Contacts of the helix formed by residues 24 - 32 (chain C) in PDB entry 5W5T
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 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLY* 3.5 2.0 - - - -
23C ARG* 1.3 76.9 - - - +
25C SER* 1.3 65.1 + - - +
26C ARG 3.3 2.7 - - - -
27C LEU* 3.0 18.4 + - - +
31C THR* 2.7 23.2 + - - -
36C LYS* 4.0 26.3 - - - +
272C GLY 5.7 1.3 - - - -
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Residues in contact with SER 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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23C ARG* 4.2 18.8 - - - +
24C GLY* 1.3 77.0 - - - +
26C ARG* 1.3 59.9 + - - +
28C LYS* 2.9 31.7 + - - +
31C THR* 4.7 1.1 - - - -
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Residues in contact with ARG 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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24C GLY 3.3 1.0 - - - -
25C SER* 1.3 76.2 - - - +
27C LEU* 1.3 58.5 + - - +
28C LYS* 3.1 32.1 + - - +
36C LYS* 5.8 0.4 - - - +
270C ASP* 3.8 11.7 + - - -
272C GLY* 3.3 40.5 + - - +
273C THR* 3.5 27.2 - - + +
274C ILE* 4.1 12.6 + - - +
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Residues in contact with LEU 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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24C GLY* 3.0 14.6 + - - +
26C ARG* 1.3 74.8 - - - +
28C LYS* 1.3 70.8 + - - +
29C GLU 3.3 0.2 + - - -
30C LEU* 3.3 25.9 + - + +
31C THR* 3.9 24.5 - - + -
36C LYS* 4.2 20.2 - - + -
39C VAL* 4.4 12.8 - - + -
271C VAL* 3.6 20.2 - - + +
272C GLY* 3.8 7.9 - - - +
273C THR 3.4 33.4 - - - +
274C ILE* 3.6 18.2 - - + +
277C TYR* 4.2 11.0 - - + -
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Residues in contact with LYS 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 GLY 3.8 0.4 + - - -
25C SER 2.9 24.5 + - - +
26C ARG* 3.5 27.1 + - - +
27C LEU* 1.3 79.2 - - - +
29C GLU* 1.3 80.1 + - - +
31C THR* 3.0 17.7 + - - -
32C ASP* 3.2 14.4 - - - +
274C ILE* 4.1 10.8 - - + -
402C ARG* 3.3 40.7 - - - +
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Residues in contact with GLU 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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27C LEU 3.3 0.2 + - - -
28C LYS* 1.3 83.3 - - - +
30C LEU* 1.3 62.3 + - - +
31C THR 3.0 0.9 + - - -
32C ASP* 3.1 34.0 + - + +
33C ARG* 4.8 8.1 + - - -
34C ARG* 5.1 0.5 + - - -
379C ASP* 5.1 2.3 - - - +
402C ARG* 3.1 48.2 + - - +
410C LEU* 3.6 5.5 - - + +
412C THR* 3.6 28.9 - - + +
414C SER* 5.9 1.6 - - - +
415C MET* 3.7 20.3 - - + +
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Residues in contact with LEU 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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27C LEU* 3.3 30.6 + - + +
28C LYS 3.0 0.4 + - - -
29C GLU* 1.3 78.4 - - - +
31C THR* 1.3 58.7 + - - +
33C ARG 5.1 0.5 + - - -
34C ARG* 2.9 39.0 + - - +
39C VAL* 4.6 13.9 - - + -
274C ILE* 5.2 5.8 - - + -
277C TYR* 3.5 41.3 - - + +
362C LEU* 4.1 16.2 - - + -
377C VAL* 4.6 7.4 - - + -
379C ASP* 3.8 20.2 - - + +
410C LEU* 3.7 22.0 - - + +
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Residues in contact with THR 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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23C ARG 3.1 18.0 + - - +
24C GLY* 2.7 26.2 + - - +
25C SER* 4.7 1.7 - - - -
27C LEU* 3.9 14.8 - - + +
28C LYS 3.0 9.2 + - - -
30C LEU* 1.3 83.1 - - - +
32C ASP* 1.3 59.1 + - - +
33C ARG 3.2 2.5 - - - -
34C ARG* 3.0 25.3 - - - +
36C LYS* 4.2 7.2 - - - -
39C VAL* 3.8 23.8 - - + -
70C LYS* 3.0 21.7 + - - +
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Residues in contact with ASP 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 LYS 3.2 13.0 - - - +
29C GLU* 3.1 42.7 + - + +
31C THR* 1.3 78.8 - - - +
33C ARG* 1.3 72.7 + - + +
70C LYS* 3.7 19.9 + - - +
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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