Contacts of the helix formed by residues 257 - 266 (chain F) in PDB entry 6ACQ
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 HIS 257 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLU* 3.8 20.1 + - - -
196F ASN* 2.9 25.1 + - - +
199F VAL* 3.6 19.1 - - + -
200F GLY* 3.2 31.9 + - - -
203F ALA* 3.5 25.4 - - + +
204F GLU* 5.7 2.8 + - - +
255F ARG* 3.7 1.9 + - - -
256F PRO* 1.3 74.7 - - - +
258F THR* 1.3 79.9 + - + +
259F LEU* 3.0 16.7 + - + +
260F LEU* 2.9 20.9 + - + +
261F LYS* 3.2 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU 5.8 1.3 - - - +
182B ALA* 5.2 7.9 - - + -
183B PRO* 4.1 27.7 - - + +
248B GLU* 3.9 15.9 + - - +
249B THR* 4.4 9.7 + - - +
204C GLU* 4.4 10.1 - - - +
206C ILE* 6.3 1.1 - - + -
256F PRO 3.4 3.5 + - - -
257F HIS* 1.3 85.9 + - + +
259F LEU* 1.3 66.0 + - + +
261F LYS* 3.4 14.4 - - - +
262F LYS* 3.3 20.7 + - - +
265F ARG* 5.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 4.2 2.5 - - + -
199F VAL* 4.2 13.0 - - + +
202F LEU* 4.3 14.1 - - + -
203F ALA* 3.9 28.3 - - + +
257F HIS* 3.0 19.0 + - + +
258F THR* 1.3 79.3 - - + +
260F LEU* 1.3 64.9 + - - +
262F LYS* 3.3 28.4 + - - +
263F TYR* 3.1 49.1 + - + +
277F PHE* 5.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F ILE* 6.0 3.8 - - + -
196F ASN* 4.1 17.0 - - + +
199F VAL* 4.0 23.2 - - + +
235F LEU* 4.1 42.4 - - + +
238F CYS* 4.5 8.7 - - + +
239F LEU* 3.9 37.9 - - + +
242F MET* 4.8 4.0 - - + -
256F PRO* 4.8 3.6 - - + -
257F HIS 2.9 12.3 + - - +
259F LEU* 1.3 74.1 - - - +
261F LYS* 1.3 67.7 + - - +
262F LYS 3.1 0.3 + - - -
263F TYR* 3.2 6.3 + - - +
264F VAL* 3.1 26.9 + - + +
277F PHE* 4.6 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER 3.5 14.3 + - - -
248B GLU* 3.0 42.9 + - - +
249B THR 5.3 0.4 - - - -
250B GLY* 5.3 1.4 - - - +
239F LEU* 3.9 27.3 - - + +
243F ASP* 5.1 3.7 + - - -
256F PRO* 4.0 32.9 - - - +
257F HIS 3.2 6.2 + - - +
258F THR* 3.4 12.8 - - - +
260F LEU* 1.3 78.8 - - - +
262F LYS* 1.3 57.1 - - - +
264F VAL* 3.5 1.6 + - - +
265F ARG* 3.0 51.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 262 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B THR* 3.7 24.5 - - + +
153B ARG 5.1 0.4 + - - -
155B ILE* 3.8 28.0 - - + +
180B ALA* 4.4 9.7 - - - +
181B GLU* 3.0 49.8 + - + +
206C ILE* 6.0 0.8 - - - +
258F THR* 3.3 11.9 + - - +
259F LEU* 3.7 29.4 - - - +
260F LEU 3.1 1.0 - - - -
261F LYS* 1.3 77.9 - - - +
263F TYR* 1.3 65.4 + - - +
265F ARG* 3.4 12.4 + - - +
266F ALA* 3.1 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 263 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ILE* 3.8 21.7 - - + +
202F LEU* 4.6 6.1 - - - +
235F LEU* 3.9 17.7 - - + -
259F LEU* 3.1 42.6 + - + +
260F LEU* 3.7 7.0 - - - +
262F LYS* 1.3 74.6 - - - +
264F VAL* 1.3 63.5 + - - +
266F ALA* 3.0 13.6 + - - +
268F TRP* 3.1 52.2 + + + +
276F GLY 3.4 33.6 + - - -
277F PHE* 3.5 37.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F LEU* 3.7 38.4 - - + +
236F ASP* 3.9 20.2 - - + +
239F LEU* 4.0 26.5 - - + -
260F LEU* 3.1 17.1 + - + +
261F LYS 3.8 3.6 - - - +
263F TYR* 1.3 74.1 - - - +
265F ARG* 1.3 61.9 + - + +
267F GLY* 2.8 21.8 + - - -
269F LEU* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.6 29.0 + - - -
122B THR* 3.7 7.7 - - + +
123B GLU* 3.2 46.8 + - + +
126B SER* 2.7 23.7 + - - -
181B GLU* 4.4 5.1 + - - -
248B GLU* 2.9 42.0 + - - -
258F THR 5.6 0.4 + - - -
261F LYS* 3.0 41.2 + - - +
262F LYS* 3.6 9.7 - - - +
263F TYR 3.3 0.2 - - - -
264F VAL* 1.3 78.2 - - + +
266F ALA* 1.3 57.0 + - - +
267F GLY 3.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B THR* 3.6 7.8 - - + +
126B SER* 3.2 13.7 + - - -
155B ILE* 3.4 32.8 - - + -
156B ALA* 5.6 2.0 - - + -
262F LYS 3.1 5.6 + - - +
263F TYR 3.0 13.9 + - - +
265F ARG* 1.3 77.6 - - - +
267F GLY* 1.3 58.6 + - - +
268F TRP* 3.6 26.3 + - + +
----------------------------------------------------------
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