Contacts of the strand formed by residues 159 - 167 (chain D) in PDB entry 6QPA
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 THR 159 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D THR* 5.7 1.1 - - - +
158D ARG* 1.3 78.2 + - - +
160D VAL* 1.3 73.2 + - - +
161D VAL* 4.2 1.3 - - + -
257D ILE 3.9 0.2 - - - +
258D GLU* 3.3 4.7 - - - +
259D TRP* 2.8 33.6 + - - +
260D GLU 4.4 0.2 + - - -
261D SER* 3.4 12.5 - - - -
262D PRO* 3.2 31.5 - - + +
265D ALA* 4.1 22.4 - - + -
298D PHE* 4.2 18.4 - - + -
299D PHE 3.7 10.3 + - - +
300D SER* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLU* 6.1 0.7 - - - +
48D LEU* 4.1 34.8 - - + -
158D ARG* 4.8 5.6 - - - +
159D THR* 1.3 78.3 - - - +
161D VAL* 1.3 68.5 + - - +
162D ILE* 4.4 3.4 - - + -
256D HIS* 3.4 32.3 - - + +
257D ILE 3.6 2.9 - - - +
258D GLU* 4.1 21.8 - - + +
298D PHE* 3.7 0.9 - - - -
299D PHE* 2.7 45.4 + - + +
301D PRO* 4.4 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D THR* 4.2 1.8 - - + -
160D VAL* 1.3 78.0 - - - +
162D ILE* 1.3 62.2 + - - +
255D VAL 3.5 0.3 - - - +
256D HIS* 3.5 3.6 - - - -
257D ILE* 2.7 44.0 + - + +
259D TRP* 4.1 6.1 - - + +
265D ALA* 3.8 22.0 - - + -
269D LEU* 3.8 12.6 - - + -
296D TYR* 3.2 36.3 - - + -
297D MET 3.4 4.7 - - - +
298D PHE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 4.0 8.1 - - + -
77D PHE* 3.7 24.9 - - + -
79D TYR* 3.5 25.4 - - + +
160D VAL* 4.4 5.8 - - + -
161D VAL* 1.3 78.2 - - - +
163D GLY* 1.3 61.1 - - - +
164D ASP* 3.8 1.1 + - + +
199D MET* 5.2 0.9 - - + -
254D LEU* 3.9 39.9 - - + -
255D VAL 3.3 5.6 - - - +
256D HIS* 4.8 2.2 - - - +
295D TYR 3.3 3.6 - - - +
296D TYR* 3.4 2.9 - - - -
297D MET* 3.0 34.0 + - + +
299D PHE* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 1.3 71.2 - - - +
164D ASP* 1.3 60.8 + - - -
165D HIS* 3.0 13.7 + - - -
254D LEU* 3.3 7.2 - - - -
255D VAL 2.7 38.2 + - - -
295D TYR 3.4 2.5 - - - -
296D TYR* 3.3 31.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 3.8 1.7 + - + +
163D GLY* 1.3 71.5 - - - -
165D HIS* 1.3 61.9 + - - +
166D TRP* 3.6 18.8 + - - -
252D GLN* 3.0 33.8 + - - +
253D TYR 3.9 1.8 - - - -
254D LEU* 3.9 8.2 - - + +
292D LYS* 4.2 0.6 - - - +
293D GLY* 3.7 5.5 - - - -
294D PRO* 3.4 8.3 - - - +
295D TYR* 2.8 45.1 + - + +
297D MET* 6.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D GLY* 3.0 32.4 + - - -
164D ASP* 1.3 72.7 + - - +
166D TRP* 1.3 64.3 + - - +
167D VAL* 4.1 1.5 + - + -
175D PHE* 3.8 28.5 - + + -
251D THR 3.8 0.2 - - - +
252D GLN* 3.4 3.6 - - - -
253D TYR* 2.8 44.0 + - + +
255D VAL* 3.4 27.6 - - + +
282D HIS* 5.2 1.4 + - - -
286D VAL* 3.9 11.4 - - + +
290D LEU* 3.9 26.0 - - + -
292D LYS 3.6 4.9 - - - -
294D PRO* 3.5 26.7 - - + +
296D TYR* 3.8 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D ASP* 3.6 20.9 + - - -
165D HIS* 1.3 80.5 - - - +
167D VAL* 1.3 56.7 + - - +
248D GLN* 3.5 33.5 + - - +
249D THR 5.6 0.2 - - - -
250D PRO* 4.1 29.6 - - + -
251D THR 3.5 4.0 - - - +
252D GLN* 4.2 12.7 - - + +
290D LEU* 3.3 6.3 - - - +
291D ASP* 2.7 31.7 + - + -
292D LYS* 3.0 64.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D HIS* 4.7 2.7 - - + -
166D TRP* 1.3 75.7 - - - +
168D MET* 1.3 76.8 + - - +
169D ASP* 3.4 1.0 + - - -
171D HIS 3.7 25.1 - - - +
172D GLU* 3.8 14.7 - - + +
175D PHE* 3.6 29.4 - - + -
250D PRO* 3.3 18.0 - - - +
251D THR* 2.9 18.8 + - - +
253D TYR* 3.4 30.3 - - + -
289D HIS 3.5 8.7 - - - +
290D LEU* 4.1 5.6 - - + -
291D ASP* 4.2 1.6 - - - -
----------------------------------------------------------
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