Contacts of the helix formed by residues 14 - 30 (chain A) in PDB entry 5D0Y
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 ARG 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 1.3 74.2 - - + +
15A GLU* 1.3 62.0 + - - +
16A LEU 3.0 4.9 - - - -
17A VAL* 2.9 60.8 + - - +
18A LEU* 3.5 11.3 + - + +
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Residues in contact with GLU 15 (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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13A LEU* 2.9 40.4 - - - +
14A ARG* 1.3 80.3 + - - +
16A LEU* 1.3 71.6 + - + +
18A LEU* 3.1 14.8 - - + +
19A LEU* 2.9 22.5 + - - +
55A PHE* 3.5 20.6 - - + -
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Residues in contact with LEU 16 (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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13A LEU* 3.9 34.5 - - + +
14A ARG 2.9 1.0 + - - -
15A GLU* 1.3 87.9 - - + +
17A VAL* 1.3 65.2 + - - +
18A LEU 3.2 0.2 - - - -
19A LEU* 3.9 26.9 - - + +
20A ALA* 3.4 18.9 + - - +
55A PHE* 5.8 0.9 - - + -
59A TRP* 5.2 13.0 - - + -
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Residues in contact with VAL 17 (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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13A LEU 4.2 6.7 - - - +
14A ARG* 3.2 43.7 - - - +
16A LEU* 1.3 78.1 - - - +
18A LEU* 1.3 66.5 + - + +
20A ALA* 3.4 5.7 + - - +
21A MET* 3.1 40.2 + - + +
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Residues in contact with LEU 18 (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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14A ARG* 3.5 13.2 + - + +
15A GLU* 3.1 17.7 + - - +
16A LEU 3.2 0.2 - - - -
17A VAL* 1.3 80.6 - - + +
19A LEU* 1.3 67.3 + - - +
21A MET* 2.9 28.3 + - + +
22A VAL* 3.0 15.4 + - + +
54A LEU* 4.9 14.8 - - + -
55A PHE* 3.7 15.7 - - + -
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Residues in contact with LEU 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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15A GLU 2.9 18.5 + - - +
16A LEU* 3.9 27.4 - - + +
17A VAL 3.4 0.4 - - - -
18A LEU* 1.3 71.6 - - - +
20A ALA* 1.3 62.1 + - - +
22A VAL* 3.0 6.0 - - - +
23A ILE* 3.0 48.6 + - + +
51A LEU* 4.2 11.0 - - + -
55A PHE* 3.5 27.1 - - + -
59A TRP* 4.6 24.2 - - + +
62A ALA* 6.2 1.3 - - + -
63A GLY* 4.3 9.4 - - - +
66A LEU* 6.2 2.0 - - + -
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Residues in contact with ALA 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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16A LEU 3.4 9.5 + - - +
17A VAL* 3.6 10.1 - - - +
18A LEU 3.1 1.0 - - - -
19A LEU* 1.3 78.9 - - - +
21A MET* 1.3 59.8 + - + +
23A ILE* 2.9 11.1 + - - +
24A ALA* 2.8 28.9 + - - +
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Residues in contact with MET 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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17A VAL* 3.1 33.7 - - + +
18A LEU* 2.9 17.2 + - + +
20A ALA* 1.3 77.6 - - + +
22A VAL* 1.3 51.3 - - - +
24A ALA* 3.2 9.2 + - - +
25A ILE* 2.7 43.8 + - + +
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Residues in contact with VAL 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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18A LEU* 3.0 15.7 + - + +
19A LEU 3.0 21.1 - - - +
21A MET* 1.3 73.9 - - - +
23A ILE* 1.3 61.1 + - - +
