Contacts of the helix formed by residues 29 - 37 (chain C) in PDB entry 2CX9
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 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C GLU 5.3 0.6 + - - -
26C VAL 3.4 3.2 + - - -
27C ALA 3.3 0.8 - - - -
28C PRO* 1.3 80.3 - - - +
30C ALA* 1.3 62.0 - - - +
31C ALA 3.5 1.8 - - - -
32C GLU* 3.6 15.7 + - - +
33C ARG* 3.0 45.4 + - - +
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Residues in contact with ALA 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 VAL 3.4 5.4 + - - +
27C ALA* 3.0 17.3 + - - +
28C PRO 3.4 0.4 - - - -
29C GLY* 1.3 75.8 - - - +
31C ALA* 1.3 66.1 + - - +
33C ARG* 3.4 13.7 + - - +
34C ASP* 3.1 20.8 + - - +
81C TYR 3.4 25.8 - - - +
82C ASP* 3.8 8.9 - - - +
357C ARG* 3.7 18.2 + - - +
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Residues in contact with ALA 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 4.7 0.6 + - - -
28C PRO 4.8 3.7 + - - +
29C GLY 3.5 0.2 - - - -
30C ALA* 1.3 78.6 - - - +
32C GLU* 1.3 65.2 + - - +
34C ASP* 3.0 18.0 + - - +
35C ARG* 3.2 32.1 + - - +
351C LYS 5.8 3.4 - - - +
357C ARG* 4.1 17.4 - - - +
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Residues in contact with GLU 32 (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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28C PRO 5.3 1.2 + - - +
29C GLY* 3.6 17.4 + - - +
30C ALA 3.3 0.4 - - - -
31C ALA* 1.3 79.1 - - - +
33C ARG* 1.3 52.4 + - - +
35C ARG* 2.9 30.1 + - - +
36C THR* 2.7 55.4 + - + +
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Residues in contact with ARG 33 (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 GLU 4.7 2.0 + - - -
26C VAL* 3.7 8.7 + - - +
29C GLY* 3.0 42.3 + - - +
30C ALA* 3.6 5.4 - - - +
32C GLU* 1.3 77.2 - - - +
34C ASP* 1.3 56.9 + - - +
36C THR* 3.5 8.5 - - - +
37C GLY* 2.7 31.5 + - - -
38C ALA* 3.6 11.4 - - + +
40C PRO* 3.5 37.6 - - - +
43C LEU* 3.4 27.1 - - - +
82C ASP* 2.5 35.3 + - - +
85C LEU* 4.9 0.8 - - - +
211C THR* 3.8 2.4 - - - -
212C ALA* 3.4 25.7 + - + -
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Residues in contact with ASP 34 (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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30C ALA 3.1 6.1 + - - +
31C ALA* 3.0 12.2 + - - +
33C ARG* 1.3 78.0 - - - +
35C ARG* 1.3 63.5 + - - +
209C GLY* 4.8 1.2 - - - -
211C THR* 2.7 53.4 + - - +
212C ALA 5.1 0.7 - - - +
351C LYS* 4.8 4.3 + - - +
356C GLU* 4.4 1.2 - - - +
357C ARG* 3.5 28.9 - - - +
360C ARG* 2.8 42.0 + - - -
361C ASP* 4.8 1.4 - - - +
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Residues in contact with ARG 35 (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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31C ALA* 3.2 23.8 + - - +
32C GLU* 2.9 42.0 + - - +
34C ASP* 1.3 85.2 - - - +
36C THR* 1.3 66.3 + - + +
211C THR* 4.7 2.6 - - - +
351C LYS* 5.2 14.2 + - + +
206D GLU* 6.4 2.7 - - - -
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Residues in contact with THR 36 (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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32C GLU* 2.7 45.0 + - + +
33C ARG* 3.5 8.7 - - - +
35C ARG* 1.3 77.5 - - + +
37C GLY* 1.3 70.6 + - - +
38C ALA* 3.1 23.4 + - - +
211C THR* 4.5 0.8 - - - +
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Residues in contact with GLY 37 (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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33C ARG 2.7 19.1 + - - -
35C ARG 3.5 0.8 - - - -
36C THR* 1.3 76.7 + - - +
38C ALA* 1.3 62.9 + - - +
39C PHE 3.4 3.3 + - - -
204C LYS* 5.8 3.3 + - - +
211C THR* 3.3 26.2 - - - +
212C ALA* 3.8 14.9 - - - +
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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