Contacts of the helix formed by residues 21 - 35 (chain C) in PDB entry 1OY1
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 GLU 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C VAL* 3.5 18.2 - - + +
19C GLY 3.7 1.6 + - - -
20C SER* 1.3 68.5 - - - +
22C ILE* 1.3 61.5 + - - +
23C HIS* 2.7 34.0 + - - +
24C GLU* 3.2 45.2 - - + +
25C ALA* 2.8 30.0 + - - +
95C PRO* 5.0 0.5 - - - +
96C GLY 3.0 14.1 + - - +
97C GLY* 3.7 11.2 - - - +
138C CYS* 5.7 0.2 - - - -
195C TYR* 3.8 6.5 - - - -
72D ARG 5.6 0.3 - - - +
75D ARG* 2.8 42.4 + - - +
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Residues in contact with ILE 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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14C CYS* 3.8 22.4 - - - +
15C GLY* 3.8 16.8 - - - +
16C VAL* 4.6 2.2 - - - +
20C SER 3.0 1.9 + - - +
21C GLU* 1.3 74.6 + - - +
23C HIS* 1.3 64.9 + - + +
25C ALA* 3.7 4.9 - - - +
26C VAL* 3.0 23.6 + - + +
73C ILE* 4.3 7.0 - - + -
14D CYS* 3.7 30.3 - - - -
22D ILE* 3.5 28.0 - - + -
26D VAL* 3.5 14.8 - - + -
72D ARG 3.8 26.5 - - - +
73D ILE* 3.9 9.4 - - + +
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Residues in contact with HIS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLU* 2.7 22.1 + - - +
22C ILE* 1.3 71.8 - - + +
24C GLU* 1.3 54.5 + - - +
26C VAL* 3.7 0.9 - - - +
27C LEU* 2.7 41.7 + - + +
195C TYR* 2.9 34.4 + - + +
201C ILE* 3.6 28.9 - - + +
26D VAL* 4.0 21.8 - - + -
29D LEU* 3.9 14.9 - - + +
72D ARG 5.9 0.2 - - - -
73D ILE 2.8 28.3 + - - -
74D THR* 5.0 2.9 - - - -
75D ARG* 4.2 16.3 - - + +
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Residues in contact with GLU 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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21C GLU* 3.2 25.4 + - + +
23C HIS* 1.3 78.7 - - - +
25C ALA* 1.3 54.7 + - - +
27C LEU* 3.8 1.0 - - - +
28C THR* 2.7 38.1 + - - -
95C PRO* 4.3 4.5 - - + -
96C GLY* 2.6 36.4 + - - -
137C MSE 3.6 9.3 - - - +
138C CYS* 3.3 15.1 - - - +
194C ALA* 2.9 34.0 - - + +
195C TYR* 3.2 23.7 + - + +
208C ILE* 3.6 18.6 - - + +
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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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9C VAL* 5.7 0.8 - - + +
11C LEU* 4.0 26.0 - - + -
20C SER* 4.7 1.1 - - - -
21C GLU 2.8 21.1 + - - +
22C ILE 3.7 3.4 - - - +
24C GLU* 1.3 74.4 - - - +
26C VAL* 1.3 58.8 + - - +
28C THR* 3.0 4.7 + - - -
29C LEU* 2.9 34.8 + - + +
73C ILE* 4.0 21.8 - - + -
95C PRO* 4.0 14.6 - - + +
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Residues in contact with VAL 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 ILE 3.0 19.7 + - - +
25C ALA* 1.3 74.3 - - - +
27C LEU* 1.3 58.1 + - + +
29C LEU* 3.2 9.1 + - - +
30C LEU* 2.9 27.4 + - - +
73C ILE* 4.2 8.1 - - + -
22D ILE* 3.7 28.9 - - + -
23D HIS* 4.0 21.3 - - + +
26D VAL* 3.4 31.9 - - + -
27D LEU* 4.6 6.3 - - + -
201D ILE* 3.7 20.5 - - + +
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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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23C HIS* 2.7 32.6 + - + +
24C GLU 3.9 3.1 - - - +
26C VAL* 1.3 73.2 - - + +
28C THR* 1.3 62.7 + - - +
30C LEU* 3.4 8.3 + - + +
31C ALA* 3.1 23.2 + - - +
34C ARG* 6.3 0.4 - - - +
201C ILE* 3.7 29.8 - - + +
204C ALA* 4.2 5.8 - - + -
205C ALA* 3.8 32.5 - - + +
208C ILE* 4.0 22.3 - - + +
209C ASP* 4.6 4.9 - - - +
26D VAL* 4.7 4.5 - - + -
27D LEU* 6.2 0.4 - - + -
30D LEU* 3.4 37.2 - - + -
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Residues in contact with THR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.7 9.0 - - + -
