Contacts of the helix formed by residues 17 - 32 (chain C) in PDB entry 8ATC
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 ARG 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C SER* 1.3 72.6 - - - +
18C ASP* 1.3 69.2 + - - +
20C LEU* 3.3 10.7 + - - +
21C ASN* 3.0 43.6 + - - +
153C ASP* 4.2 20.8 + - - -
178C LYS* 4.0 33.8 + - + +
179C PHE* 3.5 36.8 - - + +
180C ASP* 4.3 11.3 + - - -
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Residues in contact with ASP 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* 2.7 13.6 + - - +
17C ARG* 1.3 82.0 + - - +
19C ASP* 1.3 68.3 - - - +
21C ASN* 3.0 20.9 + - - +
22C LEU* 3.0 13.1 + - - +
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Residues in contact with ASP 19 (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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3C PRO* 4.2 14.7 - - - +
4C LEU* 3.7 30.3 - - + +
7C LYS* 4.0 17.0 + - - -
14C ASP 4.5 1.4 - - - +
15C LEU* 3.5 19.0 - - + +
16C SER* 2.7 38.7 + - - +
18C ASP* 1.3 73.6 - - - +
20C LEU* 1.3 66.3 + - - +
22C LEU* 3.1 14.1 + - - +
23C VAL* 3.2 17.1 + - - +
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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
----------------------------------------------------------
12C ILE* 4.6 11.4 - - + -
15C LEU* 3.9 32.1 - - + -
16C SER 3.0 15.6 + - - +
17C ARG* 3.5 8.5 - - - +
19C ASP* 1.3 78.3 - - - +
21C ASN* 1.3 64.2 + - - +
23C VAL* 3.1 14.7 + - - +
24C LEU* 3.1 16.5 + - + +
139C LEU* 4.3 15.1 - - + +
142C LEU* 3.4 31.9 - - + -
175C ALA* 3.9 20.2 - - + +
178C LYS* 4.3 8.5 - - + -
179C PHE* 3.9 20.6 - - + -
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Residues in contact with ASN 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 ARG* 3.0 42.8 + - - +
18C ASP* 3.0 14.6 + - - +
20C LEU* 1.3 72.1 - - - +
22C LEU* 1.3 52.7 - - - +
24C LEU* 3.3 10.0 + - - +
25C ALA* 2.6 37.6 + - - +
146C GLN* 5.2 3.8 + - - -
152C LEU* 4.8 7.5 - - - +
179C PHE* 3.8 21.8 - - - -
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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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2C ASN* 4.3 7.6 - - - +
3C PRO* 3.5 39.5 - - + -
4C LEU* 4.8 5.8 - - + -
18C ASP 3.0 10.8 + - - +
19C ASP* 3.5 11.7 - - - +
21C ASN* 1.3 77.2 - - - +
23C VAL* 1.3 50.6 + - - +
25C ALA* 3.1 7.6 + - + -
26C THR* 2.7 52.7 + - - +
302C LEU* 4.1 13.9 - - + -
308C LEU* 4.2 20.2 - - + -
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Residues in contact with VAL 23 (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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4C LEU* 3.4 30.1 - - + -
15C LEU* 5.5 3.4 - - + -
19C ASP 3.2 7.8 + - - +
20C LEU* 3.1 8.2 + - - +
22C LEU* 1.3 76.5 - - - +
24C LEU* 1.3 61.1 + - + +
26C THR 3.4 1.0 + - - -
27C ALA* 3.0 27.9 + - - +
139C LEU* 3.8 35.9 - - + -
295C ALA* 4.2 19.1 - - - +
298C ALA* 3.4 7.4 - - + +
299C LEU* 4.4 14.4 - - + +
302C LEU* 3.9 11.7 - - + -
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Residues in contact with LEU 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* 3.1 17.6 + - + +
21C ASN* 3.8 12.3 - - - +
23C VAL* 1.3 78.8 - - + +
25C ALA* 1.3 68.2 + - - +
27C ALA* 3.3 6.2 + - + +
28C ALA* 3.2 22.5 + - - +
139C LEU* 3.6 12.3 - - + +
142C LEU* 3.9 19.3 - - + +
143C PHE* 3.3 47.5 - - + +
146C GLN* 4.0 21.0 + - - +
