Contacts of the helix formed by residues 21 - 35 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ARG 5.4 0.5 - - - +
75C ARG* 2.7 42.0 + - - +
16D VAL* 3.5 19.5 - - + +
19D GLY 3.6 1.4 + - - -
20D SER* 1.3 69.1 - - - +
22D ILE* 1.3 63.0 + - - +
23D HIS* 2.6 34.5 + - - +
24D GLU* 3.3 44.8 - - + +
25D ALA* 2.8 29.7 + - - +
95D PRO* 5.0 0.5 - - - +
96D GLY 3.1 9.0 + - - +
97D GLY* 3.7 16.9 - - - +
138D CYS* 5.7 0.2 - - - -
195D TYR* 3.9 4.9 - - - -
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Residues in contact with ILE 22 (chain D).
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* 3.6 30.7 - - - -
22C ILE* 3.5 28.7 - - + -
26C VAL* 3.7 13.2 - - + -
72C ARG* 3.7 33.0 + - + +
73C ILE* 3.9 10.5 - - + +
14D CYS* 3.8 17.7 - - - +
15D GLY* 3.8 15.0 - - - +
16D VAL 4.6 1.8 - - - +
20D SER 3.0 2.7 + - - +
21D GLU* 1.3 74.0 + - - +
23D HIS* 1.3 65.0 + - + +
25D ALA* 4.5 4.9 - - - -
26D VAL* 3.0 23.7 + - + +
73D ILE* 4.3 5.6 - - + -
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Residues in contact with HIS 23 (chain D).
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* 4.0 22.0 - - + -
29C LEU* 3.8 15.7 - - + +
73C ILE 2.6 30.1 + - - -
74C THR* 4.8 4.3 - - - -
75C ARG* 4.1 15.2 - - + +
21D GLU* 2.6 21.7 + - - +
22D ILE* 1.3 73.8 - - + +
24D GLU* 1.3 52.9 + - - +
26D VAL* 3.7 0.5 - - - +
27D LEU* 2.7 41.8 + - + +
195D TYR* 2.8 35.8 + - + -
201D ILE* 3.7 28.3 - - + +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLU* 3.1 23.0 + - + +
23D HIS* 1.3 78.4 - - - +
25D ALA* 1.3 54.4 + - - +
27D LEU* 3.8 1.1 - - - +
28D THR* 2.7 38.9 + - - -
95D PRO* 4.3 4.7 - - + -
96D GLY* 2.6 36.6 + - - -
137D MSE 3.6 7.8 - - - +
138D CYS* 3.3 14.8 - - - +
194D ALA* 2.8 35.4 - - + +
195D TYR* 3.2 22.7 + - + +
204D ALA* 5.3 0.2 - - + -
208D ILE* 3.7 20.3 - - + +
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 5.7 0.8 - - - +
11D LEU* 4.0 26.0 - - + -
20D SER* 4.7 1.3 - - - -
21D GLU 2.8 16.5 + - - +
22D ILE 3.8 3.1 - - - +
24D GLU* 1.3 74.5 - - - +
26D VAL* 1.3 66.0 + - - +
28D THR* 3.1 4.5 + - - -
29D LEU* 2.9 29.1 + - + +
73D ILE* 4.1 21.8 - - + -
95D PRO* 4.0 14.5 - - + +
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Residues in contact with VAL 26 (chain D).
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* 3.5 30.3 - - + +
23C HIS* 4.0 20.4 - - + +
26C VAL* 3.4 31.6 - - + -
27C LEU* 4.7 7.0 - - + -
201C ILE* 3.8 20.8 - - + +
22D ILE* 3.0 20.3 + - + +
25D ALA* 1.3 74.8 - - - +
27D LEU* 1.3 57.1 + - + +
29D LEU* 3.2 9.3 + - - +
30D LEU* 2.8 27.4 + - - +
73D ILE* 4.3 7.9 - - + -
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Residues in contact with LEU 27 (chain D).
