Contacts of the strand formed by residues 255 - 263 (chain C) 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 THR 255 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C THR* 4.3 13.0 - - + -
178C ASP 3.3 16.6 - - - +
179C THR* 4.0 18.3 + - - +
253C GLY 4.5 1.2 + - - -
254C GLN* 1.3 75.4 + - - +
256C LEU* 1.3 70.9 + - - +
273C VAL* 3.3 5.9 - - - -
274C GLN* 2.9 50.1 + - + +
275C GLU* 2.7 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C THR* 3.2 8.5 - - - -
178C ASP* 2.7 39.2 + - + +
180C THR* 3.9 16.6 - - - +
214C LEU* 5.3 1.8 - - + -
219C THR* 3.8 31.2 - - + -
222C PHE* 3.7 43.5 - - + -
223C SER* 5.5 0.2 - - - +
250C VAL* 3.9 28.3 - - + -
254C GLN 5.5 0.2 - - - +
255C THR* 1.3 79.0 - - - +
257C GLN* 1.3 59.8 + - - +
258C THR* 4.1 4.0 - - - +
271C THR* 4.4 7.9 - - + -
272C LYS 3.4 9.4 - - - +
273C VAL* 4.4 2.9 - - + -
280C VAL* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 4.1 15.3 - - + -
176C LEU 3.8 2.7 - - - -
177C THR* 3.9 21.2 - - + +
256C LEU* 1.3 74.4 - - - +
258C THR* 1.3 61.2 + - - +
259C GLU* 3.7 9.4 + - + +
271C THR* 3.2 4.7 - - - +
272C LYS* 2.8 62.8 + - + +
274C GLN* 2.8 45.1 - - - +
277C GLY* 5.7 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C VAL* 3.2 21.5 - - - -
176C LEU 2.9 19.6 + - - -
178C ASP* 5.0 2.4 + - - -
222C PHE* 5.0 0.7 - - - +
223C SER* 2.8 50.1 + - - +
226C ARG* 4.6 8.2 - - - +
227C VAL* 4.9 0.2 - - + -
256C LEU* 5.1 3.6 - - - +
257C GLN* 1.3 72.9 + - - +
259C GLU* 1.3 59.5 + - - +
260C MET* 3.8 26.2 + - + +
269C PHE* 4.1 10.3 - - + -
270C GLN 3.5 7.0 - - - +
271C THR* 4.0 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PRO* 4.1 16.1 - - + +
174C ALA 3.7 4.7 - - - -
175C VAL* 4.0 15.3 - - + +
257C GLN* 4.3 12.2 - - + +
258C THR* 1.3 74.3 - - - +
260C MET* 1.3 59.8 + - - +
261C TRP* 3.3 19.7 - - + -
269C PHE* 3.0 7.8 - - - +
270C GLN* 2.7 67.0 + - + +
272C LYS* 3.0 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C PRO* 3.6 0.9 - - - +
173C ASP* 2.7 33.5 + - - +
174C ALA 2.7 22.7 + - - +
176C LEU* 3.4 41.7 - - + +
226C ARG* 4.3 9.9 - - + -
227C VAL* 3.8 29.2 - - + -
230C GLN* 4.2 6.7 - - + -
231C PHE* 3.6 31.4 - - + -
258C THR* 3.8 22.2 - - + +
259C GLU* 1.3 78.1 - - - +
261C TRP* 1.3 58.7 + - - +
262C LYS 4.2 0.2 - - - -
267C ILE* 4.1 2.7 - - + -
268C HIS 3.2 6.3 - - - +
269C PHE* 4.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ILE* 3.5 32.1 - - + -
168C PRO* 3.7 43.7 + - + -
170C ARG* 2.7 45.3 + - - +
171C PRO 3.9 0.2 - - - -
172C PRO* 3.4 31.6 - - + +
173C ASP* 3.5 4.5 - - - -
259C GLU* 3.3 43.1 - - + -
260C MET* 1.3 77.2 - - - +
262C LYS* 1.3 61.0 + - - +
263C GLU 3.6 1.2 + - - -
267C ILE* 3.4 5.1 - - - -
268C HIS* 2.8 54.0 + - + +
269C PHE* 4.1 1.3 - - - -
270C GLN* 3.8 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ARG* 3.4 14.7 + - - -
173C ASP* 2.7 16.7 + - - +
231C PHE* 3.7 32.3 - - + -
260C MET 4.2 0.2 - - - -
261C TRP* 1.3 71.7 - - - +
263C GLU* 1.3 64.0 + - - +
264C GLY* 3.0 27.4 + - - +
265C ASN* 5.9 0.9 - - - +
267C ILE* 3.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C PRO* 3.9 15.4 - - + +
170C ARG* 2.8 38.0 + - - +
261C TRP 4.6 0.2 - - - +
262C LYS* 1.3 72.3 - - - +
264C GLY* 1.3 64.7 + - - +
265C ASN 3.3 0.5 + - - -
266C ARG* 3.0 28.3 + - - +
268C HIS* 3.6 28.7 - - + +
----------------------------------------------------------
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