Contacts of the helix formed by residues 17 - 32 (chain A) in PDB entry 1LDJ
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ASP* 1.3 66.7 + - + +
19A GLN* 3.2 36.3 - - + +
20A ILE* 2.4 41.6 + - + +
21A TRP 3.6 5.4 + - - -
52A TYR* 4.0 30.8 - - - +
55A SER* 4.8 16.0 + - - +
87A GLU* 5.8 1.3 - - - -
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Residues in contact with ASP 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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17A LEU* 1.3 83.1 - - + +
19A GLN* 1.3 66.4 + - - +
20A ILE 3.3 0.2 + - - -
21A TRP* 3.5 4.7 + - - +
22A ASP* 3.3 23.1 + - - +
91A ARG* 3.8 25.6 + - - +
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Residues in contact with GLN 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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17A LEU* 4.1 32.9 - - + +
18A ASP* 1.3 79.6 - - - +
20A ILE* 1.3 78.6 - - + +
22A ASP* 3.4 8.3 + - - +
23A ASP* 4.0 10.7 + - - +
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Residues in contact with ILE 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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17A LEU* 2.4 32.4 + - + +
19A GLN* 1.3 87.3 - - + +
21A TRP* 1.3 52.6 + - - +
23A ASP* 3.1 4.0 + - - +
24A LEU* 2.7 39.7 + - + +
48A HIS* 3.0 65.3 - - + +
51A ASN* 4.1 11.9 - - + +
52A TYR* 3.4 40.6 - - + +
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Residues in contact with TRP 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 LEU 3.6 1.5 + - - +
18A ASP* 3.9 9.2 - - - +
20A ILE* 1.3 81.5 - - - +
22A ASP* 1.3 58.6 + - - +
23A ASP 3.4 0.2 - - - -
24A LEU* 3.3 43.1 - - + -
25A ARG* 2.7 85.9 + - + +
28A ILE* 4.1 6.1 - - + -
52A TYR* 3.4 24.2 - + + +
88A LEU* 4.7 2.5 - - + -
91A ARG* 3.1 67.5 - - + +
92A LEU* 4.0 24.2 - - + -
95A PHE* 4.2 7.6 - + + -
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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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18A ASP 3.3 15.4 + - - +
19A GLN* 4.1 5.2 - - - +
20A ILE 3.1 1.2 + - - -
21A TRP* 1.3 78.4 - - - +
23A ASP* 1.3 65.3 + - - +
25A ARG* 4.1 4.5 + - - +
26A ALA* 3.4 17.5 + - - +
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Residues in contact with ASP 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 GLN 4.4 6.7 - - - +
20A ILE 3.1 3.7 + - - +
22A ASP* 1.3 78.6 - - - +
24A LEU* 1.3 63.3 + - - +
25A ARG 3.3 1.1 - - - -
26A ALA* 2.9 28.4 + - + +
27A GLY 3.1 5.9 + - - -
41A ARG* 4.0 10.9 + - - +
48A HIS* 3.5 23.6 + - + +
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Residues in contact with LEU 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 ILE* 2.7 32.4 + - + +
21A TRP* 3.3 24.0 - - + -
23A ASP* 1.3 77.5 - - - +
25A ARG* 1.3 58.0 + - - +
27A GLY* 3.1 3.6 + - - -
28A ILE* 2.9 53.7 + - + +
45A LEU* 3.8 11.7 - - + +
48A HIS* 3.8 18.1 - - + +
49A VAL* 3.4 33.0 - - + -
52A TYR* 4.1 8.5 - - + -
88A LEU* 4.1 5.2 - - + -
92A LEU* 5.2 2.0 - - + -
136A ILE* 5.5 2.9 - - + -
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Residues in contact with ARG 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 TRP* 2.7 77.5 + - + +
22A ASP* 4.2 4.0 - - - +
23A ASP 3.3 0.2 - - - -
