Contacts of the helix formed by residues 266 - 278 (chain E) in PDB entry 2QC8
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 GLY 266 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E ALA 3.5 13.9 - - - -
261E MET* 3.4 25.0 - - - -
263E GLU 2.9 11.8 + - - -
264E GLU 4.5 0.2 - - - -
265E ASN* 1.3 72.7 - - - +
267E LEU* 1.3 59.1 + - - +
268E LYS 3.0 2.9 - - - -
269E TYR* 2.8 27.6 + - - +
270E ILE* 3.1 12.4 + - - +
333E LYS 2.9 3.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E ASN 3.1 0.9 - - - -
266E GLY* 1.3 77.5 - - - +
268E LYS* 1.3 62.9 + - - +
270E ILE* 3.5 31.8 - - + +
271E GLU* 2.9 45.8 + - - +
325E ILE* 4.3 21.3 - - + -
329E VAL* 4.4 5.8 - - + +
330E GLY* 4.3 13.7 - - - +
333E LYS* 3.0 43.5 + - + +
334E LYS* 4.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E ASN* 3.4 15.9 + - + +
266E GLY 3.0 0.4 - - - -
267E LEU* 1.3 78.7 - - - +
269E TYR* 1.3 83.3 + - + +
271E GLU* 3.3 9.7 + - - +
272E GLU* 3.1 50.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E THR* 5.3 0.2 - - - +
260E ALA* 3.8 39.3 - - + -
261E MET* 3.8 20.0 - - + +
264E GLU 5.9 0.9 - - - -
265E ASN 4.5 6.7 - - - -
266E GLY* 2.8 16.1 + - - +
268E LYS* 1.3 96.1 + - + +
270E ILE* 1.3 67.5 + - - +
271E GLU 3.2 0.9 - - - -
272E GLU* 3.7 28.4 - - - +
273E ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET* 3.9 25.3 - - + +
266E GLY 3.1 11.2 + - - +
267E LEU* 3.5 30.7 - - + +
269E TYR* 1.3 75.3 - - - +
271E GLU* 1.3 59.1 + - - +
273E ALA* 3.1 5.2 + - - +
274E ILE* 2.9 47.1 + - + +
325E ILE* 4.4 4.7 - - + -
329E VAL* 3.5 30.3 - - + -
335E GLY 3.8 11.0 - - - +
336E TYR 3.8 16.8 - - - +
337E PHE* 3.8 20.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E LEU* 2.9 47.7 + - + +
268E LYS* 3.6 7.9 - - - +
270E ILE* 1.3 78.2 - - - +
272E GLU* 1.3 56.0 + - - +
274E ILE* 3.4 8.2 + - + +
275E GLU* 3.0 28.2 + - - +
325E ILE* 4.8 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LYS* 3.1 44.6 + - + +
269E TYR* 3.7 29.1 - - - +
270E ILE 3.3 0.2 - - - -
271E GLU* 1.3 75.1 - - - +
273E ALA* 1.3 58.5 + - - +
275E GLU* 3.5 8.6 - - - +
276E LYS* 3.0 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E MET* 3.8 12.6 - - + -
269E TYR 2.9 13.7 + - - +
270E ILE 3.1 8.7 + - - +
272E GLU* 1.3 75.6 - - - +
274E ILE* 1.3 58.7 + - - +
276E LYS* 3.2 8.3 + - - +
277E LEU* 2.9 34.7 + - - +
337E PHE* 3.6 25.8 - - + -
359E CYS* 4.0 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E ILE* 2.9 30.1 + - + +
271E GLU* 3.8 7.6 - - + +
272E GLU 3.3 0.2 - - - -
273E ALA* 1.3 76.2 - - - +
275E GLU* 1.3 58.7 + - - +
277E LEU* 3.1 8.6 + - - +
278E SER* 2.9 28.3 + - - -
312E PHE* 3.7 14.7 - - + -
314E ALA* 3.7 26.2 - - + -
323E ILE* 4.0 22.4 - - + -
325E ILE* 3.7 35.0 - - + -
337E PHE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E GLU 3.0 17.6 + - - +
272E GLU* 3.5 11.0 - - - +
274E ILE* 1.3 77.9 - - - +
276E LYS* 1.3 63.5 + - + +
278E SER* 2.5 29.2 + - - -
279E LYS* 3.2 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E GLU* 3.0 35.0 + - - +
273E ALA* 3.2 8.4 + - - +
275E GLU* 1.3 80.8 - - + +
277E LEU* 1.3 62.3 + - - +
279E LYS* 3.1 22.1 + - - +
280E ARG* 3.7 5.2 + - - +
358E THR* 3.7 31.2 - - + +
359E CYS* 3.4 18.7 + - - +
362E ASN* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E ALA 2.9 17.4 + - - +
274E ILE* 3.1 9.8 + - - +
276E LYS* 1.3 75.4 - - - +
278E SER* 1.3 62.6 + - - +
279E LYS 3.0 0.4 - - - -
280E ARG 3.1 13.7 + - - -
281E HIS* 3.5 9.7 + - - -
284E HIS* 3.3 40.6 - - + +
312E PHE* 3.7 19.1 - - + -
323E ILE* 4.5 11.9 - - + -
337E PHE* 3.5 39.3 - - + -
341E ARG* 4.2 6.9 + - - +
355E LEU* 4.0 8.3 - - + -
358E THR* 3.8 12.1 - - + -
359E CYS* 3.8 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E ILE* 2.9 8.2 + - - -
275E GLU* 2.5 32.0 + - - -
276E LYS 3.1 0.2 - - - -
277E LEU* 1.3 75.8 - - - +
279E LYS* 1.3 64.0 + - - +
280E ARG 3.5 0.2 - - - -
281E HIS* 4.7 5.1 + - - +
312E PHE* 3.4 41.4 - - - +
----------------------------------------------------------
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