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* 4.6 4.5 - - + -
27C LEU* 6.2 0.7 - - + -
30C LEU* 3.5 36.3 - - + -
23D HIS* 2.7 32.2 + - + +
24D GLU 3.8 3.1 - - - +
26D VAL* 1.3 72.5 - - + +
28D THR* 1.3 61.9 + - - +
30D LEU* 3.4 8.4 + - + +
31D ALA* 3.1 23.9 + - - +
34D ARG* 5.9 0.8 + - - +
201D ILE* 3.6 29.6 - - + +
204D ALA* 4.2 5.8 - - + -
205D ALA* 3.8 31.9 - - + +
208D ILE* 4.0 22.4 - - + +
209D ASP* 4.6 5.6 - - - +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D VAL* 4.7 9.9 - - + -
24D GLU 2.7 24.5 + - - -
25D ALA 3.1 5.4 + - - -
27D LEU* 1.3 76.3 - - - +
29D LEU* 1.3 62.5 + - - +
31D ALA* 3.2 4.2 + - - +
32D ILE* 2.9 42.2 + - + +
93D ILE* 3.8 26.9 - - + -
95D PRO* 3.8 9.9 - - + +
137D MSE 3.1 22.5 - - - +
208D ILE* 3.7 9.5 - - - +
212D VAL* 4.2 7.8 - - + +
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Residues in contact with LEU 29 (chain D).
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* 3.9 25.4 - - + +
201C ILE* 3.6 12.9 - - + +
9D VAL* 4.4 12.3 - - + -
11D LEU* 5.7 1.6 - - + -
25D ALA* 2.9 18.4 + - + +
26D VAL* 3.5 8.5 - - - +
28D THR* 1.3 78.7 - - - +
30D LEU* 1.3 61.7 + - - +
32D ILE* 3.4 5.7 + - - +
33D SER* 3.0 24.4 + - - -
39D ALA* 3.6 28.5 - - + +
41D CYS* 3.7 18.4 - - - -
73D ILE* 4.2 20.0 - - + +
74D THR* 4.6 9.6 - - + -
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Residues in contact with LEU 30 (chain D).
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* 3.4 25.4 - - + -
30C LEU* 3.7 19.1 - - + -
34C ARG* 5.2 0.9 - - - +
201C ILE* 3.7 22.6 - - + +
202C ALA* 4.2 4.3 - - - -
205C ALA* 3.7 26.9 - - + -
26D VAL* 2.8 17.8 + - + +
27D LEU* 3.7 9.4 - - + +
29D LEU* 1.3 77.3 - - - +
31D ALA* 1.3 51.6 + - - +
33D SER* 3.2 2.3 + - - -
34D ARG* 2.7 76.1 + - + +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU 3.1 14.5 + - - +
28D THR 3.6 7.0 - - - +
30D LEU* 1.3 73.1 - - - +
32D ILE* 1.3 67.6 + - - +
34D ARG* 4.1 9.1 - - - +
35D SER* 2.9 31.5 + - - +
208D ILE 5.0 0.2 - - - +
209D ASP* 3.8 23.1 + - + +
212D VAL* 3.7 27.6 - - + -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 3.6 37.0 - - + -
9D VAL* 4.5 6.1 - - + -
28D THR* 2.9 40.9 + - + +
29D LEU* 3.6 8.7 - - - +
31D ALA* 1.3 78.6 - - - +
33D SER* 1.3 61.0 + - - +
35D SER* 3.3 3.9 + - - -
37D ALA* 2.9 58.1 + - + +
39D ALA* 3.9 20.6 - - + +
93D ILE* 4.4 4.9 - - + -
212D VAL* 3.9 17.0 - - + +
216D LEU* 4.9 1.6 - - + -
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C ASN* 3.6 12.9 + - - +
201C ILE* 3.4 28.4 - - - +
202C ALA* 3.1 28.6 + - - +
29D LEU 3.0 8.1 + - - -
30D LEU 3.5 1.8 - - - -
32D ILE* 1.3 74.4 - - - +
34D ARG* 1.3 65.2 + - - +
35D SER 3.1 1.6 - - - -
36D GLY* 3.0 14.0 + - - -
37D ALA 4.1 7.6 - - - -
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Residues in contact with ARG 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 5.1 1.0 - - - +
34C ARG* 3.1 35.1 - - - +
202C ALA* 4.4 13.0 - - + -
205C ALA* 5.6 4.1 - - + +
209C ASP* 5.4 1.8 + - - -
27D LEU* 6.2 0.4 - - - +
30D LEU* 2.7 58.4 + - + +
31D ALA* 4.1 6.7 - - - +
33D SER* 1.3 73.1 - - - +
35D SER* 1.3 58.9 + - - +
36D GLY 3.1 3.7 + - - -
205D ALA* 6.0 0.6 - - - +
209D ASP* 3.4 33.5 + - - -
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA* 2.9 22.5 + - - +
32D ILE 3.8 1.1 - - - -
33D SER 3.1 0.4 - - - -
34D ARG* 1.3 76.9 - - - +
36D GLY* 1.3 61.6 + - - +
37D ALA* 3.2 4.2 + - - +
212D VAL* 4.6 2.6 - - - +
213D SER* 4.5 11.4 + - - -
216D LEU* 3.2 31.0 - - - +
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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