Contacts of the strand formed by residues 34 - 39 (chain B) in PDB entry 5BOU
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 ALA 34 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLY 3.5 2.2 + - - +
33B THR* 1.3 74.7 - - - +
35B ILE* 1.3 63.3 + - - +
46B ALA 3.4 4.3 - - - -
47B ALA* 4.0 10.5 - - + -
64B LYS* 5.0 0.2 - - + -
75B ALA* 4.0 25.1 - - + -
76B VAL 4.4 11.2 - - - +
135B ILE* 3.5 3.1 - - + +
163B SER* 3.2 4.3 - - - -
164B VAL* 2.9 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.2 5.6 - - + -
34B ALA* 1.3 79.7 - - - +
36B GLY* 1.3 62.2 + - - +
37B ILE* 4.0 27.8 - - + -
44B VAL 3.9 0.2 - - - +
45B LEU* 3.5 5.8 - - - +
46B ALA* 2.6 43.8 + - + +
75B ALA* 5.5 0.2 - - - +
135B ILE* 4.0 4.9 - - - -
162B ILE 3.5 7.9 - - - +
163B SER* 3.9 13.7 - - - -
171B ALA* 4.7 4.5 - - + -
175B LEU* 4.3 9.2 - - + -
192B ALA* 4.0 9.8 - - + +
195B THR* 3.7 35.4 - - + -
196B LEU* 3.7 28.3 - - + +
199B THR* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 1.3 74.0 - - - +
37B ILE* 1.3 65.1 + - - +
44B VAL 3.3 8.7 - - - -
45B LEU* 4.1 10.8 - - - -
135B ILE* 3.9 6.3 - - - +
147B LEU* 3.4 16.7 - - - +
161B ALA* 3.3 3.3 - - - -
162B ILE* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 4.0 9.0 - - + -
36B GLY* 1.3 78.9 - - - +
38B MET* 1.3 64.3 + - - +
39B ALA 4.0 0.3 + - - -
43B ILE* 3.4 2.8 - - - +
44B VAL* 2.9 38.0 + - + +
147B LEU* 3.6 4.2 - - - +
160B LYS 3.8 2.0 - - - +
161B ALA* 4.2 3.1 - - + +
175B LEU* 3.7 24.7 - - + -
179B TYR* 3.8 28.0 - - + -
183B MET* 4.8 2.7 - - - -
188B ALA* 3.6 31.2 - - + +
191B LEU* 3.9 9.0 - - + -
192B ALA* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 1.3 74.0 - - - +
39B ALA* 1.3 82.4 - - - +
40B SER* 5.4 0.7 - - - -
42B GLY 4.0 1.8 - - - -
43B ILE* 4.1 8.3 - - + -
145B TYR* 4.1 27.4 - - + +
146B GLN* 4.6 3.4 - - - +
147B LEU* 3.4 14.7 - - + +
159B TRP 4.4 1.3 - - - +
160B LYS* 2.8 36.1 + - + +
179B TYR* 2.7 37.7 + - - +
54C ASP* 3.2 31.2 - - - +
56C ARG* 4.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE 4.0 0.4 + - - -
38B MET* 1.3 91.7 - - - +
40B SER* 1.3 65.2 + - - +
41B ASP* 3.3 3.8 - - - +
42B GLY 2.7 23.7 + - - +
145B TYR* 4.2 5.0 - - - +
179B TYR* 4.9 1.1 - - - -
181B ASP 5.7 1.3 - - - -
183B MET* 3.5 19.1 - - + +
184B LYS 3.6 23.3 - - - +
185B VAL* 3.7 7.6 - - + +
188B ALA* 4.5 7.9 - - + -
----------------------------------------------------------
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