - - - +
79B LEU* 5.9 2.2 - - + -
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Residues in contact with ASP 22 (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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17A LYS* 3.1 50.3 + - - +
18A LEU 3.2 11.4 + - - +
19A GLY* 3.1 10.6 + - - +
21A ILE* 1.3 79.0 - - - +
23A TYR* 1.3 66.0 + - + +
25A LEU* 3.3 17.6 + - - +
26A THR* 3.0 28.3 + - - -
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Residues in contact with TYR 23 (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 GLY* 2.9 36.1 + - - +
20A GLN* 3.9 26.2 - - - +
22A ASP* 1.3 81.9 - - + +
24A ALA* 1.3 65.9 + - - +
26A THR* 3.2 12.9 + - - -
27A ALA* 3.1 20.1 + - - +
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Residues in contact with ALA 24 (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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20A GLN 3.0 18.1 + - - +
21A ILE* 3.5 7.9 - - - +
23A TYR* 1.3 77.2 - - - +
25A LEU* 1.3 61.2 + - - +
27A ALA* 3.1 10.9 + - - +
28A VAL* 3.1 23.6 + - - +
129A PRO* 4.3 9.6 - - + +
130A PHE 3.8 11.7 - - - +
131A GLY* 4.4 6.8 - - - -
152A PRO* 3.8 22.9 - - + -
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Residues in contact with LEU 25 (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 ILE* 3.0 29.7 + - + +
22A ASP* 3.4 18.2 - - - +
24A ALA* 1.3 73.3 - - - +
26A THR* 1.3 59.2 + - - +
28A VAL* 3.3 9.5 + - + +
29A LYS* 3.0 30.7 + - - +
133A SER* 4.5 4.9 - - - +
151A ASP* 4.3 18.4 - - + +
152A PRO* 3.8 25.4 - - + -
153A SER* 6.3 0.2 - - - -
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Residues in contact with THR 26 (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 3.0 14.9 + - - -
23A TYR* 3.4 16.5 - - - -
24A ALA 3.2 0.2 - - - -
25A LEU* 1.3 73.6 - - - +
27A ALA* 1.3 63.7 + - - +
29A LYS* 3.2 15.6 + - + +
30A GLN* 3.2 31.0 + - + +
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Residues in contact with ALA 27 (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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23A TYR 3.1 11.9 + - - +
24A ALA* 3.1 12.5 + - - +
26A THR* 1.3 76.8 - - - +
28A VAL* 1.3 62.5 + - - +
30A GLN* 3.3 18.0 + - - +
31A GLY 3.4 8.1 + - - -
77A GLY* 4.0 8.8 - - - -
78A MET* 4.7 17.9 - - + +
131A GLY* 4.6 10.1 - - - +
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Residues in contact with VAL 28 (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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24A ALA 3.1 15.0 + - - +
25A LEU* 3.5 13.5 - - + +
27A ALA* 1.3 76.6 - - - +
29A LYS* 1.3 58.2 + - + +
31A GLY* 3.0 17.7 + - - -
76A SER* 3.6 18.2 - - - +
77A GLY* 4.1 7.0 - - - -
131A GLY 3.9 0.9 - - - +
132A VAL* 3.5 37.9 - - - +
133A SER* 3.5 24.9 - - - +
152A PRO* 4.2 6.3 - - + -
164A ILE* 5.1 1.6 - - + -
165A GLY* 3.5 19.0 - - - +
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Residues in contact with LYS 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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25A LEU* 3.0 18.0 + - + +
26A THR* 3.2 13.4 + - + +
28A VAL* 1.3 77.5 - - + +
30A GLN* 1.3 67.0 + - - +
165A GLY* 3.2 24.0 + - - +
166A LYS* 3.4 35.0 + - - +
168A SER* 3.0 25.0 + - - +
169A VAL* 4.3 15.0 - - - +
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Residues in contact with GLN 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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26A THR* 3.2 33.2 + - + +
27A ALA* 3.7 10.1 - - - +
28A VAL 3.2 1.2 - - - -
29A LYS* 1.3 81.3 - - - +
31A GLY* 1.3 64.8 + - - +
32A VAL* 5.6 0.3 - - - +
166A LYS* 3.9 19.9 + - - +
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Residues in contact with GLY 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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27A ALA 3.4 3.8 + - - -
28A VAL 3.0 14.0 + - - -
30A GLN* 1.3 81.7 - - - +
32A VAL* 1.3 63.3 + - - -
77A GLY* 3.9 22.7 - - - -
165A GLY* 4.6 0.4 - - - -
166A LYS* 2.8 30.0 + - - +
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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