Contacts of the helix formed by residues 293 - 304 (chain D) in PDB entry 5UQ9
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 LEU 293 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLY 6.2 0.2 - - - +
277C PRO* 4.4 16.6 - - + -
340C MET* 3.6 31.0 - - + -
433C TYR* 4.7 5.2 - - + -
289D CYS 3.8 11.4 - - - +
290D LEU* 3.2 15.2 + - + +
291D SER 3.1 2.2 - - - -
292D SER* 1.3 78.8 - - - +
294D LYS* 1.3 53.6 + - - +
295D ASP 3.2 2.9 - - - +
296D GLU* 3.0 35.2 + - + +
297D ARG* 2.7 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLU* 2.7 25.8 + - - +
437C MET* 3.5 18.6 - - - +
458C LEU* 4.0 14.7 - - - +
255D ARG* 3.5 37.9 - - - +
256D ASP* 2.4 34.3 + - - +
257D SER* 4.2 5.2 - - - -
291D SER 3.5 3.9 + - - +
292D SER 3.1 6.4 + - - +
293D LEU* 1.3 75.5 - - - +
295D ASP* 1.3 64.5 + - - +
297D ARG* 3.3 20.3 + - - +
298D ILE* 3.1 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ARG* 4.5 12.5 + - - +
293D LEU* 3.2 0.8 - - - -
294D LYS* 1.3 81.2 - - - +
296D GLU* 1.3 64.0 + - + +
298D ILE* 3.6 9.0 + - - +
299D GLN* 3.3 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C MET* 4.8 4.6 - - - +
387C GLN* 3.4 45.7 - - + +
388C ASN* 4.5 3.6 + - - +
391C LEU* 5.7 1.5 - - + +
433C TYR* 3.4 32.7 + - + +
293D LEU* 3.0 38.3 + - + +
295D ASP* 1.3 78.6 - - + +
297D ARG* 1.3 61.1 + - - +
299D GLN* 3.6 4.9 + - - +
300D ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C GLY 3.4 22.2 - - - +
433C TYR* 3.6 30.1 - - + +
435C HIS 3.2 15.9 + - - +
436C GLU* 3.0 22.6 + - - -
438C LEU* 3.6 15.7 - - - +
256D ASP* 2.7 39.9 + - - -
290D LEU* 3.2 23.2 + - - +
291D SER* 2.6 26.0 + - - +
293D LEU 2.7 18.8 + - - +
294D LYS* 3.6 16.6 - - - +
295D ASP 3.3 0.2 - - - -
296D GLU* 1.3 72.5 - - - +
298D ILE* 1.3 58.9 + - - +
300D ALA* 4.0 0.5 - - - +
301D SER* 3.0 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C GLU* 3.9 30.9 - - + +
294D LYS* 3.1 48.0 + - + +
295D ASP* 4.0 9.2 - - - +
296D GLU 3.3 0.2 - - - -
297D ARG* 1.3 76.8 - - - +
299D GLN* 1.3 77.4 + - - +
301D SER* 3.3 12.5 + - - -
302D LYS* 3.5 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 4.6 12.3 - - + +
295D ASP* 3.3 19.9 + - - +
296D GLU* 4.2 4.9 - - - +
297D ARG 3.4 0.2 - - - -
298D ILE* 1.3 87.5 - - - +
300D ALA* 1.3 61.7 + - - +
302D LYS* 3.0 48.0 + - - +
303D LYS* 3.9 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C LEU* 4.1 13.0 - - + +
433C TYR* 3.5 43.3 - - + +
434C ARG 4.6 0.9 - - - -
296D GLU 3.0 19.9 + - - +
297D ARG 4.0 0.2 - - - +
299D GLN* 1.3 74.9 - - - +
301D SER* 1.3 60.7 + - - +
302D LYS 3.1 2.2 + - - -
303D LYS 3.2 1.0 + - - +
304D LEU* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 301 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C ARG 3.3 25.1 + - - -
435C HIS* 4.9 0.2 - - - -
436C GLU* 3.8 26.0 + - - +
297D ARG 3.0 17.2 + - - -
298D ILE 3.3 7.3 + - - -
300D ALA* 1.3 75.8 - - - +
302D LYS* 1.3 60.7 + - - +
303D LYS 3.4 0.2 - - - -
304D LEU 3.7 12.0 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
298D ILE* 3.5 28.9 - - - +
299D GLN* 3.0 39.2 + - - +
300D ALA 3.1 1.0 - - - -
301D SER* 1.3 79.4 - - - +
303D LYS* 1.3 62.5 + - + +
305D LYS* 5.9 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 4.2 3.8 - - - -
391C LEU* 3.4 52.3 + - + +
392C ASP 4.7 2.8 + - - -
393C ASP* 5.3 3.0 - - - +
396C LYS* 3.1 43.2 - - + +
299D GLN 3.9 7.6 + - - +
300D ALA 3.2 4.8 + - - +
302D LYS* 1.3 83.0 - - + +
304D LEU* 1.3 67.0 + - + +
305D LYS* 3.6 7.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 3.3 38.4 - - + +
391C LEU* 5.4 0.7 - - + -
396C LYS* 3.8 19.5 - - + -
399C VAL* 5.9 0.7 - - + -
430C TYR* 3.8 31.0 - - + +
433C TYR* 3.7 29.6 - - + -
434C ARG* 3.7 25.2 + - + +
300D ALA* 2.8 26.3 + - + +
301D SER* 3.7 16.1 - - - +
302D LYS 4.9 0.2 - - - -
303D LYS* 1.3 74.1 - - + +
305D LYS* 1.3 60.8 + - - +
----------------------------------------------------------
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