Contacts of the strand formed by residues 249 - 256 (chain D) 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 GLU 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ARG* 3.0 23.0 + - - -
159D ASN* 3.6 14.3 + - + +
161D PHE* 2.7 49.0 + - + +
162D TRP* 3.4 6.9 + - - -
247D ASN 3.8 1.0 - - - -
248D LEU* 1.3 91.7 - - + +
250D GLY* 1.3 59.8 + - - +
251D SER* 2.9 22.8 + - - +
262D ARG* 2.9 33.4 + - - +
265D GLY 3.4 12.8 - - - +
266D VAL* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D ASN 3.0 7.2 - - - -
160D VAL* 4.4 2.0 - - - -
162D TRP* 4.4 2.9 - - - -
192D TYR* 4.1 20.2 - - - -
249D GLU* 1.3 73.7 - - - +
251D SER* 1.3 58.4 + - - +
264D GLY 3.9 0.9 - - - +
265D GLY 3.1 11.6 + - - +
266D VAL 3.5 12.4 + - - -
268D VAL* 2.9 29.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D THR 5.1 1.2 + - - -
158D VAL* 3.2 11.0 - - - +
159D ASN* 2.8 37.9 + - - +
192D TYR* 4.6 1.3 - - - -
249D GLU* 2.9 30.8 + - - -
250D GLY* 1.3 74.4 - - - +
252D ILE* 1.3 64.8 + - - +
253D THR* 5.0 1.9 + - - -
262D ARG* 3.8 14.7 + - - -
263D VAL 3.2 14.1 - - - -
264D GLY* 3.9 9.2 - - - -
268D VAL* 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 4.7 7.2 - - + -
141D VAL* 6.1 0.9 - - + -
156D VAL* 4.4 7.2 - - + -
157D THR 3.4 2.9 - - - -
158D VAL* 3.7 23.3 - - + -
195D LEU* 4.2 22.7 - - + +
196D LEU* 5.6 0.9 - - + -
199D LEU* 3.8 27.8 - - + -
200D VAL* 5.0 1.8 - - + -
251D SER* 1.3 75.0 - - - +
253D THR* 1.3 64.9 + - - +
254D ILE* 4.0 22.0 - - + -
261D VAL* 4.1 0.7 - - - +
262D ARG* 3.4 1.3 - - - +
263D VAL* 2.7 57.4 + - + +
268D VAL* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ASN* 5.7 1.4 + - - -
161C PHE* 4.1 23.9 - - + -
248C LEU* 4.9 5.6 - - + -
249C GLU* 5.5 0.7 - - - +
155D MET* 6.3 0.4 - - + -
156D VAL* 3.5 5.4 - - - +
157D THR* 3.0 44.6 + - - +
251D SER* 5.0 1.6 + - - -
252D ILE* 1.3 73.2 + - - +
254D ILE* 1.3 65.0 + - - +
255D LEU* 4.0 21.8 - - + -
261D VAL 3.3 10.5 - - - +
262D ARG* 3.3 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D VAL* 4.1 25.6 - - + -
145D ILE* 4.2 8.7 - - + -
150D PHE* 3.7 24.5 - - + -
153D ILE* 4.1 31.2 - - + -
155D MET 3.7 4.0 - - - +
156D VAL* 4.3 8.7 - - + +
199D LEU* 4.3 1.8 - - + -
200D VAL* 4.0 20.6 - - + -
252D ILE* 4.0 23.3 - - + -
253D THR* 1.3 78.1 - - - +
255D LEU* 1.3 64.4 + - - +
260D THR* 3.6 1.9 - - - -
261D VAL* 2.8 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C PHE* 3.7 40.8 - - + -
240C THR* 4.0 18.8 - - + -
243C THR* 4.3 13.9 - - + +
248C LEU* 4.3 6.1 - - + -
153D ILE* 3.9 1.3 - - - +
154D TYR* 2.9 27.0 + - + +
155D MET* 2.8 31.0 + - + +
253D THR* 4.0 15.5 - - + -
254D ILE* 1.3 83.7 - - - +
256D GLY* 1.3 58.9 + - - +
259D GLY 3.9 2.2 - - - +
260D THR* 3.5 31.9 - - + +
261D VAL 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU 4.4 2.9 - - - +
244C TYR* 3.7 9.2 + - - +
150D PHE* 4.0 11.7 - - - -
152D ARG 3.1 13.0 - - - -
153D ILE* 3.9 5.8 - - - -
154D TYR* 3.5 9.9 - - - -
254D ILE 4.3 0.2 + - - -
255D LEU* 1.3 72.8 - - - +
257D GLU* 1.3 68.0 + - - +
258D LYS 3.1 3.1 + - - -
259D GLY 2.9 20.6 + - - +
----------------------------------------------------------
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