Contacts of the helix formed by residues 265 - 280 (chain E) in PDB entry 6DWZ
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 CYS 265 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E VAL* 4.2 5.4 - - + -
247E THR 2.5 18.2 + - - +
264E ASN* 1.3 70.4 - - - +
266E SER* 1.3 58.7 + - - +
267E SER* 2.9 29.8 - - - -
268E HIS* 3.0 40.2 - - + +
269E LEU* 3.1 30.6 + - - +
319E TRP* 5.6 0.2 - - - -
566E ALA 4.2 4.9 - - - -
567E SER* 4.1 1.3 - - - -
568E SER* 3.6 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 266 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264E ASN 3.0 9.8 + - - -
265E CYS* 1.3 70.8 - - - +
267E SER* 1.3 60.2 + - - +
269E LEU* 3.9 7.9 - - - -
270E LEU* 3.0 27.4 + - - +
374E LEU* 3.7 23.1 - - - -
385E VAL* 3.8 4.9 - - - +
421E TRP* 3.6 24.7 + - - +
425E LEU* 4.9 0.7 - - - +
429E HIS* 3.6 21.1 - - - -
566E ALA 3.2 13.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 267 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E CYS* 2.9 14.1 - - - -
266E SER* 1.3 78.2 - - - +
268E HIS* 1.3 67.0 + - - +
270E LEU* 3.3 3.0 + - - -
271E SER* 2.9 20.8 + - - -
319E TRP* 3.8 10.1 - - - -
371E PHE* 3.3 27.0 - - - -
374E LEU* 4.6 9.5 - - - +
375E GLN* 3.3 31.1 + - - -
566E ALA 4.6 1.8 + - - -
567E SER* 4.1 9.6 + - - -
569E ALA 5.5 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASP* 4.2 2.7 + - - -
248E ASP* 3.2 41.2 + - + +
265E CYS* 3.0 27.4 - - + +
267E SER* 1.3 81.1 + - - +
269E LEU* 1.3 70.1 + - + +
271E SER* 2.8 15.1 + - - -
272E ASN* 3.0 17.9 + - - +
319E TRP* 3.6 26.5 - + - -
568E SER* 3.5 22.7 - - - -
572E GLU* 4.3 13.0 + - - -
7H C 4.1 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 269 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ARG* 3.7 30.7 - - + +
264E ASN* 4.2 15.9 - - + +
265E CYS 3.1 21.7 + - - +
266E SER* 3.9 8.1 - - - +
268E HIS* 1.3 85.1 - - + +
270E LEU* 1.3 64.7 + - - +
272E ASN* 2.9 21.5 + - - +
273E VAL* 3.0 16.7 + - - +
420E ILE* 3.8 7.8 - - + +
421E TRP* 4.2 17.3 - - + +
424E ASN* 3.4 44.4 - - + +
425E LEU* 6.0 0.4 - - + -
7H C 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E SER 3.0 19.5 + - - +
267E SER* 3.7 2.9 - - - +
269E LEU* 1.3 76.6 - - - +
271E SER* 1.3 59.9 + - - +
273E VAL* 3.7 12.4 - - + +
274E LEU* 3.2 39.3 + - + +
367E PHE* 3.9 17.0 - - + +
370E ILE* 4.8 9.9 - - + -
371E PHE* 3.6 44.4 - - + +
374E LEU* 4.9 5.6 - - + -
392E VAL* 4.8 4.3 - - + -
421E TRP* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 271 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267E SER 2.9 5.1 + - - -
268E HIS 2.8 11.2 + - - -
270E LEU* 1.3 75.6 - - - +
272E ASN* 1.3 55.3 + - - +
274E LEU* 3.1 7.2 + - - +
275E GLU* 2.4 44.6 + - - +
318E ARG 5.4 0.7 + - - -
319E TRP* 3.5 37.7 - - - -
320E ASN* 4.4 10.7 + - - +
371E PHE* 4.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249E ARG* 2.9 25.9 + - - +
