Contacts of the helix formed by residues 29 - 35 (chain C) in PDB entry 5LK5
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 ASP 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.5 2.5 - - - -
28C LEU* 1.3 76.5 + - + +
30C GLY* 1.3 64.9 + - - +
31C ASP 3.3 0.3 + - - -
32C GLY* 2.9 24.6 + - - -
33C TRP 4.1 1.0 + - - -
36C ARG* 2.9 44.2 + - - -
28I LEU 5.9 0.7 - - - -
30I GLY* 5.0 1.1 - - - +
61I GLU* 3.4 38.1 - - + +
64I LYS* 3.5 11.1 + - - -
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Residues in contact with GLY 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 PHE* 4.9 4.4 + - - +
28C LEU 3.5 5.3 + - - -
29C ASP* 1.3 76.3 + - - +
31C ASP* 1.3 58.7 + - - -
32C GLY 3.2 0.7 + - - -
33C TRP* 3.6 7.1 + - - -
51C LEU* 3.5 26.0 - - - +
64C LYS* 6.5 0.7 - - - -
30I GLY* 3.9 22.6 - - - -
31I ASP* 4.4 11.2 - - - -
51I LEU* 6.1 2.0 - - - -
64I LYS* 4.7 4.3 - - - -
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Residues in contact with ASP 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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29C ASP 3.3 0.5 + - - +
30C GLY* 1.3 69.0 - - - -
32C GLY* 1.3 64.3 + - - +
33C TRP* 3.1 11.9 - - - +
34C THR* 2.6 43.8 + - + +
51C LEU* 5.2 1.3 - - + -
31I ASP* 5.3 1.0 + - - -
64I LYS* 5.0 8.4 + - - +
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Residues in contact with GLY 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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29C ASP* 2.9 29.4 + - - -
30C GLY 3.2 0.6 - - - -
31C ASP* 1.3 79.5 + - - +
33C TRP* 1.3 62.0 + - - +
34C THR 3.0 1.0 + - - -
35C SER* 3.0 25.4 + - - -
36C ARG* 3.6 12.3 + - - -
61I GLU* 5.3 3.1 - - - -
64I LYS* 5.2 0.8 - - - +
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Residues in contact with TRP 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* 4.2 2.2 - - - +
27C PHE* 3.6 24.9 - + + -
29C ASP* 4.1 1.6 + - - -
30C GLY 3.6 18.8 + - - +
31C ASP* 3.0 7.5 + - - +
32C GLY* 1.3 74.9 - - - +
34C THR* 1.3 81.7 + - + +
35C SER 3.1 1.1 - - - -
36C ARG* 2.9 39.2 + - - +
37C TRP* 3.2 31.7 + + + -
49C PHE* 4.3 16.6 - - + -
50C VAL* 5.0 0.2 - - - -
51C LEU* 3.8 41.4 - - + +
66C LEU* 3.6 31.6 - - + -
77C LEU* 4.1 20.4 - - + -
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Residues in contact with THR 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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31C ASP* 2.6 30.3 + - + +
33C TRP* 1.3 113.5 - - + +
35C SER* 1.3 58.2 + - - +
36C ARG 3.4 0.2 - - - -
37C TRP 3.7 13.6 - - - +
38C ILE* 6.0 0.3 - - - +
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Residues in contact with SER 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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32C GLY* 3.0 17.6 + - - -
34C THR* 1.3 80.3 + - - +
36C ARG* 1.3 62.3 + - - +
37C TRP 3.7 1.3 - - - -
38C ILE* 5.8 3.3 - - - +
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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