Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 4QGC
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 LYS 247 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA* 5.6 0.4 - - - +
245A ILE* 3.5 9.2 - - - +
246A ARG* 1.3 88.3 - - - +
248A ALA* 1.3 65.4 + - - +
249A SER* 3.2 25.4 - - - +
250A ASP* 2.9 39.9 + - - +
251A VAL 3.7 0.7 + - - -
253A GLU* 6.0 0.4 - - - -
275A GLU* 4.7 5.1 + - - +
279A ARG* 3.6 27.1 - - - +
282A GLU* 3.5 14.1 - - - +
283A ILE* 3.7 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LYS* 1.3 74.6 - - - +
249A SER* 1.3 58.3 + - - +
251A VAL* 2.9 26.6 + - - +
252A HIS* 3.0 26.3 + - + -
282A GLU* 3.0 49.5 + - + +
283A ILE* 4.6 0.2 - - - +
285A GLU* 6.1 0.4 - - - +
286A ALA* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LYS* 3.2 32.3 - - - +
248A ALA* 1.3 78.6 - - - +
250A ASP* 1.3 61.2 + - - +
252A HIS* 3.7 14.0 + - - +
253A GLU* 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA* 3.4 28.8 - - + +
221A VAL* 4.4 1.6 - - - +
244A PHE 4.3 1.0 - - - +
245A ILE* 3.8 19.9 - - + -
246A ARG* 3.1 28.1 + - - +
247A LYS* 2.9 45.6 + - - +
248A ALA 3.1 0.2 - - - -
249A SER* 1.3 80.1 + - - +
251A VAL* 1.3 60.3 + - - +
253A GLU* 3.4 12.0 + - - +
254A VAL* 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.7 20.6 - - + -
247A LYS 3.9 3.1 - - - +
248A ALA* 2.9 10.0 + - - +
250A ASP* 1.3 75.0 - - - +
252A HIS* 1.3 59.8 + - + +
254A VAL* 3.2 7.5 + - - +
255A ARG* 2.8 31.3 + - - +
267A ILE* 4.2 15.4 - - + +
269A SER* 3.4 22.4 - - - +
283A ILE* 4.2 4.9 - - + -
286A ALA* 3.4 35.2 - - + +
287A SER* 3.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 3.0 30.1 + - + -
249A SER* 3.7 15.6 - - - +
250A ASP 3.3 0.2 - - - -
251A VAL* 1.3 77.4 - - - +
253A GLU* 1.3 56.9 + - + +
255A ARG* 3.6 11.6 - - + +
256A LYS* 2.9 29.6 + - - +
285A GLU* 5.2 3.7 + - - -
286A ALA* 3.8 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO* 5.9 1.4 - - - +
220A ALA* 4.7 4.5 + - - +
221A VAL* 3.7 30.5 + - + +
247A LYS* 6.0 0.2 - - - -
249A SER* 3.1 24.5 + - - +
250A ASP* 3.5 19.6 - - - +
251A VAL 3.2 0.2 - - - -
252A HIS* 1.3 74.9 - - - +
254A VAL* 1.3 59.7 + - - +
256A LYS* 3.1 9.9 + - + +
257A VAL* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA 5.8 0.4 - - - +
221A VAL* 3.9 16.8 - - + -
229A LEU* 4.1 22.7 - - + -
240A VAL* 4.5 12.8 - - + -
242A ALA* 4.3 18.6 - - + -
245A ILE* 4.8 3.4 - - + -
250A ASP 3.3 15.5 + - - +
251A VAL* 3.2 9.3 + - - +
253A GLU* 1.3 76.4 - - - +
255A ARG* 1.3 63.8 + - - +
256A LYS 3.2 0.2 + - - -
257A VAL* 3.3 3.1 + - - +
258A LEU* 3.1 29.5 + - + +
267A ILE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 2.8 17.4 + - - +
252A HIS* 3.6 15.8 - - + +
254A VAL* 1.3 76.8 - - - +
256A LYS* 1.3 58.0 + - - +
258A LEU* 3.6 5.6 + - - +
259A GLY* 3.1 23.2 + - - +
263A LYS* 4.9 13.3 + - - +
265A ILE 4.2 7.3 + - - -
267A ILE* 3.6 27.6 - - + +
286A ALA 3.1 26.5 + - - -
287A SER 4.2 0.2 - - - -
288A ASP* 3.0 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A HIS 2.9 18.5 + - - +
253A GLU* 3.4 10.5 - - + +
254A VAL 3.1 0.2 - - - -
255A ARG* 1.3 77.1 - - - +
257A VAL* 1.3 68.6 + - + +
259A GLY* 3.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A VAL* 4.1 13.2 - - + -
226A ILE* 3.9 44.0 - - + +
229A LEU* 3.8 30.1 - - + -
230A LYS* 4.2 20.4 + - + +
253A GLU* 3.0 21.0 + - + +
254A VAL 3.3 4.5 + - - +
256A LYS* 1.3 82.4 - - + +
258A LEU* 1.3 63.9 + - - +
259A GLY* 3.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 4.0 26.0 - - + +
230A LYS* 5.5 2.1 + - - -
232A GLY 5.9 0.2 - - - -
233A VAL* 3.8 29.6 - - + +
240A VAL* 4.2 17.7 - - + -
254A VAL* 3.1 20.8 + - + +
255A ARG* 3.8 5.8 - - - +
257A VAL* 1.3 77.1 - - - +
259A GLY* 1.3 64.1 + - - +
261A LYS* 3.9 4.2 + - - +
262A GLY* 3.0 37.1 + - - +
265A ILE* 4.2 17.5 - - + +
267A ILE* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG 3.1 12.5 + - - +
256A LYS* 3.1 17.8 + - - -
257A VAL 4.1 0.9 - - - -
258A LEU* 1.3 83.0 - - - +
260A GLU* 1.3 60.6 + - - -
262A GLY 3.6 0.2 - - - -
263A LYS* 3.2 19.4 + - - +
----------------------------------------------------------
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