Contacts of the helix formed by residues 16 - 31 (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 SER 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C ALA* 1.3 76.3 - - - +
17C CYS* 1.3 65.0 + - - +
18C LEU* 3.8 7.1 + - - +
19C GLU* 3.3 35.8 + - - +
20C LEU* 3.0 26.1 + - - +
46C VAL* 4.4 5.4 - - - -
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Residues in contact with CYS 17 (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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16C SER* 1.3 73.5 - - - +
18C LEU* 1.3 60.0 + - - +
20C LEU 3.1 3.5 + - - -
21C ALA* 2.8 26.4 + - - +
43C ALA* 3.2 39.5 - - - +
44C VAL* 5.4 0.2 - - - -
46C VAL* 3.8 12.2 - - + +
47C GLY 3.4 17.5 - - - +
48C THR* 3.6 34.5 - - - -
53C THR* 5.4 4.3 - - - -
54C LEU* 6.0 0.7 - - - -
57C ILE* 5.1 10.1 - - - -
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Residues in contact with LEU 18 (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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16C SER* 3.4 7.0 + - - +
17C CYS* 1.3 80.9 - - - +
19C GLU* 1.3 58.2 + - + +
21C ALA* 4.4 3.4 - - - -
22C LEU* 2.8 55.1 + - + +
53C THR* 4.7 15.3 - - + +
52F ILE* 4.1 25.6 - - + +
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ALA* 3.3 23.9 + - - -
16C SER* 3.3 31.9 + - - +
17C CYS 3.2 0.8 - - - -
18C LEU* 1.3 79.8 - - + +
20C LEU* 1.3 63.7 + - + +
22C LEU* 3.3 11.4 + - + +
23C GLU* 3.0 21.8 + - - +
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Residues in contact with LEU 20 (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* 4.3 23.3 - - + +
16C SER 3.0 13.5 + - - +
17C CYS 3.5 0.4 - - - +
19C GLU* 1.3 76.7 - - + +
21C ALA* 1.3 59.3 + - - +
23C GLU* 3.0 7.4 + - - +
24C GLY 2.9 25.3 + - - -
39C PHE* 3.4 35.4 - - + +
42C ALA* 3.6 15.9 - - + -
43C ALA* 3.4 31.9 - - + +
46C VAL* 3.8 18.2 - - + -
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Residues in contact with ALA 21 (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 2.8 16.8 + - - +
18C LEU* 3.8 6.1 - - - +
20C LEU* 1.3 76.4 - - - +
22C LEU* 1.3 63.8 + - - +
24C GLY 3.4 0.3 + - - -
25C GLU* 3.1 22.3 + - - +
40C PHE* 3.5 14.9 - - - -
43C ALA* 3.7 6.0 - - + +
53C THR* 5.2 1.8 - - + -
57C ILE* 3.2 34.5 - - + -
52F ILE* 3.6 15.1 - - + +
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Residues in contact with LEU 22 (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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18C LEU* 2.8 51.2 + - + +
19C GLU* 3.5 9.4 - - + +
20C LEU 3.2 0.2 - - - -
21C ALA* 1.3 73.4 - - - +
23C GLU* 1.3 60.0 + - - +
25C GLU* 3.6 8.0 + - - +
26C ARG* 3.3 20.8 + - - +
52F ILE* 3.8 10.5 - - + +
53F SER* 3.6 40.4 - - - +
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Residues in contact with GLU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 4.9 6.4 - - - -
19C GLU 3.0 10.7 + - - +
20C LEU* 3.0 10.1 + - - +
22C LEU* 1.3 73.5 - - - +
24C GLY* 1.3 66.2 + - - +
25C GLU 3.1 1.6 - - - -
26C ARG* 2.6 53.1 + - - +
27C LEU* 3.0 21.7 + - + +
39C PHE* 3.1 41.1 - - + -
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Residues in contact with GLY 24 (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 2.9 15.3 + - - -
21C ALA 3.4 2.2 + - - -
23C GLU* 1.3 72.1 - - - +
25C GLU* 1.3 61.4 + - - +
27C LEU* 3.3 4.1 + - - +
28C CYS* 3.1 27.7 + - - -
36C GLY* 3.6 16.2 - - - -
39C PHE* 3.5 20.3 - - - +
40C PHE* 3.5 12.1 - - - -
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 3.1 15.8 + - - +
22C LEU* 3.6 8.0 - - - +
23C GLU 3.1 0.4 - - - -
24C GLY* 1.3 76.1 - - - +
26C ARG* 1.3 63.7 + - - +
28C CYS* 3.1 5.4 + - - +
29C LYS* 2.9 37.7 + - + +
40C PHE* 3.3 10.2 - - + -
60C GLN* 3.2 27.5 + - - +
51F PRO* 3.3 8.8 - - - +
52F ILE* 2.8 30.6 + - + +
53F SER* 3.0 31.8 + - - -
58F ALA 4.5 7.7 - - - +
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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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23A GLU* 3.0 38.4 + - - -
26A ARG* 3.8 6.7 - - - +
22C LEU 3.3 10.1 + - - +
23C GLU* 2.6 49.0 + - - +
25C GLU* 1.3 79.6 + - - +
27C LEU* 1.3 67.3 + - - +
29C LYS* 3.4 11.3 + - + +
30C SER* 3.0 25.6 + - - -
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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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26A ARG* 3.8 36.6 - - - +
23C GLU* 3.0 22.0 + - + +
24C GLY 3.5 6.3 - - - +
25C GLU 3.1 0.2 - - - -
26C ARG* 1.3 89.1 - - - +
28C CYS* 1.3 63.8 + - - +
30C SER* 2.4 24.3 + - - +
32C ASP* 3.0 24.7 + - + +
35C ALA* 3.3 38.6 - - + +
36C GLY* 3.5 4.3 - - - +
39C PHE* 3.4 27.4 - - + -
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Residues in contact with CYS 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 3.1 15.9 + - - -
25C GLU* 3.1 7.4 + - - +
27C LEU* 1.3 77.8 - - - +
29C LYS* 1.3 64.1 + - + +
31C GLY* 3.0 14.6 + - - -
32C ASP 3.8 6.5 - - - -
33C CYS* 4.0 30.6 - - - -
36C GLY* 4.1 6.5 - - - -
40C PHE* 3.8 18.2 - - - -
60C GLN* 5.0 5.6 - - - +
64C ALA* 4.1 17.3 - - - -
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Residues in contact with LYS 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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25C GLU* 2.9 34.9 + - + +
26C ARG* 3.7 11.0 - - + +
28C CYS* 1.3 77.2 - - + +
30C SER* 1.3 62.1 + - - +
31C GLY* 4.6 0.2 - - - -
58F ALA* 3.4 35.1 - - + +
59F GLN* 4.6 0.2 - - - +
60F GLY* 2.9 38.1 + - - +
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Residues in contact with SER 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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23A GLU* 5.1 10.3 - - - -
26A ARG* 5.1 4.2 + - - -
26C ARG* 3.0 15.1 + - - -
27C LEU* 2.4 31.5 + - - +
29C LYS* 1.3 77.2 - - - +
31C GLY* 1.3 57.6 + - - +
32C ASP* 3.6 8.3 + - - +
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Residues in contact with GLY 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 LEU 3.9 0.2 - - - -
28C CYS 3.0 12.2 + - - -
29C LYS 4.6 0.2 - - - -
30C SER* 1.3 80.7 - - - +
32C ASP* 1.3 61.5 + - - +
33C CYS* 3.5 6.4 + - - -
67C TYR* 4.6 18.3 + - - -
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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