Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 5F0P
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 VAL 36 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 3.6 42.4 - - + +
29B MSE 3.5 7.4 - - - +
30B LYS* 4.8 9.4 - - + -
34B GLY 3.8 10.3 + - - +
35B LYS* 1.3 77.9 - - - +
37B GLU* 1.3 60.3 + - - +
38B LYS* 4.0 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU* 3.3 6.8 - - - +
29B MSE 3.1 34.7 + - + +
31B THR* 3.4 29.3 - - + +
35B LYS* 4.0 2.4 - - + -
36B VAL* 1.3 76.5 - - - +
38B LYS* 1.3 61.0 + - - +
39B HIS* 3.5 33.3 + - + +
122B ILE* 4.3 8.5 - - - +
148B ASP* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MSE 3.5 42.7 - - + +
27B ALA 3.3 17.7 - - - +
28B GLU* 4.4 18.6 - - + +
36B VAL* 4.0 2.2 + - + +
37B GLU* 1.3 76.1 - - - +
39B HIS* 1.3 72.2 + - - +
404B EDO 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B MSE 3.4 10.4 - - - -
27B ALA 2.9 30.5 + - - +
29B MSE 5.2 1.3 - - + -
37B GLU* 3.5 43.8 + - + +
38B LYS* 1.3 90.0 + - - +
40B TYR* 1.3 64.1 + - - +
148B ASP* 3.8 41.1 - - + +
149B LEU 5.0 0.2 - - - -
150B ILE* 3.6 35.1 - - + +
404B EDO 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.7 23.6 - - + -
21B GLY* 2.6 40.7 + - - -
24B ARG* 3.8 38.6 - - + -
25B LYS 4.1 1.8 - - - -
26B MSE 3.7 31.3 - - + -
39B HIS* 1.3 74.2 - - - +
41B LEU* 1.3 60.0 + - - +
42B PHE* 3.9 1.5 + - + -
147B TYR* 3.3 23.1 - + - -
148B ASP 4.7 0.6 + - - -
149B LEU* 3.7 13.0 - - + +
150B ILE 2.9 25.8 + - - +
404B EDO 3.2 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 2.7 32.7 + - - +
25B LYS* 3.1 34.1 + - + +
26B MSE 4.9 3.6 - - - +
27B ALA* 4.3 12.6 - - + -
39B HIS 3.6 0.4 + - - -
40B TYR* 1.3 71.8 - - - +
42B PHE* 1.3 58.8 + - - +
43B TYR* 3.3 34.0 - - + +
46B GLU* 4.2 0.2 - - - +
150B ILE* 3.4 10.8 - - + +
152B HIS* 3.2 59.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.0 12.8 - - + -
20B ASP* 5.0 1.1 - - - -
24B ARG* 3.5 44.4 - - - -
40B TYR* 4.1 4.3 - - + -
41B LEU* 1.3 78.3 - - - +
43B TYR* 1.3 64.3 + - - +
46B GLU* 3.3 21.3 - - + -
47B SER 3.6 17.0 - - - -
48B VAL* 3.8 24.7 - - + -
116B LYS* 3.9 22.4 - - - -
149B LEU* 3.8 38.6 - - + -
150B ILE 2.8 11.1 + - - +
151B VAL* 3.2 27.6 - - + -
152B HIS 3.3 8.3 + - - -
----------------------------------------------------------
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