24C GLU 2.7 25.3 + - - -
25C ALA 3.3 5.4 - - - -
27C LEU* 1.3 76.5 - - - +
29C LEU* 1.3 63.3 + - - +
31C ALA* 3.2 4.5 + - - +
32C ILE* 2.9 42.4 + - + +
93C ILE* 3.8 27.1 - - + -
95C PRO* 3.9 9.2 - - + +
137C MSE 3.1 22.5 - - - +
208C ILE* 3.6 9.8 - - - +
212C VAL* 4.3 7.4 - - + -
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Residues in contact with LEU 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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9C VAL* 4.5 11.9 - - + -
11C LEU* 5.8 1.3 - - + -
25C ALA* 2.9 18.6 + - + +
26C VAL* 3.5 9.2 - - - +
28C THR* 1.3 78.4 - - - +
30C LEU* 1.3 61.8 + - - +
32C ILE* 3.4 7.0 + - - +
33C SER* 3.0 24.8 + - - -
39C ALA* 3.7 28.2 - - + +
41C CYS* 3.7 19.5 - - - -
73C ILE* 4.2 20.2 - - + +
74C THR* 4.6 8.3 - - + -
23D HIS* 3.8 26.7 - - + +
201D ILE* 3.6 13.6 - - + +
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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 VAL 2.9 16.5 + - - +
27C LEU* 3.7 10.1 - - + +
28C THR 3.2 0.2 - - - -
29C LEU* 1.3 76.9 - - - +
31C ALA* 1.3 53.8 + - - +
33C SER* 3.2 1.4 + - - -
34C ARG* 2.7 76.8 + - + +
27D LEU* 3.5 24.5 - - + -
30D LEU* 3.7 20.2 - - + -
34D ARG* 5.1 1.1 - - - +
201D ILE* 3.8 20.8 - - + +
202D ALA* 4.2 4.9 - - - -
205D ALA* 3.6 26.7 - - + -
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Residues in contact with ALA 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 3.1 16.4 + - - +
28C THR 3.7 3.6 - - - +
30C LEU* 1.3 75.4 - - - +
32C ILE* 1.3 66.4 + - - +
34C ARG* 4.1 8.5 - - - +
35C SER* 2.9 31.0 + - - +
208C ILE* 5.3 0.2 - - + -
209C ASP* 3.7 24.0 + - - +
212C VAL* 3.8 27.1 - - + -
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Residues in contact with ILE 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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7C ILE* 3.6 33.7 - - + -
9C VAL* 4.6 5.8 - - + -
28C THR* 2.9 34.9 + - + +
29C LEU* 3.6 8.7 - - - +
31C ALA* 1.3 77.1 - - - +
33C SER* 1.3 60.6 + - - +
35C SER* 3.4 4.5 + - - -
37C ALA* 2.9 58.0 + - + +
39C ALA* 3.8 23.1 - - + +
93C ILE* 4.4 4.5 - - + -
212C VAL* 3.9 19.7 - - + +
216C LEU* 4.9 1.1 - - + -
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Residues in contact with SER 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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29C LEU 3.0 14.6 + - - -
30C LEU 3.5 2.0 - - - -
32C ILE* 1.3 77.1 - - - +
34C ARG* 1.3 65.4 + - - +
35C SER 3.1 1.1 - - - -
36C GLY* 3.0 14.6 + - - -
37C ALA 4.1 8.7 - - - +
200D ASN* 3.5 13.4 + - - +
201D ILE* 3.4 18.1 - - - +
202D ALA* 2.9 33.1 + - - +
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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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27C LEU* 6.3 0.2 - - - +
30C LEU* 2.7 58.7 + - + +
31C ALA* 4.1 6.3 - - - +
33C SER* 1.3 73.6 - - - +
35C SER* 1.3 59.1 + - - +
36C GLY 3.0 3.7 + - - -
205C ALA* 6.0 0.6 - - - +
209C ASP* 3.4 33.3 + - - -
30D LEU* 5.2 1.2 - - - +
34D ARG* 3.1 36.1 - - - +
202D ALA* 4.5 11.7 - - + +
205D ALA* 5.7 3.2 - - + +
209D ASP* 5.3 2.0 + - - -
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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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31C ALA* 2.9 20.9 + - - +
32C ILE 3.8 1.1 - - - -
33C SER 3.1 0.4 - - - -
34C ARG* 1.3 77.1 - - - +
36C GLY* 1.3 61.8 + - - +
37C ALA* 3.2 2.9 + - - +
212C VAL* 4.6 2.4 - - - +
213C SER* 4.5 11.3 + - - -
216C LEU* 3.2 31.5 - - - +
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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