Contacts of the strand formed by residues 143 - 149 (chain F) in PDB entry 5B6N
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 143 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU* 5.0 0.7 - - + -
5F LEU* 3.8 17.3 - - + +
6F LEU 3.1 33.7 - - - +
7F LEU* 4.1 11.6 - - + +
8F GLY* 3.5 19.2 + - - +
9F ASP* 3.1 19.8 + - + +
135F PHE* 3.6 25.6 - - + -
136F VAL 3.5 11.7 - - - +
137F PHE* 3.5 24.3 - - + -
142F LYS* 1.3 73.1 - - - +
144F LYS* 1.3 66.5 + - - +
145F LEU 3.7 13.2 - - - +
146F SER* 4.5 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150E PRO* 3.6 23.9 - - - +
7F LEU* 3.7 10.0 - - - +
8F GLY* 5.7 1.8 - - - -
33F TRP* 3.6 26.0 - - + -
136F VAL* 2.7 24.0 + - + +
138F GLY* 3.8 12.1 - - - +
140F ASP* 3.1 39.6 + - - -
142F LYS* 3.7 16.7 - - - +
143F LEU* 1.3 77.0 + - - +
145F LEU* 1.3 60.1 - - - +
167F LEU* 4.0 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E LEU 3.3 13.7 - - - +
149E TYR* 3.6 42.6 - - + -
150E PRO* 3.7 18.6 - - + -
153E THR* 4.9 3.4 - - + -
7F LEU* 4.3 3.1 - - - -
134F VAL* 3.9 3.7 - - + +
136F VAL* 3.2 42.6 + - + +
143F LEU* 3.7 11.6 - - - +
144F LYS* 1.3 79.6 - - - +
146F SER* 1.3 61.7 + - - +
147F ILE* 4.0 15.3 - - + -
160F ILE* 5.6 3.6 - - + -
163F VAL* 4.1 30.1 - - + -
167F LEU* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E SER* 5.1 2.9 + - - -
147E ILE 3.3 0.5 - - - -
148E LEU* 2.3 68.3 + - - +
5F LEU 5.3 2.5 - - - -
134F VAL 3.7 7.9 - - - -
135F PHE* 4.7 10.5 - - - -
143F LEU* 4.5 11.2 - - - -
145F LEU* 1.3 75.3 - - - +
147F ILE* 1.3 70.3 + - - +
148F LEU* 4.9 7.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E SER 3.5 6.1 - - - +
147E ILE* 4.0 16.6 - - + -
149E TYR* 4.3 7.9 - - + +
132F ARG 4.7 0.9 - - - +
133F VAL* 3.5 5.4 - - - +
134F VAL* 3.4 53.7 + - + +
135F PHE* 6.1 0.3 - - - -
145F LEU* 4.0 17.7 - - + +
146F SER* 1.3 81.0 - - - +
148F LEU* 1.3 66.7 + - - +
149F TYR* 3.5 36.8 - - + +
155F ARG* 3.9 14.4 - - + -
156F ASN 5.9 0.2 - - - +
160F ILE* 4.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E LEU 5.4 2.7 - - - +
6E LEU* 4.7 4.7 - - - -
7E LEU* 3.6 47.0 - - + +
143E LEU* 5.8 0.9 - - + -
145E LEU* 3.2 11.3 - - - +
146E SER* 2.4 57.2 + - - +
115F GLY 5.7 4.7 - - - +
116F MET* 5.6 5.6 - - + -
117F LEU 5.9 1.3 - - - +
131F ALA* 5.4 1.3 - - + -
132F ARG 3.8 1.3 - - - -
133F VAL* 4.0 25.4 - - + -
135F PHE* 5.7 7.2 - - + -
146F SER* 4.9 7.4 - - - +
147F ILE* 1.3 81.2 - - - +
149F TYR* 1.3 64.3 + - - +
150F PRO* 4.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 149 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E LEU* 4.5 2.5 - - - -
145E LEU* 3.6 17.9 - - + +
147E ILE* 4.3 11.9 - - + +
159E GLU* 2.9 33.8 + - - +
160E ILE* 5.8 1.0 - - - +
162E ARG* 4.1 5.8 - - - -
163E VAL* 3.4 24.9 - - + +
131F ALA* 3.6 4.3 - - - +
132F ARG* 2.6 53.0 + - + +
147F ILE* 3.5 33.5 - - + +
148F LEU* 1.3 82.0 - - - +
150F PRO* 1.3 62.0 - - + +
153F THR* 3.8 22.7 - - + +
155F ARG* 3.8 23.1 - - + -
156F ASN* 4.6 1.7 - - - +
159F GLU* 6.0 0.5 - - - +
----------------------------------------------------------
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