Contacts of the strand formed by residues 276 - 284 (chain D) in PDB entry 6Q0R
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 276 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR* 2.7 26.6 + - - -
267D ARG* 4.2 11.9 + - - +
270D PHE* 3.8 9.0 - - + -
271D GLU* 3.7 46.5 + - + +
274D GLY 3.6 8.5 + - - +
275D ARG* 1.4 76.3 - - - +
277D GLU* 1.4 59.6 + - - +
278D SER 3.4 20.9 - - - +
279D ILE* 3.6 24.9 - - + -
296D ILE* 3.8 19.1 - - + -
297D THR 3.3 20.4 - - - +
298D PHE* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 2.7 26.3 + - - -
159B THR* 4.3 7.3 + - - +
267D ARG* 5.2 0.7 - - - -
275D ARG* 3.4 25.0 + - - -
276D ILE* 1.4 70.9 - - - +
278D SER* 1.4 63.4 + - - +
297D THR* 2.8 19.6 + - + +
298D PHE 4.6 1.8 - - - +
299D SER* 2.7 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 5.4 4.0 - - - -
267D ARG* 5.1 2.7 - - - +
276D ILE* 3.4 4.1 - - - +
277D GLU* 1.4 82.3 - - - +
279D ILE* 1.3 65.7 + - - +
280D GLN* 6.1 2.2 - - - -
295D PHE 3.9 0.8 - - - +
296D ILE* 3.5 0.9 - - - -
297D THR* 2.8 51.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU* 3.4 44.5 - - + +
266D LEU* 4.6 10.5 - - + -
267D ARG* 3.4 61.0 - - + +
276D ILE* 3.6 22.2 - - + -
278D SER* 1.3 79.4 - - - +
280D GLN* 1.3 64.5 + - - +
281D LEU 4.8 2.0 - - - +
295D PHE 3.4 4.7 - - - +
296D ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D ARG* 6.1 2.4 - - - +
263D GLU* 4.2 3.1 - - - -
278D SER* 6.1 2.5 - - - -
279D ILE* 1.3 76.7 - - - +
281D LEU* 1.3 64.2 + - - +
282D MET* 3.7 23.1 + - - +
294D GLY* 3.3 3.3 - - - -
295D PHE* 3.0 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU* 4.4 7.4 - - + -
261D ILE* 3.3 26.5 - - + +
262D THR* 4.0 2.7 - - - -
263D GLU* 3.5 44.8 + - + +
266D LEU* 3.8 22.4 - - + -
279D ILE* 4.8 0.4 - - - +
280D GLN* 1.3 72.1 - - - +
282D MET* 1.3 62.1 + - - +
283D MET* 3.6 25.1 + - + +
290D SER* 3.4 28.3 - - - +
293D TYR 3.4 25.8 - - - +
294D GLY* 4.2 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D GLN* 3.8 28.7 - - - +
281D LEU* 1.3 71.4 - - - +
283D MET* 1.3 53.1 + - - +
290D SER* 3.7 5.7 + - - -
291D LYS* 2.8 45.2 + - + +
293D TYR* 3.1 64.8 + - + +
294D GLY* 4.3 6.1 - - - -
295D PHE* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D THR* 6.1 1.6 - - - -
263D GLU* 5.9 4.5 - - + +
281D LEU* 3.6 36.4 + - + +
282D MET* 1.3 74.3 - - - +
284D ASP* 1.4 63.9 + - - +
285D SER* 3.6 6.1 + - - -
288D GLY 5.3 1.3 - - - -
289D ARG* 3.8 21.1 - - - +
290D SER* 3.8 18.6 - - - +
291D LYS* 3.4 17.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D MET* 1.4 72.0 - - - +
285D SER* 1.4 60.9 + - - +
286D GLU* 3.2 25.3 + - - +
287D THR* 2.9 39.0 - - + +
288D GLY* 2.9 28.9 + - - -
289D ARG 2.9 10.9 + - - +
290D SER 5.3 0.9 - - - +
291D LYS* 3.8 21.1 - - + +
----------------------------------------------------------
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