Contacts of the helix formed by residues 19 - 26 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A LEU 4.2 0.2 + - - -
18A SER* 1.3 72.3 - - - +
20A TYR* 1.3 60.5 + - - +
22A ILE* 3.2 7.0 + - - +
23A THR* 3.0 27.3 + - - -
41A ILE* 4.4 3.5 - - - +
42A TYR* 3.7 18.8 - - - -
45A LEU* 3.6 30.7 - - - +
68A LYS 4.1 4.4 + - - -
70A TYR* 4.6 1.6 - - - -
8I T 3.6 4.4 + - - -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 3.0 6.5 - - - +
19A GLY* 1.3 76.1 - - - +
21A ASP* 1.3 66.0 + - - +
23A THR* 3.2 12.9 + - + -
24A SER* 3.0 38.2 + - - -
42A TYR* 4.0 2.5 - - - -
5I A 3.8 3.3 - - - +
6I C 2.6 67.4 + + + -
7I A 3.7 53.8 - + - +
8I T 2.9 29.2 + - + +
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Residues in contact with ASP 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.7 27.1 - - + +
18A SER* 2.8 46.0 + - - +
20A TYR* 1.3 73.8 - - - +
22A ILE* 1.3 62.3 + - - +
24A SER* 3.2 9.3 + - - -
25A TYR* 3.1 32.6 + - + -
67A LYS* 5.4 2.1 + - - -
69A MET* 4.2 10.0 - - - +
7I A 4.4 9.5 + - - -
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Residues in contact with ILE 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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8A ILE* 4.2 17.9 - - + -
11A LEU* 4.1 17.0 - - + -
12A LEU* 4.4 14.4 - - + -
17A LEU* 4.3 17.5 - - + +
18A SER 3.0 23.0 + - - +
19A GLY* 3.2 8.0 + - - +
21A ASP* 1.3 72.3 - - - +
23A THR* 1.3 67.3 + - - +
25A TYR* 3.1 18.9 + - - +
26A PHE* 3.3 36.2 + - + -
41A ILE* 3.9 15.7 - - + -
45A LEU* 4.1 27.4 - - + -
70A TYR* 5.4 0.2 - - + -
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Residues in contact with THR 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 GLY 3.0 14.5 + - - -
20A TYR* 3.2 19.6 + - + -
22A ILE* 1.3 76.0 - - - +
24A SER* 1.3 63.2 + - - +
26A PHE* 3.4 13.7 + - - +
27A LYS* 3.4 19.3 + - + +
36A ALA 5.1 4.4 - - - +
37A LYS* 5.6 0.2 - - - -
38A HIS* 3.6 36.2 - - + +
41A ILE* 3.6 18.5 - - + +
42A TYR* 5.2 0.9 + - - -
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Residues in contact with SER 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 TYR* 3.0 30.9 + - - -
21A ASP* 3.3 12.5 - - - -
22A ILE 3.1 0.2 - - - -
23A THR* 1.3 74.1 - - - +
25A TYR* 1.3 62.1 + - - +
27A LYS* 2.8 26.0 + - - +
28A GLU* 3.1 17.6 + - - +
6I C 4.9 2.6 + - - -
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Residues in contact with TYR 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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11A LEU* 3.8 26.5 - - + -
17A LEU* 4.0 36.0 - - + +
21A ASP* 3.1 29.2 + - + -
22A ILE* 3.1 8.9 + - - +
24A SER* 1.3 76.5 - - - +
26A PHE* 1.3 57.5 + - - +
28A GLU* 3.1 27.7 + - + +
29A GLU* 4.9 4.5 - - - -
30A LEU* 3.7 18.1 - - + +
103B TYR* 3.7 23.5 + - - -
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Residues in contact with PHE 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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4A LEU* 4.3 9.4 - - + -
7A ALA* 3.8 20.0 - - + -
8A ILE* 5.2 0.7 - - + -
11A LEU* 3.7 22.4 - - + -
22A ILE* 3.3 32.4 + - + -
23A THR 3.5 7.0 - - - +
24A SER 3.2 0.6 - - - -
25A TYR* 1.3 77.3 - - - +
27A LYS* 1.3 58.8 + - + +
28A GLU 3.4 0.4 - - - -
30A LEU* 4.0 14.6 - - + -
31A GLY* 3.1 25.0 - - - +
34A TRP* 3.3 34.3 - + + -
35A SER* 3.9 17.5 - - - -
36A ALA* 3.8 21.8 - - + +
41A ILE* 3.6 24.9 - - + -
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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