Contacts of the helix formed by residues 18 - 28 (chain C) 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 SER 18 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 1.3 76.7 - - - +
19C GLY* 1.3 64.9 + - - +
20C TYR* 3.6 8.0 + - - +
21C ASP* 3.1 33.3 + - - -
22C ILE* 3.0 25.5 + - - +
67C LYS* 4.1 15.2 - - - -
68C LYS 3.4 16.2 - - - -
69C MET* 3.9 14.5 - - - -
70C TYR* 4.8 0.2 - - - -
21M A 4.4 0.2 + - - -
22M T 4.0 11.7 - - - -
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Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 1.3 73.6 - - - +
20C TYR* 1.3 56.1 + - - +
22C ILE* 3.4 5.1 + - - +
23C THR* 2.8 32.3 + - - -
41C ILE* 4.3 2.9 - - - +
42C TYR* 3.7 17.3 - - - -
45C LEU* 3.7 30.1 - - - +
68C LYS 4.2 4.0 + - - -
70C TYR* 4.6 2.6 - - - -
22M T 3.6 5.0 + - - -
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Residues in contact with TYR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER* 3.1 6.7 - - - +
19C GLY* 1.3 74.9 - - - +
21C ASP* 1.3 68.3 + - - +
23C THR* 3.4 12.0 + - + -
24C SER* 3.0 39.2 + - - -
42C TYR* 3.5 2.4 + - - -
19M A 4.3 1.0 - - - +
20M C 2.4 60.0 + + + -
21M A 3.5 54.7 - + - -
22M T 3.0 30.6 + - + +
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Residues in contact with ASP 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.0 25.8 - - + +
18C SER* 3.1 37.4 + - - +
20C TYR* 1.3 78.9 - - - +
22C ILE* 1.3 62.7 + - - +
24C SER* 3.3 9.9 + - - -
25C TYR* 3.1 30.5 + - + -
67C LYS* 5.3 4.2 + - - -
69C MET* 4.8 7.3 - - - +
21M A 4.1 10.7 + - - -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.3 14.6 - - + -
11C LEU* 3.9 22.4 - - + -
12C LEU* 4.3 18.2 - - + -
17C LEU* 4.4 17.9 - - + +
18C SER 3.0 22.6 + - - +
19C GLY* 3.6 7.6 - - - +
21C ASP* 1.3 73.7 - - - +
23C THR* 1.3 66.6 + - - +
25C TYR* 2.9 20.4 + - - +
26C PHE* 3.3 18.8 + - + -
41C ILE* 3.8 24.0 - - + -
45C LEU* 3.8 29.4 - - + -
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Residues in contact with THR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLY 2.8 20.3 + - - -
20C TYR* 3.4 17.2 + - + -
22C ILE* 1.3 76.2 - - - +
24C SER* 1.3 62.6 + - - +
26C PHE* 3.4 11.8 + - - +
27C LYS* 3.5 40.2 + - + +
36C ALA 4.7 1.7 - - - +
37C LYS 4.6 1.1 - - - -
38C HIS* 3.6 36.7 - - + +
41C ILE* 3.5 20.5 - - + +
42C TYR* 5.1 0.5 - - - -
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C TYR* 3.0 29.0 + - - -
21C ASP* 3.3 13.8 + - - -
22C ILE 3.1 0.2 - - - -
23C THR* 1.3 77.4 - - - +
25C TYR* 1.3 58.3 + - - +
27C LYS* 2.9 25.9 + - - +
28C GLU* 3.1 24.6 + - - +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 3.8 28.3 - - + -
17C LEU* 3.8 39.3 - - + +
21C ASP* 3.1 27.9 + - + -
22C ILE* 2.9 10.4 + - - +
24C SER* 1.3 75.0 - - - +
26C PHE* 1.3 61.2 + - - +
28C GLU* 3.2 22.5 + - + +
29C GLU* 4.7 6.7 - - - +
30C LEU* 3.4 20.4 + - + +
103D TYR* 3.9 21.5 - - - -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.9 13.0 - - + -
7C ALA* 3.5 27.8 - - + -
8C ILE* 5.2 0.7 - - + -
11C LEU* 4.3 8.3 - - + -
22C ILE* 3.3 24.1 + - + -
23C THR 3.7 4.7 - - - +
24C SER 3.2 0.8 - - - -
25C TYR* 1.3 77.2 - - - +
27C LYS* 1.3 58.6 + - + +
28C GLU 3.3 0.2 - - - -
30C LEU* 3.5 26.9 - - + -
31C GLY* 3.0 27.7 - - - +
34C TRP* 3.8 35.1 - + + +
35C SER* 4.0 6.9 - - - -
36C ALA* 3.7 42.2 - - + +
41C ILE* 3.8 19.1 - - + -
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C THR* 3.5 38.4 + - + +
24C SER* 2.9 14.3 + - - +
26C PHE* 1.3 77.7 - - - +
28C GLU* 1.3 71.7 + - - +
31C GLY* 5.2 0.4 - - - -
36C ALA 5.3 3.1 - - - -
37C LYS* 5.0 20.5 - - - +
38C HIS* 5.5 4.9 + - - +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C SER* 3.1 25.1 + - - +
25C TYR* 3.2 17.4 + - + +
27C LYS* 1.3 90.4 - - - +
29C GLU* 1.3 80.4 + - - +
30C LEU 3.3 2.0 - - - -
31C GLY* 3.1 13.7 + - - -
32C GLN* 4.4 2.4 + - - +
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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