Contacts of the helix formed by residues 32 - 47 (chain C) in PDB entry 3SF4
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 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ARG* 4.5 16.1 + - - +
30A SER* 5.5 6.1 + - - -
27C LEU* 3.0 23.2 + - + +
28C CYS* 3.6 0.4 + - - -
30C SER* 3.6 5.7 + - - +
31C GLY* 1.3 76.7 - - - +
33C CYS* 1.3 55.8 + - - +
34C ARG* 3.0 11.8 + - - +
35C ALA* 2.7 43.4 + - + +
36C GLY 3.3 14.7 + - - -
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Residues in contact with CYS 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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28C CYS* 4.0 31.9 - - - -
31C GLY* 3.5 4.3 + - - -
32C ASP* 1.3 71.9 - - - +
34C ARG* 1.3 59.8 + - - +
36C GLY 3.7 0.6 - - - -
37C VAL* 2.9 35.7 + - - +
64C ALA* 4.2 12.6 - - + +
67C TYR* 3.4 36.5 - - + -
68C LEU* 3.9 26.6 - - + +
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Residues in contact with ARG 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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32C ASP* 3.0 7.2 + - - +
33C CYS* 1.3 81.1 - - - +
35C ALA* 1.3 59.4 + - - +
37C VAL* 3.6 10.9 + - - +
38C SER* 3.6 13.9 + - - -
65C TYR* 5.0 10.7 - - - -
68C LEU* 3.3 50.6 + - + +
70C ASP* 5.4 4.8 + - - +
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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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26A ARG* 5.2 3.6 - - - +
27C LEU* 3.4 19.7 - - + -
32C ASP* 2.7 32.4 + - + +
34C ARG* 1.3 71.6 - - - +
36C GLY* 1.3 65.7 + - - +
38C SER* 3.3 12.5 + - - -
39C PHE* 3.2 26.4 - - + -
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Residues in contact with GLY 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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24C GLY* 3.6 24.5 - - - -
27C LEU* 3.5 12.3 - - - +
28C CYS* 4.1 3.8 - - - -
32C ASP 3.3 10.1 + - - -
33C CYS 3.4 3.1 + - - -
34C ARG 3.3 0.2 - - - -
35C ALA* 1.3 80.0 - - - +
37C VAL* 1.3 61.0 + - - +
39C PHE 3.4 1.7 + - - -
40C PHE* 2.9 33.6 + - - -
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Residues in contact with VAL 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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28C CYS* 4.9 0.2 - - - -
33C CYS 2.9 26.1 + - - +
34C ARG* 3.7 8.1 - - - +
35C ALA 3.2 0.2 - - - -
36C GLY* 1.3 74.1 - - - +
38C SER* 1.3 61.1 + - - +
40C PHE* 3.0 7.3 + - - +
41C GLU* 2.8 47.6 + - + +
61C LEU* 4.1 3.4 - - + -
64C ALA* 4.0 20.2 - - + -
65C TYR* 3.0 46.4 - - + +
68C LEU* 4.2 11.4 - - + -
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Residues in contact with SER 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 ARG 3.6 9.3 + - - -
35C ALA* 3.3 11.6 + - - -
36C GLY 3.3 0.4 - - - -
37C VAL* 1.3 80.8 - - - +
39C PHE* 1.3 62.6 + - - +
40C PHE 3.1 0.5 + - - -
41C GLU* 3.3 8.9 + - - +
42C ALA* 2.9 31.9 + - - +
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Residues in contact with PHE 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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26A ARG* 6.5 0.7 - - - -
20C LEU* 3.4 36.4 - - + +
23C GLU* 3.1 38.1 - - + -
24C GLY* 3.5 22.7 - - - +
27C LEU* 3.4 15.5 - - + -
35C ALA* 3.2 23.9 + - + -
36C GLY 3.8 0.2 - - - +
37C VAL 3.3 0.4 - - - -
38C SER* 1.3 82.8 - - - +
40C PHE* 1.3 57.3 + - - +
42C ALA* 3.9 5.8 - - - -
43C ALA* 3.3 18.7 + - - +
