Contacts of the helix formed by residues 20 - 31 (chain A) in PDB entry 3LAW
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 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A GLY 3.3 0.4 - - - -
19A VAL* 1.3 81.4 - - - +
21A LYS* 1.3 58.1 + - - +
22A THR 3.2 2.7 - - - -
23A SER* 2.9 1.7 + - - -
24A LEU* 2.8 42.4 + - - +
125A ASN* 3.7 1.3 - - - +
1400A GNP 2.9 40.8 + - - -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.6 43.3 - - + +
14A LEU 3.6 1.1 - - - -
15A GLY* 2.7 36.5 + - - +
16A ASP 2.6 31.1 + - - -
17A SER 3.9 0.2 - - - +
19A VAL* 3.6 10.3 - - + -
20A GLY* 1.3 77.0 - - - +
22A THR* 1.3 62.7 + - - +
24A LEU* 3.6 9.2 + - - +
25A MET* 3.3 20.3 + - - +
63A ASP* 4.3 6.8 - - - +
64A THR* 4.0 12.1 - - - -
66A GLY* 4.0 4.0 - - - +
87A VAL* 3.8 7.9 - - + -
1400A GNP 2.8 35.7 + - - +
1401A MG 4.0 7.0 - - - -
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Residues in contact with THR 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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21A LYS* 1.3 72.9 - - - +
23A SER* 1.3 58.3 + - - +
25A MET* 3.3 3.2 + - + +
26A ASN* 2.8 48.5 + - - +
38A LYS* 5.3 6.3 - - + +
40A THR* 2.7 12.2 + - + +
63A ASP* 2.9 17.0 + - - +
1400A GNP 2.6 22.4 + - - -
1401A MG 2.3 31.7 - - - -
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Residues in contact with SER 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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20A GLY 2.9 7.9 + - - -
22A THR* 1.3 74.9 - - - +
24A LEU* 1.3 60.5 + - - +
26A ASN* 3.6 3.7 + - - +
27A GLN* 3.0 31.0 + - - +
32A LYS 4.6 2.0 - - - +
33A PHE* 4.2 11.5 - - - +
34A SER 4.9 2.4 + - - -
156A ALA* 3.7 12.0 - - - +
1400A GNP 2.7 51.4 + - - -
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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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13A ILE* 5.7 3.1 - - + -
20A GLY 2.8 20.0 + - - +
21A LYS* 3.8 5.4 - - - +
23A SER* 1.3 76.4 - - - +
25A MET* 1.3 58.1 + - - +
27A GLN* 3.9 2.7 - - - +
28A TYR* 3.1 28.4 + - - +
87A VAL* 3.8 38.8 - - + -
123A LEU* 4.0 13.9 - - + -
125A ASN* 3.5 30.5 - - + +
154A THR* 3.6 16.6 - - + +
156A ALA* 4.0 13.9 - - + +
162A VAL* 4.2 11.9 - - + +
166A PHE* 3.9 16.9 - - + -
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Residues in contact with MET 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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13A ILE* 4.4 6.3 - - + -
21A LYS 3.3 8.7 + - - +
22A THR* 3.3 9.1 + - + +
23A SER 3.1 0.4 - - - -
24A LEU* 1.3 76.5 - - - +
26A ASN* 1.3 68.0 + - - +
27A GLN 3.1 1.9 + - - -
28A TYR* 3.2 3.2 + - - +
29A VAL* 2.8 38.4 + - + +
44A ASP 5.9 0.4 - - - -
45A PHE* 5.0 2.2 - - - +
46A LEU* 3.3 36.3 - - + +
61A ILE* 3.6 43.5 - - + +
63A ASP* 3.1 40.4 - - + +
166A PHE* 5.2 2.2 - - + -
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Residues in contact with ASN 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A THR* 2.8 40.7 + - - +
23A SER* 4.4 3.1 - - - +
25A MET* 1.3 92.6 - - - +
27A GLN* 1.3 56.4 + - - +
30A ASN* 2.9 46.4 + - + +
31A LYS 3.1 7.1 + - - -
32A LYS* 3.3 21.6 + - + +
46A LEU* 4.1 8.5 - - - +
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Residues in contact with GLN 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 SER 3.0 19.4 + - - +
24A LEU* 3.9 6.7 - - - +
26A ASN* 1.3 75.7 - - - +
28A TYR* 1.3 62.4 + - - +
31A LYS* 2.7 49.0 + - - +
32A LYS 3.5 21.1 + - - +
33A PHE* 4.0 5.7 - - - +
156A ALA* 2.9 29.5 + - + +
157A LYS 4.3 4.4 + - - -
159A ALA* 3.6 17.8 - - + +
162A VAL* 3.9 24.2 - - + -
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Residues in contact with TYR 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 LEU 3.1 16.8 + - - +
25A MET* 3.8 2.0 - - - +
27A GLN* 1.3 81.7 - - - +
29A VAL* 1.3 61.5 + - - +
31A LYS* 4.6 3.8 + - - +
48A LYS* 2.8 49.2 + - + +
50A VAL* 3.8 30.3 - - - +
59A MET* 3.4 27.3 - - + +
61A ILE* 4.1 11.0 - - + -
162A VAL* 3.8 10.9 - - + +
163A GLU* 3.3 32.9 + - - +
166A PHE* 3.3 54.3 + + + +
167A GLN* 5.0 0.5 + - - -
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Residues in contact with VAL 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 MET* 2.8 23.1 + - + +
28A TYR* 1.3 76.9 - - + +
30A ASN* 1.3 83.5 + - - +
31A LYS* 3.8 7.8 + - - +
46A LEU* 4.1 23.8 - - + -
47A THR 3.9 17.7 - - - +
48A LYS* 4.0 28.0 + - + +
61A ILE* 3.9 28.0 - - + -
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Residues in contact with ASN 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 ASN* 2.9 32.3 + - - +
29A VAL* 1.3 94.1 - - - +
31A LYS* 1.3 66.5 + - - +
32A LYS* 2.8 49.6 + - - +
46A LEU* 4.2 13.9 - - - +
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Residues in contact with LYS 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 GLN* 2.7 44.7 + - - +
28A TYR 5.0 3.4 - - - +
29A VAL 4.5 8.1 - - - +
30A ASN* 1.3 75.0 + - - +
32A LYS* 1.3 58.4 + - - +
33A PHE 4.4 0.2 + - - -
48A LYS* 6.0 2.5 - - - +
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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