268E HIS 3.4 12.3 + - - +
269E LEU* 2.9 12.9 + - - +
271E SER* 1.3 74.9 - - - +
273E VAL* 1.3 58.3 + - - +
275E GLU* 2.7 46.1 + - - +
276E ASN* 2.8 22.8 + - - +
420E ILE* 3.9 18.4 - - + -
6H A 4.4 5.8 - - - +
7H C 3.4 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E LEU 3.0 15.5 + - - +
270E LEU* 3.7 15.9 - - + +
272E ASN* 1.3 72.6 - - - +
274E LEU* 1.3 65.0 + - + +
277E SER* 2.7 33.9 + - - +
392E VAL* 6.1 0.4 - - + -
413E ILE* 4.2 8.1 - - + +
416E ASN* 3.7 7.2 - - + +
417E VAL* 3.5 37.5 - - + +
420E ILE* 3.6 22.6 - - + +
421E TRP* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E LEU* 3.2 38.6 + - + +
271E SER* 3.1 9.1 + - - +
273E VAL* 1.3 79.7 - - + +
275E GLU* 1.3 68.0 + - - +
277E SER* 3.8 4.2 - - - -
278E PHE* 3.1 35.3 + - + +
320E ASN* 3.1 42.2 - - + +
364E LEU* 4.0 18.6 - - + -
367E PHE* 3.5 28.7 - - + -
371E PHE* 5.1 6.3 - - + -
413E ILE* 5.5 8.7 - - + -
----------------------------------------------------------
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 SER* 2.4 34.4 + - - +
272E ASN* 2.7 37.0 + - - +
274E LEU* 1.3 69.1 - - - +
276E ASN* 1.3 70.1 + - - +
278E PHE* 3.6 5.2 + - - +
279E GLU* 3.3 28.8 + - - +
320E ASN* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ASN* 2.8 20.0 + - - +
273E VAL 4.5 0.2 - - - +
275E GLU* 1.3 83.3 - - - +
277E SER* 1.3 53.8 + - - +
278E PHE 2.6 6.0 + - - -
279E GLU* 2.5 47.0 + - - +
280E GLU* 2.9 33.7 + - - +
416E ASN* 4.3 6.5 - - - +
420E ILE* 3.4 24.6 - - + +
6H A 4.8 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E VAL 2.7 25.3 + - - -
274E LEU* 3.8 4.3 - - - -
276E ASN* 1.3 75.4 - - - +
278E PHE* 1.3 59.9 + - - +
280E GLU* 3.9 10.0 - - - +
281E THR* 3.4 14.6 + - - -
409E LEU* 3.3 19.4 - - - +
412E ASN* 4.2 6.0 - - - +
413E ILE* 3.1 34.8 - - - +
416E ASN* 3.0 23.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E LEU* 3.1 29.1 + - + +
275E GLU* 3.8 4.7 - - - +
276E ASN 2.6 5.3 + - - -
277E SER* 1.3 73.4 - - - +
279E GLU* 1.3 65.0 + - - +
280E GLU 3.0 2.9 + - - -
281E THR 3.1 10.0 + - - +
284E LEU* 4.4 9.6 - - + -
285E ASN* 3.3 29.4 - - - +
288E ILE* 3.1 35.0 - - + -
320E ASN* 4.6 11.9 - - - -
322E THR* 5.8 1.1 - - + -
360E MET* 3.2 31.9 - - + -
364E LEU* 4.2 28.7 - - + -
409E LEU* 4.0 27.4 - - + -
413E ILE* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLU* 3.3 17.9 + - - +
276E ASN* 2.5 47.8 + - - +
278E PHE* 1.3 71.6 - - - +
280E GLU* 1.3 61.2 + - + +
281E THR 3.5 2.6 + - - -
282E PRO* 3.8 14.6 - - - +
285E ASN* 4.0 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E ASN* 2.9 38.1 + - - +
277E SER* 3.9 4.0 - - - +
279E GLU* 1.3 83.1 - - + +
281E THR* 1.3 57.8 + - - +
282E PRO* 3.3 9.4 - - - +
408E LYS* 4.0 6.2 + - - +
412E ASN* 3.2 33.0 + - - +
415E LYS* 5.7 1.9 - - - +
416E ASN* 3.6 16.0 - - - +
----------------------------------------------------------
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