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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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21C ALA* 3.5 27.1 - - - -
24C GLY* 3.6 14.1 - - - -
25C GLU* 3.3 17.9 - - - -
28C CYS* 3.8 15.9 - - - -
36C GLY 2.9 21.6 + - - -
37C VAL* 3.0 9.9 + - - +
39C PHE* 1.3 75.2 - - - +
41C GLU* 1.3 66.2 + - - +
42C ALA 3.0 1.7 + - - -
43C ALA* 3.1 5.7 + - - +
44C VAL* 3.0 26.6 + - - +
57C ILE* 4.0 17.1 - - + +
60C GLN* 3.4 37.2 - - + -
61C LEU* 3.5 27.1 - - + -
64C ALA* 5.4 0.9 - - + -
52F ILE* 3.7 15.9 - - + -
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Residues in contact with GLU 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 VAL* 2.8 32.6 + - + +
38C SER* 3.9 8.3 + - - +
40C PHE* 1.3 71.6 - - - +
42C ALA* 1.3 61.8 + - - +
44C VAL* 3.4 11.1 + - - +
45C GLN* 3.1 26.9 + - - +
61C LEU* 4.0 10.3 - - + -
65C TYR* 2.7 27.7 + - - -
73C LYS* 5.3 3.8 + - - -
77C TYR* 3.9 16.1 + - - +
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Residues in contact with ALA 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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20C LEU* 3.6 20.2 - - + -
38C SER 2.9 17.8 + - - +
39C PHE* 3.7 7.4 - - + +
41C GLU* 1.3 74.6 - - - +
43C ALA* 1.3 61.3 + - - +
45C GLN* 2.8 27.2 + - - +
46C VAL* 3.0 13.2 + - - +
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Residues in contact with ALA 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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17C CYS* 3.2 48.2 - - - +
20C LEU* 3.4 19.9 - - + +
21C ALA* 3.7 12.3 - - + +
39C PHE 3.3 5.4 + - - +
40C PHE* 3.1 9.1 + - - +
42C ALA* 1.3 79.5 - - - +
44C VAL* 1.3 57.3 + - - +
46C VAL* 3.4 2.6 + - - +
47C GLY 3.0 21.0 + - - -
57C ILE* 4.8 5.2 - - + -
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Residues in contact with VAL 44 (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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40C PHE 3.0 17.5 + - - +
41C GLU* 3.5 9.6 - - - +
42C ALA 3.0 0.2 + - - -
43C ALA* 1.3 72.7 - - - +
45C GLN* 1.3 72.4 + - + +
47C GLY* 2.9 16.5 + - - +
54C LEU* 4.6 11.4 - - + +
57C ILE* 3.6 22.4 - - + -
58C TYR* 4.4 27.1 - - + +
61C LEU* 4.1 13.2 - - + -
77C TYR* 5.5 2.2 - - + -
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Residues in contact with GLN 45 (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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41C GLU* 3.1 17.5 + - + +
42C ALA* 2.8 12.4 + - - +
44C VAL* 1.3 78.1 - - + +
46C VAL* 1.3 67.8 + - + +
47C GLY* 3.1 1.9 + - - -
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Residues in contact with VAL 46 (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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15C ALA 4.1 10.5 - - - +
16C SER* 4.4 2.5 - - - -
17C CYS* 3.8 19.7 - - - +
20C LEU* 3.8 21.5 - - + -
42C ALA 3.0 16.7 + - - +
43C ALA 3.5 7.6 - - - +
45C GLN* 1.3 77.5 - - + +
47C GLY* 1.3 69.3 + - - +
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Residues in contact with GLY 47 (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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17C CYS* 3.4 15.3 - - - +
43C ALA 3.0 7.1 + - - -
44C VAL* 2.9 19.0 + - - -
45C GLN 4.0 0.9 - - - -
46C VAL* 1.3 86.0 - - - +
48C THR* 1.3 66.7 + - - -
54C LEU* 6.1 1.1 - - - -
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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