Contacts of the helix formed by residues 298 - 310 (chain L) in PDB entry 6PST
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 PRO 298 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296L LYS 3.3 9.6 - - - +
297L MET* 1.3 96.2 - - + +
299L LYS* 1.3 65.7 + - - +
300L LYS* 3.1 11.2 + - + +
301L ASN* 3.2 31.4 + - - +
302L PHE 3.6 0.9 + - - -
326L TRP* 4.0 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 299 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288L MET* 5.8 5.8 - - - -
292L VAL* 4.9 19.7 - - + -
297L MET* 4.3 7.9 - - - +
298L PRO* 1.3 72.3 - - - +
300L LYS* 1.3 57.3 + - - +
301L ASN 3.3 0.2 - - - -
302L PHE* 3.1 15.0 - - + +
303L ILE* 2.9 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 300 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298L PRO* 3.1 7.5 - - + -
299L LYS* 1.3 79.6 - - - +
301L ASN* 1.3 65.8 + - - +
303L ILE* 3.3 6.9 + - + +
304L THR* 2.6 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L MET* 4.0 3.6 - - + -
298L PRO* 3.2 25.6 + - - +
300L LYS* 1.3 88.7 - - - +
302L PHE* 1.3 57.3 + - - +
304L THR* 4.5 5.4 - - - +
305L LEU* 2.9 38.6 + - + +
322L MET* 3.4 21.2 - - + +
326L TRP* 3.1 38.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 302 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L GLU* 5.3 7.2 - - + -
287L ILE* 5.7 1.1 - - + -
288L MET* 4.2 35.4 - - + -
297L MET* 3.3 31.3 - - + +
299L LYS* 3.1 19.3 + - + +
301L ASN* 1.3 77.4 - - - +
303L ILE* 1.3 82.9 + - + +
306L PHE* 2.6 85.6 + + + +
307L THR* 3.2 8.2 + - - -
315L TRP* 5.8 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299L LYS* 2.9 25.6 + - + +
300L LYS* 3.9 7.6 - - + +
302L PHE* 1.3 91.1 - - + +
304L THR* 1.3 59.7 + - - +
307L THR* 3.2 47.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 304 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300L LYS* 2.6 32.4 + - - +
301L ASN* 4.1 5.6 - - - -
303L ILE* 1.3 81.0 - - - +
305L LEU* 1.3 69.6 + - + +
307L THR 4.1 3.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297L MET* 5.9 2.2 - - + -
301L ASN* 2.9 21.8 + - + +
302L PHE* 5.2 0.4 - - - -
304L THR* 1.3 88.3 - - + +
306L PHE* 1.3 68.4 + - - +
307L THR 3.6 4.6 - - - +
309L ASN* 4.3 9.0 + - - +
314L THR* 4.8 9.9 - - + +
315L TRP* 3.2 45.9 - - + +
318L ALA 5.7 0.9 - - - +
319L ALA* 4.5 3.6 - - + -
322L MET* 3.7 37.9 - - + -
326L TRP* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 306 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L GLU* 3.7 33.0 - - + -
287L ILE* 4.5 11.2 - - + -
302L PHE* 2.6 62.0 + + + +
305L LEU* 1.3 74.9 - - - +
307L THR* 1.3 61.4 + - - +
310L GLU* 2.6 71.1 + - + -
315L TRP* 3.3 60.5 - + + +
344L LEU* 4.8 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 307 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302L PHE* 3.2 11.2 + - - -
303L ILE* 3.2 54.1 - - + +
304L THR 4.1 4.7 - - - +
305L LEU 3.6 8.0 - - - +
306L PHE* 1.3 84.4 - - - +
308L GLY* 1.3 61.7 + - - +
309L ASN 3.6 0.3 + - - -
310L GLU* 4.6 7.7 + - - +
356L GLU* 5.2 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 308 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L PHE 3.5 0.2 + - - -
307L THR* 1.3 80.2 - - - +
309L ASN* 1.3 58.8 + - - +
310L GLU* 5.2 1.4 + - - +
356L GLU* 6.2 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 309 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305L LEU 4.3 9.6 + - - +
306L PHE 3.4 0.2 + - - -
307L THR 3.4 4.0 + - - -
308L GLY* 1.3 77.7 - - - +
310L GLU* 1.3 59.7 + - - +
311L THR* 2.8 47.0 + - - +
312L SER* 3.1 33.6 + - - +
314L THR* 5.0 7.9 - - - -
315L TRP* 4.9 4.6 - - + -
354L THR* 5.6 1.4 - - - +
356L GLU* 5.5 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 310 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284L GLU* 4.0 4.3 - - - +
306L PHE* 2.6 57.3 + - + +
307L THR* 4.6 9.2 + - - +
308L GLY 5.2 1.2 + - - +
309L ASN* 1.3 72.7 - - - +
311L THR* 1.3 59.2 + - + +
315L TRP* 3.6 15.2 + - - +
344L LEU* 3.0 23.8 - - + +
348L GLU* 3.6 0.3 - - - +
355L ILE* 3.0 32.9 - - + +
356L GLU* 4.1 23.6 - - + +
359L LYS* 3.1 24.7 + - - +
----------------------------------------------------------
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