24A LEU* 1.3 74.2 - - - +
26A ALA* 1.3 58.9 + - - +
28A ILE* 4.1 9.0 - - - -
29A GLN* 2.7 38.0 + - + +
91A ARG* 4.0 14.1 + - - +
94A GLU* 4.1 20.4 + - - +
95A PHE* 4.3 34.3 - - + +
98A ASN* 6.1 0.8 - - - +
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Residues in contact with ALA 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 3.4 6.9 + - - +
23A ASP* 2.9 34.6 + - + +
25A ARG* 1.3 80.7 - - - +
27A GLY* 1.3 54.6 - - - +
29A GLN* 3.8 5.8 - - - +
30A GLN* 3.1 30.1 + - - +
41A ARG* 4.8 2.2 - - - +
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Residues in contact with GLY 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 ASP 3.1 3.6 + - - -
24A LEU 3.1 6.0 + - - -
25A ARG 3.0 0.2 - - - -
26A ALA* 1.3 77.3 - - - +
28A ILE* 1.3 52.4 + - - +
29A GLN 3.0 1.8 - - - -
30A GLN* 2.4 33.5 + - - +
31A VAL* 2.6 18.5 + - - +
37A MET* 4.5 0.9 - - - +
41A ARG* 3.5 23.3 - - - +
45A LEU* 4.0 10.5 - - - -
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Residues in contact with ILE 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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21A TRP* 4.1 7.9 - - + -
24A LEU* 2.9 46.7 + - + +
25A ARG* 3.9 6.7 - - - +
27A GLY* 1.3 71.0 - - - +
29A GLN* 1.3 59.0 + - - +
31A VAL* 2.9 12.0 - - + +
32A TYR* 2.9 41.6 - - + -
45A LEU* 4.5 3.5 - - + +
92A LEU* 3.5 19.3 - - + -
95A PHE* 3.1 32.8 - - + -
133A LEU* 3.5 31.0 - - + -
136A ILE* 5.5 4.9 - - + -
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Residues in contact with GLN 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 ARG* 2.7 22.6 + - + +
26A ALA* 3.8 7.6 - - - +
28A ILE* 1.3 73.6 - - - +
30A GLN* 1.3 61.4 + - + +
32A TYR* 3.7 13.7 + - - +
95A PHE* 3.4 29.6 - - + -
99A TYR* 5.2 17.6 - - - +
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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 ALA* 3.1 21.5 + - - +
27A GLY* 2.4 27.6 + - - +
29A GLN* 1.3 74.5 - - + +
31A VAL* 1.3 53.6 + - - -
32A TYR 2.7 23.4 + - - +
34A ARG* 3.2 14.6 - - - -
35A GLN* 3.4 30.2 + - - +
37A MET* 4.0 10.0 - - - +
41A ARG* 4.4 20.0 - - - +
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Residues in contact with VAL 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 GLY 2.6 13.2 + - - +
28A ILE* 2.9 37.7 - - + +
30A GLN* 1.3 72.2 - - - +
32A TYR* 1.3 74.9 + - + +
34A ARG* 2.8 24.9 - - + +
37A MET* 3.7 17.2 - - + -
42A TYR* 4.8 7.4 - - + +
45A LEU* 5.8 0.4 - - + -
129A SER* 3.5 11.4 + - - +
132A VAL* 3.4 39.9 - - + -
133A LEU* 4.8 3.4 - - + +
136A ILE* 4.6 11.7 - - + -
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Residues in contact with TYR 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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28A ILE* 2.9 34.8 - - + +
29A GLN* 3.7 11.8 - - - +
30A GLN* 2.7 15.7 - - - +
31A VAL* 1.3 94.2 - - + +
33A THR* 1.3 67.7 + - - +
34A ARG 2.8 4.3 - - - -
35A GLN* 4.9 0.7 + - - -
95A PHE* 4.4 4.9 - + - -
96A LEU* 3.4 14.2 - - + +
99A TYR* 3.3 42.2 - + + +
125A ASP 4.9 0.2 - - - -
126A TYR* 4.1 28.3 - + - -
129A SER* 3.3 31.0 - - - +
130A SER* 4.0 8.4 + - - -
133A LEU* 3.0 28.2 - - + +
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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