Contacts of the strand formed by residues 153 - 161 (chain P) in PDB entry 3Q2K
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 ILE 153 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213O LEU* 4.5 1.2 - - - +
145P ILE* 4.3 33.2 - - + -
150P PHE* 3.9 22.7 - - + -
151P GLY 3.5 4.2 + - - +
152P ARG* 1.3 86.2 + - - +
154P TYR* 1.3 69.5 + - - +
156P VAL* 4.1 24.2 - - + -
200P VAL* 4.6 20.6 - - + +
231P HIS* 4.4 16.2 + - + +
233P ALA* 3.7 20.9 + - + +
254P ILE* 4.1 12.3 - - + -
255P LEU 3.9 7.9 - - - +
256P GLY* 4.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 154 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213O LEU* 3.7 37.6 + - + +
214O ALA* 3.8 13.5 - - - +
222O THR* 3.7 12.1 - - - +
240O THR* 4.6 10.5 - - + +
242O LEU* 3.5 42.8 - - + -
152P ARG* 4.0 19.8 - - + +
153P ILE* 1.3 82.7 - - - +
155P MET* 1.3 67.6 - - + +
233P ALA* 3.7 6.1 - - - -
234P MET 3.3 19.2 + - - +
255P LEU* 2.9 10.8 + - + +
256P GLY* 3.7 6.1 - - - -
257P GLU* 3.0 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161O PHE* 3.7 23.6 - - + -
222O THR* 3.6 12.6 - - + -
223O GLY 3.2 26.5 - - - +
224O VAL* 3.7 13.2 - - + -
238O ASN* 3.9 18.4 - - - -
239O VAL 3.4 22.7 - - - +
240O THR* 4.2 15.5 - - + -
153P ILE* 4.3 0.6 - - - +
154P TYR* 1.3 81.6 - - + +
156P VAL* 1.3 79.5 + - - +
157P THR* 4.7 0.2 - - - +
234P MET 3.4 9.0 - - - +
253P THR* 3.8 1.2 - - + +
254P ILE* 3.6 0.5 - - - -
255P LEU* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P ILE* 4.1 16.8 - - + -
155P MET* 1.3 84.1 - - - +
157P THR* 1.3 64.6 + - - +
158P VAL* 4.6 6.7 - - + -
196P LEU* 4.7 3.1 - - + -
200P VAL* 4.1 25.8 - - + -
229P TRP* 3.7 37.4 - - + -
233P ALA* 4.7 1.1 - - + -
234P MET 3.3 4.9 + - - +
235P GLY* 2.9 25.6 - - - -
236P SER 3.0 5.5 + - - +
252P ILE* 4.5 12.6 - - + -
253P THR 3.2 10.1 - - - +
254P ILE* 4.5 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157O THR* 5.5 0.7 - - + -
159O ASN* 4.1 9.6 - - - +
161O PHE* 3.2 28.7 - - - -
238O ASN* 3.9 18.7 - - - +
155P MET* 4.7 0.7 - - - +
156P VAL* 1.3 74.1 + - - +
158P VAL* 1.3 65.3 + - - +
159P ASN* 4.2 14.4 + - - +
236P SER* 3.4 22.7 - - - +
238P ASN* 4.0 9.2 - - - +
251P SER* 3.7 1.9 + - - +
252P ILE* 3.3 2.3 - - - -
253P THR* 2.7 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156P VAL* 4.6 2.9 - - + -
157P THR* 1.3 77.4 - - - +
159P ASN* 1.3 63.0 + - - +
160P VAL* 4.3 3.1 - - + -
192P TYR* 3.9 29.4 - - + +
195P LEU* 5.3 1.3 - - + -
196P LEU* 3.8 21.3 - - + -
236P SER 3.0 6.3 + - - +
237P ILE* 3.3 30.1 - - + -
238P ASN* 3.0 31.1 + - - -
251P SER 3.0 9.9 - - - +
252P ILE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 159 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157O THR* 3.9 11.2 + - - +
159O ASN* 5.2 5.3 - - - +
262O ARG* 6.0 1.8 - - - +
157P THR* 4.2 12.9 + - - +
158P VAL* 1.3 73.3 - - - +
160P VAL* 1.3 67.2 + - - +
161P PHE* 3.6 30.1 - - + -
238P ASN* 3.1 33.2 + - - +
249P GLU* 3.9 15.5 + - - -
250P GLY* 3.2 4.3 - - - -
251P SER* 2.8 47.3 + - - +
262P ARG* 5.6 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158P VAL* 4.4 3.8 - - + -
159P ASN* 1.3 78.5 - - - +
161P PHE* 1.3 60.2 + - - +
162P TRP* 3.6 43.7 - - + -
189P ALA* 4.1 22.4 - - + -
192P TYR* 3.4 40.6 - - + -
237P ILE* 5.3 0.4 - - + -
238P ASN 2.9 8.0 + - - +
239P VAL* 3.2 11.8 - - + +
240P THR 2.9 27.5 + - - +
241P MET* 4.1 5.6 - - + -
249P GLU 3.5 2.2 - - - -
250P GLY* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155O MET* 3.8 24.7 - - + -
157O THR* 4.3 15.0 - - + -
253O THR* 3.9 20.9 - - + -
255O LEU* 3.5 18.6 - - + -
159P ASN* 3.6 27.1 - - + -
160P VAL* 1.3 79.0 - - - +
162P TRP* 1.3 58.0 + - - +
238P ASN* 3.6 19.5 - - + -
240P THR 3.7 4.7 - - - -
243P THR* 3.2 17.5 + - - +
248P LEU* 2.9 44.0 + - + -
249P GLU* 2.7 40.8 + - + +
----------------------------------------------------------
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