Contacts of the strand formed by residues 253 - 267 (chain C) in PDB entry 5IXM
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 253 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C HIS* 3.1 23.9 - - - -
233C TYR 3.4 3.8 - - - -
234C GLN* 4.2 10.0 + - - -
251C LYS* 4.0 13.0 - - - +
252C ASP* 1.3 81.6 - - - +
254C VAL* 1.3 65.2 + - - +
255C ASN* 5.2 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C THR 3.8 0.9 - - - +
232C HIS* 3.4 7.5 + - - -
233C TYR* 2.8 49.0 + - + -
235C GLN* 4.2 5.8 - - - +
251C LYS* 3.6 30.3 - - + +
253C SER* 1.3 80.3 + - - +
255C ASN* 1.3 75.3 + - - +
256C ARG* 5.2 0.4 - - + -
299C ASP* 3.8 26.7 - - - +
300C ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C THR 3.7 2.8 - - - +
232C HIS* 3.0 33.2 + - - +
253C SER* 5.3 2.6 + - - -
254C VAL* 1.3 80.7 - - - +
256C ARG* 1.3 62.3 + - - +
257C VAL* 4.2 6.1 - - + -
295C ARG* 4.2 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C HIS* 4.8 0.8 + - - -
229C LEU* 3.4 7.7 + - - +
231C THR* 2.9 76.1 + - - +
233C TYR* 4.4 4.5 - - + -
254C VAL* 5.2 0.9 - - + -
255C ASN* 1.3 76.0 - - - +
257C VAL* 1.3 62.3 + - - +
258C LEU* 4.1 23.1 - - + +
295C ARG* 4.5 15.0 - - + +
297C GLN* 2.8 47.1 + - + -
300C ILE* 4.2 16.1 - - + +
324C LEU* 2.4 36.0 + - - +
325C ASP* 3.5 12.5 + - - +
327C ILE* 3.8 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 3.8 28.7 - - + -
229C LEU 3.3 4.7 - - - +
230C ALA* 4.2 15.7 - - + -
231C THR 5.0 0.9 - - - +
255C ASN* 4.2 5.6 - - + -
256C ARG* 1.3 80.3 - - - +
258C LEU* 1.3 69.1 + - - +
259C PRO* 4.1 6.0 - - + +
295C ARG* 5.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 4.2 2.5 - - - -
229C LEU* 2.9 48.6 + - + +
256C ARG* 4.1 22.9 - - + -
257C VAL* 1.3 82.5 - - - +
259C PRO* 1.3 70.0 - - + +
292C VAL* 4.5 8.7 - - + -
293C PRO* 3.6 32.3 - - + +
294C TYR 4.7 0.7 - - - +
295C ARG* 3.6 21.1 - - + +
297C GLN* 4.3 4.9 - - - +
327C ILE* 3.8 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LYS 3.5 7.9 - - - +
228C LEU* 4.0 15.4 - - + -
229C LEU* 5.8 0.2 - - - -
257C VAL* 4.1 6.3 - - + +
258C LEU* 1.3 86.8 - - - +
260C GLN* 1.3 60.6 + - - +
261C PHE 4.3 0.2 - - - -
291C TYR* 4.1 1.4 - - + +
292C VAL* 4.0 3.3 - - - +
293C PRO* 3.1 46.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLU* 3.7 5.5 + - - +
226C ALA* 3.7 4.0 - - - -
227C LYS* 2.9 53.0 + - + +
229C LEU* 4.0 9.6 - - + +
259C PRO* 1.3 75.6 - - - +
261C PHE* 1.3 63.3 + - - +
262C LYS* 3.9 9.9 - - + +
290C LEU* 3.7 16.1 - - + +
291C TYR 3.5 3.6 - - - -
292C VAL* 3.7 14.6 - - + -
318C ASP* 2.9 35.0 + - - +
319C ARG* 2.6 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C THR* 3.8 24.2 - - + -
225C GLU 3.7 7.6 - - - -
226C ALA* 5.1 3.4 - - + +
260C GLN* 1.3 73.9 - - - +
262C LYS* 1.3 67.6 + - - +
263C VAL* 4.1 22.2 - - + -
289C TYR* 4.0 31.4 - + - -
290C LEU* 3.6 2.9 - - - +
291C TYR* 2.9 48.5 + - + +
603C C8E 5.3 2.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
223C ASN* 3.8 3.1 - - - +
224C THR* 3.7 2.3 - - - +
225C GLU* 2.8 70.4 + - + +
260C GLN* 3.9 9.6 - - + +
261C PHE* 1.3 79.8 - - - +
263C VAL* 1.3 64.9 + - - +
264C ASP* 4.7 7.6 - - + +
288C GLN* 3.6 32.2 - - + +
289C TYR 3.4 10.8 - - - +
290C LEU* 4.0 8.5 - - + -
316C PHE 5.0 3.4 + - - -
318C ASP* 3.6 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ILE* 4.3 13.2 - - + -
223C ASN 3.5 7.9 - - - +
224C THR* 4.3 13.2 - - + +
261C PHE* 4.1 21.3 - - + -
262C LYS* 1.3 75.5 - - - +
264C ASP* 1.3 63.3 + - - +
265C GLY 4.3 0.2 - - - -
288C GLN* 3.2 4.6 - - - -
289C TYR* 2.9 56.0 + - + +
603C C8E 4.1 11.2 - - - +
607C C8E 3.9 25.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C SER 4.1 0.5 - - - +
222C ILE* 3.4 4.8 - - - -
223C ASN* 2.9 47.6 + - + +
262C LYS* 4.7 7.0 - - + -
263C VAL* 1.3 75.9 - - - +
265C GLY* 1.3 65.8 + - - +
266C LYS* 5.5 0.2 - - - +
286C ARG* 3.0 35.8 + - - +
287C ALA 3.1 11.0 - - - +
288C GLN* 2.9 34.0 + - - +
607C C8E 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C SER 3.4 7.2 - - - -
222C ILE* 4.1 6.5 - - - -
264C ASP* 1.3 76.3 + - - +
266C LYS* 1.3 61.6 + - - +
286C ARG* 3.4 4.5 - - - +
287C ALA 2.9 36.1 + - - +
601C C8E 3.8 11.0 - - - +
607C C8E 3.7 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C GLY* 3.3 1.1 - - - -
221C SER* 2.9 43.9 + - - +
264C ASP* 5.5 0.2 - - - +
265C GLY* 1.3 74.2 - - - +
267C VAL* 1.3 74.4 + - - +
268C VAL* 4.2 15.0 - - + +
284C GLU* 3.8 27.3 + - + -
285C PRO 3.5 13.0 - - - +
286C ARG* 4.3 22.2 - - + +
340C ARG* 5.5 4.6 - - - +
601C C8E 3.9 3.0 - - - +
133D GLN* 5.3 6.1 + - - -
137D ARG* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C TRP* 3.7 26.9 - - + +
220C GLY* 4.3 0.2 - - - -
266C LYS* 1.3 81.0 - - - +
268C VAL* 1.3 68.7 + - - +
269C PHE* 3.8 30.5 - - + -
284C GLU* 3.3 7.4 - - - +
285C PRO* 3.0 39.2 + - + +
601C C8E 3.6 39.2 - - + +
605C C8E 4.4 9.6 - - - +
7D THR* 4.4 5.8 - - + -
----------------------------------------------------------
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