Contacts of the helix formed by residues 20 - 31 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D VAL* 1.3 79.5 - - - +
21D LYS* 1.3 57.8 + - - +
23D SER* 3.7 0.7 - - - -
24D LEU* 2.7 45.8 + - - +
125D ASN* 3.9 0.7 - - - -
1400D GNP 3.0 44.1 + - - -
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 3.3 43.8 - - + +
14D LEU 3.7 12.3 - - - -
15D GLY 2.8 29.5 + - - +
16D ASP 3.2 4.2 + - - -
19D VAL* 3.7 19.5 - - + +
20D GLY* 1.3 76.8 - - - +
22D THR* 1.3 64.0 + - - +
24D LEU* 3.2 7.1 + - - +
25D MET* 2.9 24.8 + - - +
63D ASP* 4.0 9.2 - - - +
64D THR* 3.7 18.4 - - - -
65D ALA 5.0 0.2 - - - -
66D GLY* 3.6 6.5 - - - +
87D VAL* 4.0 5.6 - - + -
1400D GNP 2.7 37.4 + - - +
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Residues in contact with THR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 1.3 76.4 - - - +
23D SER* 1.3 58.8 + - - +
25D MET* 3.0 8.8 + - + +
26D ASN* 2.9 47.5 + - - +
38D LYS 5.0 6.2 + - - +
40D THR* 3.0 8.1 + - - +
63D ASP* 2.7 19.7 + - - +
1400D GNP 2.6 18.3 + - - +
1401D MG 2.3 32.6 - - - -
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Residues in contact with SER 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLY 3.7 3.8 - - - -
22D THR* 1.3 75.4 - - - +
24D LEU* 1.3 63.6 + - - +
26D ASN* 3.4 6.3 + - - +
27D GLN* 2.9 25.6 + - - +
32D LYS 4.5 2.4 - - - +
33D PHE* 4.3 14.8 - - - +
34D SER 4.7 3.3 + - - -
156D ALA* 3.9 12.7 - - - +
1400D GNP 2.9 53.4 + - - -
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Residues in contact with LEU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 5.9 2.9 - - + -
20D GLY 2.7 27.1 + - - +
21D LYS* 3.6 4.5 - - - +
23D SER* 1.3 72.6 - - - +
25D MET* 1.3 58.8 + - - +
27D GLN* 3.3 4.0 + - - +
28D TYR* 2.9 28.9 + - - +
87D VAL* 3.9 30.5 - - + -
123D LEU* 4.0 21.5 - - + -
125D ASN* 3.8 29.4 - - + +
154D THR* 3.8 11.0 - - + +
156D ALA* 3.9 14.1 - - + +
162D VAL* 4.1 26.5 - - + +
166D PHE* 5.0 11.0 - - + -
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Residues in contact with MET 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ILE* 4.2 10.9 - - + +
21D LYS 2.9 13.2 + - - +
22D THR* 3.0 10.7 + - + +
24D LEU* 1.3 78.2 - - - +
26D ASN* 1.3 62.8 + - - +
28D TYR* 3.2 4.8 + - - +
29D VAL* 3.0 33.7 + - + +
44D ASP* 6.0 0.9 - - + -
45D PHE* 5.2 2.0 - - - -
46D LEU* 3.8 31.8 - - + +
61D ILE* 3.5 45.3 - - + +
63D ASP* 3.7 35.7 - - + +
166D PHE* 5.0 4.3 - - - -
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Residues in contact with ASN 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 2.9 40.2 + - - +
23D SER* 4.0 5.1 - - - +
25D MET* 1.3 74.9 - - - +
27D GLN* 1.3 60.3 + - - +
30D ASN* 2.8 54.3 + - + +
31D LYS 3.1 5.4 + - - -
32D LYS* 3.5 19.0 + - + +
33D PHE* 5.9 0.2 - - - -
46D LEU* 3.4 14.9 - - - +
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Residues in contact with GLN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D SER 2.9 18.1 + - - +
24D LEU* 3.5 6.5 - - - +
26D ASN* 1.3 75.2 - - - +
28D TYR* 1.3 62.9 + - - +
31D LYS* 2.9 47.0 + - - +
32D LYS* 3.4 26.5 + - - +
33D PHE* 3.9 5.3 - - - +
156D ALA* 3.4 25.8 + - - +
157D LYS 4.4 4.4 + - - -
159D ALA* 3.5 32.5 - - + +
162D VAL* 4.3 12.3 - - + -
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Residues in contact with TYR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU 2.9 16.0 + - - +
25D MET* 3.2 4.0 + - - +
27D GLN* 1.3 79.0 - - - +
29D VAL* 1.3 56.7 + - + +
31D LYS* 4.5 3.8 + - - +
48D LYS* 2.7 48.9 + - + -
50D VAL* 3.5 33.1 - - - +
59D MET* 3.6 12.9 - - + +
61D ILE* 3.7 16.6 - - + -
162D VAL* 3.9 13.4 - - + +
163D GLU* 3.4 34.7 + - - +
166D PHE* 3.3 64.0 - + + +
167D GLN* 4.4 2.3 + - - -
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D MET* 3.0 16.7 + - + +
28D TYR* 1.3 81.1 - - + +
30D ASN* 1.3 77.8 + - - +
31D LYS* 3.5 9.1 + - - -
46D LEU* 4.0 26.9 - - + -
47D THR 3.5 20.2 - - - +
48D LYS* 3.9 30.6 + - + +
61D ILE* 4.1 20.0 - - + -
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN* 2.8 39.8 + - - +
29D VAL* 1.3 88.1 - - - +
31D LYS* 1.3 73.0 + - - +
32D LYS* 3.1 34.7 - - + +
46D LEU* 3.7 16.8 - - - +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASN 3.1 0.2 + - - -
27D GLN* 2.9 41.3 + - - +
28D TYR 4.7 2.9 - - - +
29D VAL 4.1 8.4 + - - -
30D ASN* 1.3 80.4 - - - +
32D LYS* 1.3 60.4 + - - +
48D LYS* 4.0 19.6 - - - +
163D GLU* 6.1 0.4 - - - +
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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