152C LEU* 3.7 29.8 - - + -
179C PHE* 5.8 0.2 - - + -
295C ALA* 5.5 0.9 - - + -
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Residues in contact with ALA 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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21C ASN 2.6 21.9 + - - +
22C LEU* 3.7 9.0 - - + +
24C LEU* 1.3 73.5 - - - +
26C THR* 1.3 64.4 + - - +
28C ALA* 3.3 7.2 + - - +
29C LYS* 3.0 32.5 + - - +
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Residues in contact with THR 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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22C LEU* 2.7 30.0 + - - +
23C VAL 3.7 4.3 - - - -
25C ALA* 1.3 72.4 - - - +
27C ALA* 1.3 49.8 + - - +
29C LYS* 3.1 10.9 + - - +
30C LEU* 2.8 40.7 + - + +
298C ALA* 3.8 18.2 - - + +
301C ALA* 5.0 0.9 - - + -
302C LEU* 3.7 32.9 - - + +
308C LEU* 5.2 1.7 - - - +
309C VAL* 4.4 22.4 - - + +
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Residues in contact with ALA 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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23C VAL 3.0 18.8 + - - +
24C LEU* 3.4 7.9 - - + +
26C THR* 1.3 71.0 - - - +
28C ALA* 1.3 56.3 + - - +
30C LEU* 3.7 2.1 - - - +
31C LYS* 2.8 35.6 + - - +
143C PHE* 3.5 23.3 - - + -
294C PHE* 3.7 27.9 - - - +
295C ALA* 4.2 4.7 - - + -
298C ALA* 3.4 10.5 - - + +
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Residues in contact with ALA 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 LEU 3.2 9.0 + - - +
25C ALA* 3.5 11.4 - - - +
27C ALA* 1.3 76.1 - - - +
29C LYS* 1.3 69.5 - - - +
31C LYS* 3.3 6.3 + - - +
32C ALA* 3.2 21.8 + - - +
143C PHE* 3.8 12.7 - - + -
146C GLN* 5.7 4.9 - - - +
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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 ALA* 3.0 24.2 + - - +
26C THR* 3.1 12.8 + - - +
28C ALA* 1.3 80.7 - - + +
30C LEU* 1.3 57.6 + - - +
32C ALA* 3.2 5.5 - - - +
33C ASN* 2.9 32.8 + - - +
308C LEU* 5.4 8.1 - - - +
309C VAL* 2.9 35.2 + - + +
310C LEU* 3.3 27.2 + - - +
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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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26C THR* 2.8 18.6 + - + +
27C ALA* 4.2 3.6 - - - +
29C LYS* 1.3 73.4 - - - +
31C LYS* 1.3 67.4 + - - +
32C ALA 3.1 0.8 + - - -
33C ASN 3.7 5.4 - - - +
34C PRO* 3.4 22.1 - - + +
35C GLN* 3.3 39.5 - - + +
38C LEU* 4.5 5.2 - - + -
66C LEU* 4.8 5.8 - - + -
294C PHE* 4.9 4.4 - - + +
297C GLN* 3.8 25.9 + - + +
298C ALA* 3.6 36.8 - - + +
301C ALA* 4.3 9.9 - - + -
309C VAL* 3.8 16.8 - - + -
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Residues in contact with LYS 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 ALA 2.8 25.5 + - - +
28C ALA* 3.7 6.7 - - - +
29C LYS 3.3 0.8 - - - -
30C LEU* 1.3 74.1 - - - +
32C ALA* 1.3 58.3 + - - +
34C PRO* 4.7 3.1 - - - +
143C PHE* 4.2 12.1 - - + -
147C GLN* 3.4 23.8 + - - -
291C ASN* 4.0 10.3 - - - +
294C PHE* 3.6 48.6 - - + -
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Residues in contact with ALA 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 ALA 3.2 11.6 + - - +
29C LYS* 3.2 11.0 - - - +
31C LYS* 1.3 79.6 - - - +
33C ASN* 1.3 74.6 - - - +
34C PRO* 3.6 8.1 - - - +
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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