Contacts of the strand formed by residues 266 - 273 (chain D) in PDB entry 1S9C
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 ARG 266 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D VAL* 3.9 26.3 - - - +
263D GLU* 3.0 35.7 + - + +
264D GLY 3.3 0.4 - - - -
265D ASN* 1.3 79.5 - - - +
267D ILE* 1.3 63.9 + - - +
268D HIS* 3.6 32.8 + - + +
285D TYR* 3.2 38.6 + - + -
286D VAL 3.6 3.6 - - - -
287D ASP* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D VAL* 3.9 21.1 - - + -
231D PHE* 3.5 44.4 - - + -
260D MET* 4.1 7.4 - - + -
261D TRP 3.4 6.5 - - - +
262D LYS* 3.5 34.3 - - + -
264D GLY 4.8 3.4 - - - +
265D ASN 5.1 0.4 - - - -
266D ARG* 1.3 76.0 - - - +
268D HIS* 1.3 67.1 + - - +
269D PHE* 3.8 0.3 + - - -
285D TYR* 3.2 3.3 - - - -
286D VAL* 2.9 35.9 + - + +
288D LEU* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D VAL* 3.8 22.7 - - + +
166D ALA 3.6 16.9 + - - -
167D ILE* 4.4 3.3 - - - -
168D PRO* 3.6 25.5 - - + +
260D MET* 3.3 3.3 - - - -
261D TRP* 2.8 39.3 + - + +
263D GLU* 3.6 33.9 - - + +
266D ARG* 3.6 36.3 - - + +
267D ILE* 1.3 73.1 - - - +
269D PHE* 1.3 61.2 + - - +
284D ALA 3.5 13.0 + - - +
285D TYR* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 4.3 4.9 - - - +
220D PHE* 5.2 8.3 - + - -
223D SER* 3.6 27.4 - - - -
224D ALA* 4.9 9.4 - - + -
227D VAL* 4.2 15.5 - - + -
242D VAL* 5.3 2.9 - - + -
243D LYS 4.4 0.4 - - - -
244D ALA* 4.4 9.2 - - + -
258D THR* 4.2 4.0 - - + -
259D GLU 3.0 15.9 - - - +
260D MET* 4.2 10.1 - - + -
261D TRP* 4.1 3.8 - - - -
267D ILE 4.1 4.0 - - - -
268D HIS* 1.3 74.9 - - - +
270D GLN* 1.3 64.4 + - - +
271D THR* 3.8 15.5 - - - -
281D ILE* 4.0 9.6 - - + -
283D ASN 4.4 0.3 + - - -
284D ALA* 3.0 58.7 + - + +
285D TYR* 3.5 28.7 - - - -
286D VAL* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 3.5 34.2 - - + +
257D GLN 3.6 0.7 - - - +
258D THR* 3.5 1.9 - - - +
259D GLU* 2.7 58.1 + - - +
261D TRP* 3.8 10.5 - - + -
269D PHE* 1.3 75.6 - - - +
271D THR* 1.3 62.8 + - - +
272D LYS* 3.8 11.0 - - - +
279D ILE* 3.2 32.3 - - + +
281D ILE 3.5 15.7 - - - +
282D SER* 4.4 8.9 - - - -
283D ASN 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D THR* 4.0 12.1 - - + -
223D SER* 2.8 33.5 + - - +
256D LEU* 4.4 5.8 - - + -
257D GLN 3.3 11.9 - - - +
258D THR* 3.9 4.9 - - - +
269D PHE* 3.8 3.8 - - - -
270D GLN* 1.3 75.7 + - - +
272D LYS* 1.3 64.4 + - - +
279D ILE* 3.6 4.3 - - - +
280D VAL* 2.8 43.5 + - + +
281D ILE* 2.9 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D LEU* 3.4 6.6 - - - +
257D GLN* 2.8 49.9 + - + +
259D GLU* 3.0 40.9 + - - +
270D GLN* 3.8 12.0 - - - +
271D THR* 1.3 80.5 - - - +
273D VAL* 1.3 67.1 + - - +
274D GLN 3.8 0.7 - - - -
277D GLY* 4.0 16.1 + - - +
278D ASP 3.0 14.8 - - - +
279D ILE* 3.9 18.8 - - + -
280D VAL* 4.3 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D PRO 4.5 2.0 - - - +
250D VAL* 3.9 16.4 - - + -
254D GLN* 3.8 33.0 - - + +
255D THR 3.3 4.0 - - - +
256D LEU* 4.5 6.1 - - + -
272D LYS* 1.3 78.0 - - - +
274D GLN* 1.3 49.7 + - - +
275D GLU* 2.7 32.0 + - + +
276D THR* 3.0 16.0 + - - +
277D GLY* 2.7 32.6 + - - -
278D ASP* 3.0 8.6 + - + +
280D VAL* 3.5 26.5 - - + -
----------------------------------------------------------
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