Contacts of the strand formed by residues 241 - 249 (chain O) in PDB entry 3K9Q
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 SER 241 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177O ILE 3.3 12.3 - - - -
178O HIS* 3.3 9.1 + - - -
179O ALA 3.0 18.0 + - - -
240O GLY* 1.3 67.5 - - - -
242O LEU* 1.3 59.0 + - - +
280O SER* 5.0 0.4 - - - -
283O VAL* 4.7 1.8 - - - +
313O TRP* 3.3 11.9 - - - -
314O TYR* 2.8 64.8 + - - -
316O ASN* 2.8 23.5 + - - -
206P ILE* 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175O THR 4.0 0.2 - - - +
176O THR* 2.9 5.4 + - - -
177O ILE* 2.8 43.5 + - + +
241O SER* 1.3 74.5 - - - +
243O THR* 1.3 62.1 + - - +
244O GLU* 4.0 7.9 - - + +
296O GLN* 3.8 17.9 - - - +
311O ALA* 4.0 11.7 - - + -
312O ALA 3.6 20.0 - - - +
313O TRP* 3.4 44.4 - - + +
314O TYR* 4.0 0.2 - - - -
206P ILE* 4.8 4.0 - - + -
233P GLN* 3.3 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152O THR* 3.9 2.4 - - - +
155O SER* 2.7 29.1 + - - +
156O LEU* 4.5 17.5 - - + -
174O MET* 3.9 29.6 - - + -
175O THR 3.7 2.7 - - - -
176O THR* 3.7 8.3 + - - -
242O LEU* 1.3 69.4 - - - +
244O GLU* 1.3 64.8 + - - +
245O LEU* 4.9 2.8 - - + +
310O VAL 3.7 0.2 - - - +
311O ALA* 3.0 6.7 - - - -
312O ALA* 2.8 37.3 + - + -
314O TYR* 3.2 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174O MET* 3.2 5.5 - - - +
175O THR* 2.7 50.1 + - - +
177O ILE* 4.0 18.0 - - + +
242O LEU* 4.0 3.8 - - + -
243O THR* 1.3 75.6 - - - +
245O LEU* 1.3 59.9 + - - +
246O THR* 5.3 1.3 - - - +
296O GLN* 4.1 4.7 + - - -
309O LYS* 4.0 18.1 - - + +
310O VAL 3.4 6.5 - - - +
311O ALA* 4.3 10.5 - - + -
175P THR* 2.6 39.7 + - - +
233P GLN* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156O LEU* 3.8 31.2 - - + -
159O VAL* 4.3 10.3 - - + -
160O ALA* 4.7 8.7 - - + -
163O LEU* 3.7 27.1 - - + -
169O LEU* 6.1 0.2 - - + -
173O LEU 3.5 18.8 - - - +
174O MET* 4.1 8.7 - - + -
228O LEU* 3.9 26.2 - - + -
243O THR* 4.1 3.6 - - + +
244O GLU* 1.3 75.3 - - - +
246O THR* 1.3 60.5 + - - +
247O VAL* 3.6 13.2 - - + +
308O VAL 3.6 1.4 - - - +
309O LYS* 3.2 4.9 - - - +
310O VAL* 3.0 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172O GLY* 3.1 1.7 - - - -
173O LEU 2.8 38.3 + - - -
244O GLU* 5.3 1.4 - - - +
245O LEU* 1.3 74.0 + - - +
247O VAL* 1.3 62.2 + - - +
307O LEU* 4.4 15.5 - - + -
308O VAL 3.3 4.5 - - - +
309O LYS* 3.8 20.8 - - + +
173P LEU* 4.1 28.0 - - + +
246P THR* 4.1 33.8 + - + -
307P LEU* 3.9 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163O LEU* 4.1 13.9 - - + -
169O LEU* 3.8 20.4 - - + -
171O GLU 3.4 6.7 - - - +
172O GLY* 3.9 6.5 - - - -
228O LEU* 4.6 0.4 - - + -
245O LEU* 3.6 32.3 - - + +
246O THR* 1.3 81.0 - - - +
248O VAL* 1.3 62.9 + - - +
249O LEU* 3.7 22.8 + - + -
306O GLN 4.2 0.3 - - - +
307O LEU* 3.5 9.1 - - - -
308O VAL* 2.8 55.1 + - + +
310O VAL* 6.3 0.2 - - + -
307P LEU* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169O LEU* 4.0 0.7 - - - +
170O VAL* 2.8 38.4 + - + +
171O GLU* 2.7 32.9 + - + +
247O VAL* 1.3 72.5 - - - +
249O LEU* 1.3 69.8 + - - +
306O GLN 4.5 9.6 - - - +
307O LEU* 3.6 26.0 - - + -
248P VAL* 4.9 4.3 - - + -
305P ARG* 3.4 31.6 - - - +
307P LEU* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163O LEU* 4.3 14.4 - - + +
167O PHE* 3.7 37.5 - - + +
168O GLY 3.2 11.4 - - - +
169O LEU* 4.2 12.1 - - + -
170O VAL* 3.6 8.0 - - - +
247O VAL* 3.7 22.9 + - + -
248O VAL* 1.3 84.5 - - - +
250O GLU* 1.3 62.9 + - - +
251O LYS 3.5 10.4 - - - +
252O GLN* 3.7 10.0 - - - +
254O VAL* 4.4 10.8 - - + -
259O VAL* 5.3 0.2 - - + -
306O GLN 5.0 3.2 + - - -
308O VAL* 3.7 34.3 - - + +
305P ARG* 4.9 3.3 + - - -
----------------------------------------------------------
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