Contacts of the strand formed by residues 152 - 160 (chain A) in PDB entry 5MJ3
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 152 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.7 29.6 - - + -
146A THR* 3.9 12.3 - - + -
148A ILE* 3.7 32.3 - - + +
149A SER 5.3 1.3 - - - -
150A THR 3.9 11.0 - - - +
151A ASP* 1.3 77.3 - - - +
153A THR* 1.3 64.6 + - - +
154A PHE* 3.7 33.8 - - + -
189A TYR* 3.9 13.8 + - - +
215A VAL 3.5 11.2 - - - +
216A HIS* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ASP 5.2 0.9 - - - -
152A LEU* 1.3 78.0 + - - +
154A PHE* 1.3 75.4 + - - +
213A ASP 3.8 0.3 - - - +
214A ALA* 3.5 4.0 - - - -
215A VAL* 2.9 39.0 + - - +
407A PG4 3.8 37.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.2 3.6 - - + -
117A LEU* 3.8 16.6 - - + -
144A TRP* 3.4 45.8 - + + -
146A THR* 4.7 2.0 - - + -
152A LEU* 3.7 39.0 - - + -
153A THR* 1.3 85.8 - - - +
155A SER* 1.3 62.2 + - - +
156A VAL* 5.2 0.9 - - - -
173A ALA* 4.2 14.8 + - + +
189A TYR* 3.9 31.4 - + - -
212A VAL* 4.2 8.7 - - + -
213A ASP 3.2 13.5 - - - +
214A ALA* 3.7 20.2 - - + -
407A PG4 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A PHE* 1.3 76.2 - - - +
156A VAL* 1.3 67.6 + - - +
157A LYS* 4.3 5.8 + - - +
211A MET 3.7 1.0 - - - +
212A VAL* 3.4 4.0 - - - -
213A ASP* 2.9 42.6 + - - +
407A PG4 3.5 39.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 3.6 30.3 - - + -
155A SER* 1.3 81.8 + - - +
157A LYS* 1.3 72.5 + - - +
170A CYS* 4.0 32.4 - - + +
171A GLY 4.6 5.0 + - - +
173A ALA* 4.2 11.2 - - + +
191A VAL* 4.1 29.6 - - + -
193A CYS* 4.4 0.2 - - - -
210A VAL* 4.2 13.2 - - + -
211A MET 3.4 7.9 - - - +
212A VAL* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER* 5.2 6.1 - - - +
156A VAL* 1.3 78.6 - - - +
158A SER* 1.3 63.7 + - - +
170A CYS* 4.4 5.2 - - - -
210A VAL* 3.6 2.9 - - - +
211A MET* 2.8 49.1 + - + +
213A ASP* 5.9 2.9 - - - +
1D NAG 6.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A PHE* 3.7 3.0 - - - -
157A LYS* 1.3 79.2 - - - +
159A SER* 1.3 64.0 + - - +
168A VAL* 3.4 48.8 + - - +
170A CYS* 3.7 15.6 - - - -
208A ILE* 3.4 14.7 - - - +
209A GLU 2.8 20.0 + - - -
210A VAL* 4.0 7.6 - - - +
211A MET* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 1.3 77.3 + - - +
160A ARG* 1.3 60.1 + - - +
161A GLY 2.9 16.6 + - - -
162A SER* 5.0 0.7 - - - -
165A PRO* 3.6 21.8 - - - +
166A GLN 3.2 13.9 - - - -
167A GLY* 5.5 0.4 - - - -
168A VAL* 3.6 9.4 - - - -
208A ILE* 3.4 4.0 - - - +
209A GLU* 2.8 36.8 + - - +
211A MET* 4.2 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 1.3 70.6 - - - +
161A GLY* 1.3 61.1 + - - +
164A ASP 3.9 0.9 - - - +
165A PRO* 3.5 0.7 - - - +
166A GLN* 2.8 68.4 + - + +
168A VAL* 3.8 2.8 - - + +
195A GLU* 2.7 43.2 + - + +
204A GLU* 2.8 44.8 + - - +
205A SER 6.1 0.2 - - - +
206A LEU* 2.8 46.7 + - + +
207A PRO* 3.6 5.6 - - - +
208A ILE* 3.6 26.9 - - + +
229A ILE* 3.6 10.1 - - - +
----------------------------------------------------------
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