24A ALA 3.2 0.2 - - - -
25A ILE* 3.5 9.6 - - + +
26A LYS* 2.8 28.6 + - - +
47A GLY 4.5 2.7 - - - +
50A MET* 3.6 46.4 - - + -
51A LEU* 3.6 28.6 - - + +
54A LEU* 5.0 3.6 - - + -
55A PHE* 3.7 16.2 - - + -
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Residues in contact with ILE 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 LEU* 3.0 32.1 + - + +
20A ALA* 2.9 11.3 + - - +
22A VAL* 1.3 76.3 - - - +
24A ALA* 1.3 54.6 + - - +
26A LYS* 3.2 3.6 + - - +
27A VAL* 2.8 38.7 + - + +
51A LEU* 3.6 16.2 - - + -
63A GLY* 3.2 40.6 - - - +
66A LEU* 4.9 11.4 - - + -
67A SER* 3.4 26.5 - - - +
70A VAL* 5.0 9.9 - - + -
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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 ALA 2.8 11.8 + - - +
21A MET* 3.2 13.7 - - - +
23A ILE* 1.3 76.0 - - - +
25A ILE* 1.3 64.6 + - + +
27A VAL* 3.5 6.0 + - - +
28A VAL* 3.0 32.5 + - + +
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Residues in contact with ILE 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 MET* 2.7 25.9 + - + +
22A VAL* 3.5 11.9 - - + +
24A ALA* 1.3 76.5 - - - +
26A LYS* 1.3 60.4 - - - +
28A VAL* 2.9 7.8 + - - +
29A LEU* 2.9 54.5 + - + +
47A GLY* 4.7 1.6 - - - -
50A MET* 3.8 37.0 - - + -
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Residues in contact with LYS 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 VAL 2.8 18.4 + - - +
23A ILE* 3.2 8.7 + - - +
25A ILE* 1.3 76.9 - - - +
27A VAL* 1.3 62.1 + - - +
29A LEU* 4.5 2.0 - - - +
30A GLY* 3.1 19.8 + - - -
44A GLY* 3.8 15.0 + - - +
47A GLY* 3.4 33.4 - - - +
48A SER* 3.5 30.1 - - - +
51A LEU* 4.7 6.3 - - + -
64A GLY* 4.9 8.3 - - - -
67A SER* 3.3 25.1 - - - +
89A ALA* 4.4 12.8 - - - +
92A GLU* 3.7 14.5 + - - -
93A SER* 4.7 3.4 - - - -
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Residues in contact with VAL 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 ILE* 2.8 26.2 + - + +
24A ALA* 3.8 6.7 - - - +
26A LYS* 1.3 73.1 - - - +
28A VAL* 1.3 65.7 + - + +
30A GLY* 3.4 8.0 + - - -
31A GLN* 3.6 13.5 + - - +
67A SER* 3.2 34.8 - - - +
70A VAL* 4.1 16.2 - - + -
71A SER* 4.0 24.3 + - - +
74A ILE* 5.0 3.1 - - + -
75A PHE* 3.6 26.2 - - + -
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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* 3.0 23.3 + - + +
25A ILE* 2.9 7.8 + - - +
27A VAL* 1.3 76.8 - - + +
29A LEU* 1.3 66.0 + - + +
30A GLY 3.0 1.1 - - - -
31A GLN* 2.8 29.0 + - - +
32A PHE* 3.6 17.4 - - + -
75A PHE* 5.6 4.9 - - + -
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Residues in contact with LEU 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 ILE* 2.9 40.7 + - + +
26A LYS* 4.5 2.7 - - - +
28A VAL* 1.3 77.0 - - + +
30A GLY* 1.3 63.5 + - - +
31A GLN 3.0 0.4 - - - -
32A PHE* 2.9 26.1 + - + +
43A LEU* 3.5 47.3 - - + +
44A GLY* 4.9 0.4 - - - -
46A ILE* 3.9 34.8 - - + -
47A GLY 4.3 3.8 - - - +
50A MET* 5.4 0.7 - - - -
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Residues in contact with GLY 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 LYS 3.1 18.6 + - - -
27A VAL* 3.7 3.6 - - - -
28A VAL 3.0 1.8 - - - -
29A LEU* 1.3 78.8 - - - +
31A GLN* 1.3 62.8 + - - +
32A PHE 3.2 2.7 + - - +
33A LYS* 3.4 27.7 + - - +
42A GLY* 5.8 0.2 - - - -
44A GLY* 3.9 16.8 - - - -
71A SER* 5.7 1.3 - - - -
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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