Contacts of the helix formed by residues 291 - 302 (chain D) in PDB entry 1TYE
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 291 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 4.4 9.4 - - - -
324C GLU* 2.8 32.3 + - - -
353C TYR* 4.8 1.6 - - - -
355C ARG* 4.9 4.4 + - - -
256D ILE* 6.1 0.4 - - - -
257D ALA* 3.6 20.3 - - - +
290D PRO* 1.3 76.5 - - - +
292D LEU* 1.3 67.3 + - - +
293D GLY 4.2 0.2 - - - -
294D LEU* 3.0 27.9 + - - +
295D MET* 3.1 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C MET 4.5 0.4 - - - +
286C ALA* 4.0 26.4 - - + +
314C MET* 4.1 15.5 - - + -
223D PHE* 3.6 18.4 - - + -
256D ILE* 4.9 3.7 - - + +
290D PRO 4.0 0.6 + - - -
291D SER* 1.3 70.8 - - - +
293D GLY* 1.3 58.3 + - - +
295D MET* 3.1 29.3 + - + +
296D THR* 2.9 32.4 + - - +
321D TYR* 4.2 17.0 - - + +
324D LEU* 3.7 40.4 - - + -
325D ILE* 4.2 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C MET* 3.8 19.6 - - - -
324C GLU* 4.3 11.8 + - - -
353C TYR* 3.7 13.3 + - - -
291D SER* 3.1 3.6 - - - -
292D LEU* 1.3 78.4 - - - +
294D LEU* 1.3 62.5 + - - +
296D THR* 3.1 9.4 + - - -
297D GLU* 2.9 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C TYR* 3.6 33.3 + - + +
227D MET* 3.4 36.6 - - + -
269D ASN* 4.0 18.6 - - + +
270D ASP 5.8 0.9 - - - -
271D GLY* 3.8 18.2 - - - +
290D PRO* 4.4 3.1 - - + -
291D SER* 3.0 27.8 + - - +
293D GLY* 1.3 73.5 - - - +
295D MET* 1.3 61.3 + - - +
297D GLU* 3.4 12.3 + - - +
298D LYS* 3.2 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D PHE* 3.3 63.3 - - + +
226D ILE* 4.5 16.4 - - + -
227D MET* 3.6 24.2 - - + -
290D PRO* 4.1 7.9 - - + +
291D SER 3.1 10.0 + - - +
292D LEU* 3.1 33.7 + - + +
294D LEU* 1.3 72.3 - - - +
296D THR* 1.3 62.3 + - - +
298D LYS* 3.2 2.9 + - - +
299D LEU* 2.8 44.4 + - + +
306D LEU* 5.9 1.1 - - - -
325D ILE* 4.2 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C MET* 5.3 0.7 - - - -
322C LEU 6.0 1.8 - - - +
292D LEU 2.9 17.2 + - - -
293D GLY* 3.3 12.0 - - - -
295D MET* 1.3 76.0 - - - +
297D GLU* 1.3 64.1 + - - +
299D LEU* 3.3 3.7 + - - +
300D SER* 3.1 24.9 + - - -
324D LEU 3.9 7.0 + - - +
325D ILE* 3.6 27.6 - - + +
326D PRO* 4.4 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C LEU* 4.3 7.4 - - - +
353C TYR* 2.9 41.7 + - - +
293D GLY 2.9 6.9 + - - +
294D LEU* 3.6 11.0 - - - +
295D MET 3.3 0.2 - - - -
296D THR* 1.3 78.1 - - - +
298D LYS* 1.3 79.6 + - + +
300D SER* 3.3 4.7 + - - -
301D GLN* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D MET* 3.8 22.0 - - + -
230D THR* 3.5 16.8 - - + +
231D VAL* 3.9 13.7 - - + -
270D ASP 5.3 1.2 + - - -
271D GLY* 3.7 26.3 + - - -
294D LEU* 3.2 22.0 + - + +
295D MET 3.9 2.7 - - - +
297D GLU* 1.3 89.4 + - - +
299D LEU* 1.3 66.7 + - - +
301D GLN* 3.5 37.4 + - - +
302D LYS* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE* 4.8 8.3 - - + -
230D THR* 3.5 25.8 - - + +
246D LEU* 4.9 1.3 - - + -
295D MET* 2.8 26.2 + - + +
296D THR* 3.6 5.2 - - - +
298D LYS* 1.3 76.0 - - - +
300D SER* 1.3 57.7 + - - +
303D ASN* 3.2 5.5 + - - -
304D ILE* 2.9 60.8 + - + +
306D LEU* 4.0 34.3 - - + -
325D ILE* 3.9 25.8 - - + -
328D THR* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D THR* 3.1 18.2 + - - -
297D GLU* 3.7 5.2 - - - -
299D LEU* 1.3 76.0 - - - +
301D GLN* 1.3 59.6 + - - +
302D LYS 3.2 0.2 - - - -
303D ASN* 3.0 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLU* 2.9 29.2 + - + +
298D LYS* 3.4 35.6 + - - +
300D SER* 1.3 77.5 - - - +
302D LYS* 1.3 81.6 + - + +
303D ASN* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D THR* 3.5 20.4 - - + +
231D VAL* 4.2 24.0 + - + +
233D ASP* 3.0 38.8 + - - +
238D TRP* 6.3 0.4 - - + -
244D HIS* 3.8 9.9 + - - -
298D LYS* 3.0 21.4 + - - +
301D GLN* 1.3 101.9 - - + +
303D ASN* 1.3 72.7 + - - +
304D ILE* 3.5 14.7 - - + +
----------------------------------------------------------
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