Contacts of the helix formed by residues 22 - 31 (chain C) in PDB entry 1AX4
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 ARG 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C SER* 1.3 72.9 - - - +
23C GLU* 1.3 62.6 + - - +
25C ARG* 3.3 19.2 + - - +
26C GLU* 2.6 62.8 + - - +
382C LEU* 3.1 47.2 + - - +
383C GLU* 3.1 29.7 + - - -
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Residues in contact with GLU 23 (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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21C SER* 3.2 8.6 + - - +
22C ARG* 1.3 79.3 - - - +
24C GLU* 1.3 57.2 + - + +
26C GLU* 3.3 11.8 + - - +
27C ALA* 3.0 30.4 + - + +
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Residues in contact with GLU 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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18C ARG* 3.0 37.7 + - - -
20C PRO* 3.9 8.5 - - + -
21C SER* 2.8 48.1 + - - +
23C GLU* 1.3 76.0 - - + +
25C ARG* 1.3 58.5 + - - +
27C ALA* 3.3 5.5 + - - +
28C ALA* 2.9 31.2 + - - +
381C TYR* 5.2 0.2 - - - -
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Residues in contact with ARG 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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19C VAL* 4.0 12.5 - - - +
20C PRO* 2.7 43.2 + - + +
21C SER* 2.9 12.8 + - - +
22C ARG* 3.5 30.4 - - - +
24C GLU* 1.3 75.6 - - - +
26C GLU* 1.3 56.5 + - - +
28C ALA* 3.4 0.3 + - - +
29C LEU* 2.9 28.4 + - - +
381C TYR* 3.4 47.6 + - + +
382C LEU* 2.7 38.5 + - + +
383C GLU* 3.4 21.4 + - - +
384C SER* 4.1 1.7 - - - +
385C GLY* 3.6 20.1 - - - +
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Residues in contact with GLU 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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22C ARG* 2.6 61.0 + - - +
23C GLU* 3.7 10.0 - - - +
24C GLU 3.3 0.2 - - - -
25C ARG* 1.3 76.0 - - - +
27C ALA* 1.3 65.1 + - - +
29C LEU* 3.9 1.7 - - - +
30C LYS* 3.1 28.8 + - + +
382C LEU* 3.6 15.5 - - + -
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Residues in contact with ALA 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 GLU* 3.0 18.9 + - + +
24C GLU* 3.7 5.6 - - - +
26C GLU* 1.3 78.6 - - - +
28C ALA* 1.3 58.1 + - - +
30C LYS* 3.3 7.6 + - - +
31C GLU* 2.9 36.9 + - - +
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Residues in contact with ALA 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 GLU 2.9 16.7 + - - +
25C ARG* 3.7 4.3 - - - +
27C ALA* 1.3 77.1 - - - +
29C LEU* 1.3 57.0 + - - +
31C GLU* 3.3 12.3 + - - +
32C ALA* 2.9 30.7 + - - +
39C LEU* 3.6 17.3 - - + +
40C PRO* 5.3 5.0 - - + +
43C ALA* 3.8 19.5 - - + -
381C TYR* 3.9 2.9 - - - +
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Residues in contact with LEU 29 (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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25C ARG 2.9 20.4 + - - +
26C GLU 3.9 3.6 - - - +
28C ALA* 1.3 71.4 - - - +
30C LYS* 1.3 58.5 + - - +
32C ALA* 3.2 2.6 + - + -
33C GLY 3.1 4.7 + - - -
34C TYR* 2.8 73.6 + - + -
35C ASN 3.9 4.3 - - - +
36C PRO* 4.3 20.6 - - + -
39C LEU* 4.0 7.9 - - + +
378C ASN* 3.9 20.0 - - + +
381C TYR* 4.3 12.6 - - + -
382C LEU* 3.7 34.8 - - + -
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Residues in contact with LYS 30 (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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26C GLU* 3.1 15.6 + - + +
27C ALA* 3.4 11.7 - - - +
29C LEU* 1.3 72.9 - - - +
31C GLU* 1.3 60.7 + - - +
33C GLY* 2.8 22.2 + - - -
34C TYR* 3.3 36.9 - - + +
462C ARG* 3.6 6.8 + - - -
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Residues in contact with GLU 31 (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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27C ALA* 2.9 25.9 + - - +
28C ALA* 3.4 9.5 - - - +
30C LYS* 1.3 77.7 - - - +
32C ALA* 1.3 55.1 + - + +
462C ARG* 3.1 22.9 + - - +
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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