Contacts of the helix formed by residues 19 - 28 (chain D) in PDB entry 5X11
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 19 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D SER* 1.3 73.9 - - - +
20D TYR* 1.3 55.4 + - - +
22D ILE* 3.4 4.3 + - - +
23D THR* 2.9 33.2 + - - -
41D ILE* 4.2 3.0 - - - +
42D TYR* 3.7 19.5 - - - -
45D LEU* 3.5 30.2 - - - +
68D LYS 4.2 3.6 + - - -
70D TYR* 4.6 1.6 - - - -
22I T 3.8 3.8 + - - -
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Residues in contact with TYR 20 (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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18D SER* 3.1 5.3 - - - +
19D GLY* 1.3 72.1 - - - +
21D ASP* 1.3 61.8 + - - +
23D THR* 3.3 13.5 + - + -
24D SER* 2.9 43.0 + - - -
27D LYS* 6.0 3.1 - - - -
38D HIS* 6.4 0.7 - - + -
42D TYR* 3.5 3.1 + - - +
19I A 4.1 3.3 - - - +
20I C 2.9 64.1 + + + -
21I A 3.5 50.0 - + - +
22I T 3.1 28.6 + - + +
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Residues in contact with ASP 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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17D LEU* 3.6 27.0 - - + +
18D SER* 3.0 38.7 + - - +
20D TYR* 1.3 75.1 - - - +
22D ILE* 1.3 66.4 + - - +
24D SER* 3.1 9.2 + - - -
25D TYR* 3.0 31.6 + - + -
67D LYS* 5.4 2.5 + - - +
69D MET* 4.2 9.2 - - - +
21I A 5.0 6.5 + - - -
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Residues in contact with ILE 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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8D ILE* 4.2 15.5 - - + -
11D LEU* 4.0 21.8 - - + -
12D LEU* 4.8 7.0 - - + -
17D LEU* 4.5 21.8 - - + +
18D SER 3.0 26.2 + - - +
19D GLY 3.6 5.4 - - - +
21D ASP* 1.3 75.1 - - - +
23D THR* 1.3 64.4 + - - +
25D TYR* 2.8 18.8 + - - +
26D PHE* 3.2 36.7 + - + -
41D ILE* 3.7 17.0 - - + -
45D LEU* 4.1 28.0 - - + -
70D TYR* 5.3 0.4 - - + -
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Residues in contact with THR 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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19D GLY 2.9 19.4 + - - -
20D TYR* 3.6 14.7 - - + -
22D ILE* 1.3 76.7 - - - +
24D SER* 1.3 60.5 + - - +
26D PHE* 3.4 6.2 + - - +
27D LYS* 3.4 43.4 + - - +
36D ALA 4.8 4.1 - - - +
37D LYS* 4.7 1.6 - - - -
38D HIS* 3.7 37.8 - - + +
41D ILE* 3.5 22.0 - - + +
42D TYR* 5.2 0.5 - - - -
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Residues in contact with SER 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D TYR* 2.9 31.5 + - - -
21D ASP* 3.4 11.4 - - - -
23D THR* 1.3 73.4 - - - +
25D TYR* 1.3 66.8 + - - +
27D LYS* 3.0 23.1 + - - +
28D GLU* 3.2 22.3 + - - +
20I C 5.4 1.2 + - - -
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Residues in contact with TYR 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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103C TYR* 3.7 24.6 + - - +
11D LEU* 3.8 25.1 - - + -
17D LEU* 3.9 36.1 - - + +
21D ASP* 3.0 28.1 + - + -
22D ILE* 2.8 13.1 + - - +
24D SER* 1.3 72.7 - - - +
26D PHE* 1.3 62.7 + - - +
28D GLU* 3.0 26.3 + - + +
29D GLU* 5.1 3.4 - - - -
30D LEU* 3.7 15.8 + - + +
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Residues in contact with PHE 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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4D LEU* 4.0 13.0 - - + -
7D ALA* 3.5 31.4 - - + -
8D ILE* 4.8 0.9 - - + -
11D LEU* 4.0 8.7 - - + -
22D ILE* 3.2 36.8 + - + -
23D THR 3.7 6.3 - - - +
24D SER 3.2 0.2 - - - -
25D TYR* 1.3 75.6 - - - +
27D LYS* 1.3 58.0 + - + +
30D LEU* 3.9 23.1 - - + -
31D GLY* 3.1 29.0 - - - +
34D TRP* 3.8 30.8 - + + +
35D SER* 4.6 3.7 - - - -
36D ALA* 3.8 28.9 - - + +
41D ILE* 3.5 25.1 - - + -
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Residues in contact with LYS 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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20D TYR* 6.0 3.2 - - - -
23D THR* 3.4 33.4 + - - +
24D SER* 3.0 17.7 + - - +
26D PHE* 1.3 77.6 - - - +
28D GLU* 1.3 68.2 + - + +
31D GLY* 4.9 0.8 - - - -
37D LYS* 5.7 11.2 - - - +
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Residues in contact with GLU 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 SER* 3.3 21.0 - - - +
25D TYR* 3.0 19.2 + - + +
26D PHE 3.3 0.2 - - - -
27D LYS* 1.3 86.7 - - - +
29D GLU* 1.3 78.1 + - - +
30D LEU 3.4 2.0 - - - -
31D GLY* 3.2 12.4 + - - -
32D GLN* 4.4 2.8 + - - +
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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