Contacts of the helix formed by residues 23 - 33 (chain B) in PDB entry 3OPY
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 LEU 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 3.7 32.4 - - + +
18B PRO* 4.8 5.3 - - - +
19B ASN 4.9 0.9 - - - +
21B SER 2.7 41.9 + - - +
24B GLN* 1.3 60.4 + - + +
25B ALA* 3.6 5.2 - - - +
26B SER* 4.2 12.9 + - - +
27B ILE* 3.3 24.3 + - - +
64B LEU* 5.1 9.2 - - + -
134B VAL* 5.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 3.5 13.3 + - - +
23B LEU* 1.3 75.3 - - + +
25B ALA* 1.4 60.6 + - - +
26B SER 3.2 1.3 - - - -
27B ILE* 3.2 14.3 + - - +
28B ASP* 2.9 55.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 4.5 5.2 + - - +
23B LEU 5.1 4.0 - - - +
24B GLN* 1.4 77.8 - - - +
26B SER* 1.4 56.5 + - - +
28B ASP* 3.7 8.9 + - - +
29B PHE* 3.2 23.7 + - - +
134B VAL* 5.7 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 6.1 1.3 - - - -
23B LEU* 4.1 14.1 + - - +
24B GLN 3.2 0.4 - - - -
25B ALA* 1.4 75.9 - - - +
27B ILE* 1.4 63.4 + - - +
28B ASP 3.2 0.2 - - - -
29B PHE* 3.0 7.2 + - - +
30B TYR* 3.0 49.8 + - - -
133B THR* 4.1 1.1 - - - -
134B VAL* 3.3 34.8 + - - +
135B ASP* 4.2 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 3.3 19.3 + - - +
24B GLN* 3.2 22.7 + - - +
26B SER* 1.4 77.2 - - - +
28B ASP* 1.4 51.5 + - - +
30B TYR* 4.0 2.4 + - - +
31B THR* 2.6 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 2.9 40.6 + - - +
25B ALA* 3.8 8.1 - - - +
26B SER 3.2 0.2 - - - -
27B ILE* 1.4 73.1 - - - +
29B PHE* 1.4 59.4 + - - +
31B THR* 3.1 11.5 + - - -
32B ASN* 2.9 40.8 + - - +
33B PHE* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 3.2 14.5 + - - +
26B SER* 3.0 10.6 + - - +
28B ASP* 1.4 73.5 - - - +
30B TYR* 1.3 81.1 + + - +
33B PHE* 2.8 65.8 + + + +
34B LEU* 5.1 6.7 - - + -
112B LEU* 3.9 15.7 - - + -
117B HIS* 3.4 45.3 - + - -
131B VAL* 5.0 5.2 - - + -
132B TYR 4.3 12.6 - - - -
133B THR* 3.6 28.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.1 19.6 - - + +
26B SER* 3.0 50.9 + - - +
27B ILE* 4.8 2.7 - - - +
29B PHE* 1.3 82.5 - + - +
31B THR* 1.4 56.4 + - + +
34B LEU* 3.3 39.5 + - + -
36B PHE* 3.3 41.3 + + + -
100B PHE* 5.6 7.6 - + - -
133B THR* 3.4 13.2 - - - -
135B ASP* 3.2 35.6 + - + +
138B GLY* 5.9 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ILE* 2.6 25.8 + - + +
28B ASP* 3.1 13.2 + - - -
30B TYR* 1.4 77.8 - - + +
32B ASN* 1.4 65.0 + - - +
35B GLY* 3.4 18.9 + - - -
36B PHE* 3.4 31.8 + - + +
37B ALA* 4.1 8.7 - - - +
38B ILE* 4.7 6.5 - - + +
50B GLN* 5.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP* 2.9 34.9 + - - +
31B THR* 1.4 80.8 + - - +
33B PHE* 1.3 74.2 + - + +
35B GLY* 4.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASP 5.2 0.4 - - - -
29B PHE* 2.8 51.6 + + + +
32B ASN* 1.3 86.5 - - + +
34B LEU* 1.3 70.5 + - + +
35B GLY 3.7 0.2 - - - -
108B LEU* 5.8 4.5 - - - +
111B LEU* 3.6 30.7 - - + +
112B LEU* 3.8 21.8 - - + -
115B GLY* 4.2 14.1 - - - -
117B HIS* 3.5 33.7 - + - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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