Contacts of the helix formed by residues 32 - 43 (chain C) in PDB entry 3C5C
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 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C GLY 3.2 1.2 - - - -
31C ALA* 1.3 78.7 - - - +
33C LYS* 1.3 61.1 + - - +
34C SER 3.3 1.8 - - - -
35C ALA* 3.7 0.7 - - - +
36C LEU* 2.9 37.9 + - - +
97C VAL* 4.8 0.9 - - - -
134C ASN* 3.6 3.8 + - - -
201C GDP 3.0 40.6 + - - -
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Residues in contact with LYS 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 ILE* 3.7 24.4 - - + +
26C LEU* 3.3 31.9 - - - +
27C GLY* 3.0 22.4 + - - +
28C ARG 3.3 12.1 + - - -
29C ARG* 3.9 3.2 - - - +
31C ALA* 4.7 2.2 - - + -
32C GLY* 1.3 72.2 - - - +
34C SER* 1.3 56.8 - - - +
36C LEU* 3.4 8.0 + - - +
37C THR* 2.9 31.2 + - - -
74C ASP* 3.4 12.1 - - - +
75C THR* 3.3 32.3 + - - -
76C ALA* 5.3 2.9 - - - +
77C ASP 5.9 0.9 - - - +
97C VAL* 4.0 14.6 - - + -
201C GDP 2.7 40.6 + - - +
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Residues in contact with SER 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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33C LYS* 1.3 71.5 - - - +
35C ALA* 1.3 61.3 + - - +
37C THR* 3.3 2.1 + - - -
38C VAL* 2.9 36.2 + - - +
49C TYR* 3.4 30.9 - - - -
53C LEU 4.6 1.0 + - - -
74C ASP* 2.4 26.0 + - - -
201C GDP 3.0 12.1 + - - -
202C MG 2.1 30.1 - - - -
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Residues in contact with ALA 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 3.7 1.8 - - - +
33C LYS 3.4 0.2 - - - -
34C SER* 1.3 76.3 - - - +
36C LEU* 1.3 56.3 + - - +
38C VAL* 3.9 3.7 - - - +
39C LYS* 3.0 28.9 + - - +
44C ARG 4.9 0.9 - - - +
45C PHE* 4.0 13.4 - - + -
46C ILE 4.3 14.6 + - - +
49C TYR* 5.5 0.6 - - - +
165C ALA* 3.5 22.2 - - + +
201C GDP 2.9 38.8 + - + +
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Residues in contact with LEU 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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25C ILE* 5.5 1.8 - - + -
32C GLY 2.9 21.4 + - - +
33C LYS* 3.7 4.7 - - - +
35C ALA* 1.3 74.7 - - - +
37C THR* 1.3 64.3 + - - +
39C LYS* 3.5 2.6 + - - +
40C PHE* 3.0 24.4 + - - +
95C LEU* 6.3 0.4 - - + -
97C VAL* 4.1 20.0 - - + -
132C LEU* 4.3 12.8 - - + -
134C ASN* 3.6 35.0 - - - +
163C VAL* 4.0 17.3 - - + -
165C ALA* 4.0 10.8 - - + +
172C VAL* 3.9 30.5 - - + +
175C VAL* 5.9 1.3 - - + -
176C PHE* 3.7 16.0 - - + -
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Residues in contact with THR 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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25C ILE* 3.2 20.1 - - - +
33C LYS 2.9 18.8 + - - -
34C SER* 3.6 7.4 - - - -
36C LEU* 1.3 77.2 - - - +
38C VAL* 1.3 60.5 + - + +
40C PHE* 3.3 2.8 + - - +
41C LEU* 3.0 54.1 + - + +
57C TYR* 4.3 19.7 - - + -
72C VAL* 4.1 18.6 - - + -
74C ASP* 3.9 11.2 - - + +
176C PHE* 4.1 8.5 - - + -
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Residues in contact with VAL 38 (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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34C SER 2.9 20.8 + - - +
35C ALA* 4.1 3.4 - - - +
37C THR* 1.3 77.2 - - + +
39C LYS* 1.3 56.3 + - - +
41C LEU* 4.6 3.6 - - + -
42C THR* 2.6 66.1 + - + +
44C ARG 3.9 2.9 - - - +
46C ILE* 3.7 31.6 - - + +
49C TYR* 4.0 36.1 - - + +
57C TYR* 5.6 4.9 - - + -
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Residues in contact with LYS 39 (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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35C ALA 3.0 18.1 + - - +
36C LEU* 3.7 7.2 - - - +
38C VAL* 1.3 76.1 - - - +
40C PHE* 1.3 57.4 + - - +
43C LYS* 2.7 54.3 + - - -
44C ARG 3.2 13.6 + - - +
45C PHE* 4.5 5.5 - - - +
165C ALA* 2.9 34.5 + - - +
166C CYS* 3.9 4.2 - - - +
167C LEU 2.9 28.4 + - - -
168C ASP 4.2 1.1 - - - -
169C PHE* 3.5 25.4 - - + +
172C VAL* 4.2 22.4 - - + -
204C UNX 4.5 6.5 - - - -
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Residues in contact with PHE 40 (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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36C LEU 3.0 17.7 + - - +
37C THR* 3.6 4.0 - - + +
39C LYS* 1.3 78.1 - - - +
41C LEU* 1.3 75.1 + - + +
43C LYS* 5.2 1.4 + - - +
61C GLU* 3.5 36.2 - - + +
70C LEU* 3.5 27.1 - - + -
72C VAL* 5.1 1.1 - - + -
169C PHE* 3.4 23.4 - + - -
172C VAL* 4.0 4.8 - - + +
173C GLN* 3.8 28.5 - - + -
176C PHE* 3.4 55.2 - + + -
177C HIS* 4.1 14.4 - + - -
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Residues in contact with LEU 41 (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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37C THR* 3.0 33.0 + - + +
38C VAL* 4.0 4.9 - - + +
40C PHE* 1.3 94.8 - - + +
42C THR* 1.3 68.4 + - + +
43C LYS* 5.2 5.3 + - - -
57C TYR* 3.6 40.8 - - + +
58C SER 5.5 1.6 - - - +
59C SER* 3.7 31.4 - - - +
61C GLU* 4.5 1.8 - - - +
72C VAL* 5.4 6.5 - - + -
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Residues in contact with THR 42 (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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38C VAL* 2.6 45.1 + - + +
41C LEU* 1.3 81.3 - - + +
43C LYS* 1.3 69.8 + - - +
44C ARG* 3.0 35.1 + - - +
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Residues in contact with LYS 43 (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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39C LYS* 2.7 37.5 + - - +
40C PHE 5.2 1.6 + - - +
41C LEU 3.8 5.8 + - - +
42C THR* 1.3 74.7 - - - +
44C ARG* 1.3 74.4 + - - +
169C PHE* 3.8 49.7 - - + +
204C UNX 4.0 3.5 - - - -
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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