Contacts of the helix formed by residues 286 - 299 (chain L) in PDB entry 6AHU
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 286 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L THR 4.8 8.9 + - - +
64L GLY* 5.7 3.4 - - - +
65L PRO 5.7 3.4 - - - +
91L SER 5.9 0.4 - - - +
93L TYR* 3.7 31.0 - - + -
182L ALA* 4.1 26.0 - - + -
183L TRP* 4.3 11.9 - - - +
184L HIS* 4.3 31.2 - - + +
284L PHE* 3.9 6.4 + - + +
285L ILE* 1.3 88.0 - - - +
287L PRO* 1.3 71.8 - - + +
288L GLU* 3.8 8.5 - - - +
289L LYS* 3.3 32.8 + - + +
290L ILE* 3.6 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 287 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L VAL* 3.4 17.2 - - + +
34L GLN* 4.4 7.4 - - - +
36L HIS 3.3 27.1 - - - +
37L TYR 4.3 5.8 - - - +
39L ASN* 3.8 14.8 - - - +
93L TYR* 3.6 32.3 - - + +
285L ILE 3.7 4.0 - - - +
286L LEU* 1.3 80.9 - - - +
288L GLU* 1.3 75.9 + - - +
289L LYS 3.3 0.2 - - - -
290L ILE* 3.3 8.9 + - + +
291L CYS* 3.3 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 288 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L GLN* 5.0 12.4 - - + +
91L SER* 4.9 9.8 + - - -
93L TYR* 3.5 16.3 + - - -
111L PRO* 5.7 0.5 - - - +
184L HIS* 3.8 41.3 - - + +
286L LEU* 3.2 12.2 - - + +
287L PRO* 1.3 96.4 - - - +
289L LYS* 1.3 64.1 + - - +
291L CYS* 3.3 15.5 + - - +
292L LEU* 3.3 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 289 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L LEU* 4.9 10.3 - - + +
62L ASN* 3.9 19.8 + - - +
63L THR* 3.4 39.3 - - + +
64L GLY 4.7 5.8 + - - -
184L HIS* 4.9 13.1 + - + +
285L ILE* 4.9 4.3 - - + -
286L LEU* 3.3 30.4 + - + +
287L PRO 3.3 0.4 - - - -
288L GLU* 1.3 78.9 - - + +
290L ILE* 1.3 59.2 + - - +
292L LEU* 3.5 18.0 + - + +
293L LEU* 3.1 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 290 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L VAL* 4.2 10.8 - - + -
39L ASN* 3.4 34.8 - - - +
42L VAL* 4.0 9.9 - - + -
285L ILE* 3.9 20.2 - - + -
286L LEU 3.6 9.4 - - - +
287L PRO* 3.3 8.0 + - + +
288L GLU 3.2 0.6 - - - -
289L LYS* 1.3 75.5 - - - +
291L CYS* 1.3 55.8 + - - +
293L LEU* 3.0 12.2 + - + -
294L LEU* 2.5 35.3 + - + +
312L LEU* 4.6 13.7 - - + -
314L VAL* 3.9 25.6 - - + -
339L TYR* 3.7 17.3 - - + +
341L PHE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 291 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ARG* 4.3 26.8 + - - +
33L VAL* 3.7 19.5 - - - -
34L GLN* 3.6 30.7 - - - +
287L PRO 3.3 16.7 + - - -
288L GLU* 3.6 10.8 - - - +
289L LYS 3.3 0.4 - - - -
290L ILE* 1.3 78.7 - - - +
292L LEU* 1.3 61.0 + - + +
294L LEU* 4.0 7.2 - - - +
295L GLU* 3.2 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 292 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L LEU* 3.8 23.2 - - + +
184L HIS* 6.1 2.2 - - - +
288L GLU* 3.3 22.0 + - + +
289L LYS* 3.9 19.1 - - + +
290L ILE 3.3 0.2 - - - -
291L CYS* 1.3 79.6 - - + +
293L LEU* 1.3 61.3 + - - +
295L GLU* 4.1 4.5 - - - +
296L HIS* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 3.8 29.2 - - + -
44L PHE* 4.4 19.5 - - + -
56L LEU* 3.8 29.4 - - + -
59L LEU* 3.8 14.3 - - + +
60L VAL* 5.6 2.0 - - + -
63L THR* 6.4 1.3 - - + -
281L ILE* 5.0 4.7 - - + -
289L LYS 3.1 13.8 + - - +
290L ILE* 3.0 15.8 + - + +
292L LEU* 1.3 76.4 - - - +
294L LEU* 1.3 63.2 + - - +
296L HIS* 3.5 1.3 + - - +
297L LEU* 3.2 30.0 + - + +
312L LEU* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L PHE* 4.2 13.9 - - + -
29L HIS* 3.8 39.5 - - + +
30L ARG* 4.8 7.2 - - - -
33L VAL* 4.5 7.9 - - + -
290L ILE* 2.5 22.0 + - + +
291L CYS* 4.0 7.4 - - - +
293L LEU* 1.3 73.6 - - - +
295L GLU* 1.3 59.7 + - + +
297L LEU* 3.4 2.9 + - - -
298L CYS* 2.9 25.6 + - - +
312L LEU* 3.7 24.7 - - + +
341L PHE* 4.2 24.2 - - + -
343L ILE* 3.9 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 295 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L PHE* 5.3 1.4 - - - -
29L HIS* 3.8 14.9 + - - -
30L ARG* 3.5 40.6 + - - +
291L CYS 3.2 18.2 + - - +
292L LEU* 4.5 4.5 - - - +
294L LEU* 1.3 76.3 - - + +
296L HIS* 1.3 58.4 + - - +
298L CYS* 3.5 12.8 + - - +
299L HIS* 2.4 57.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 296 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L SER* 4.3 5.8 + - - -
55L GLU* 3.6 43.6 + - + +
56L LEU* 3.5 46.0 + - + +
59L LEU* 4.4 9.4 - - + -
292L LEU 3.3 21.5 + - - +
293L LEU 3.9 4.5 - - - +
294L LEU 3.3 0.4 - - - -
295L GLU* 1.3 77.4 - - - +
297L LEU* 1.3 61.3 + - + +
299L HIS* 3.3 10.3 + - + +
300L TYR* 3.0 29.7 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 297 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L PHE* 4.6 7.0 - - + -
46L ILE* 4.6 21.8 - - + -
56L LEU* 4.9 14.4 - - + -
293L LEU* 3.2 25.2 + - + +
294L LEU 3.8 3.8 - - - +
296L HIS* 1.3 77.0 - - + +
298L CYS* 1.3 63.5 + - - +
300L TYR* 3.4 24.0 - - + +
301L PHE* 4.0 12.5 - - - -
310L VAL* 4.7 13.5 - - + +
311L THR 4.1 9.2 - - - +
312L LEU* 3.8 41.7 - - + -
343L ILE* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 298 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L PHE* 3.8 44.9 - - + -
294L LEU 2.9 17.0 + - - +
295L GLU* 3.7 20.0 - - - +
296L HIS 3.3 0.4 - - - -
297L LEU* 1.3 78.7 - - - +
299L HIS* 1.3 62.8 + - - +
300L TYR 3.2 1.1 + - - -
301L PHE* 4.1 11.6 + - - +
302L ASP* 4.6 3.1 - - - +
343L ILE* 4.7 8.7 - - - +
347L GLN* 4.9 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 299 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295L GLU* 2.4 55.7 + - + +
296L HIS* 3.3 12.4 + - + +
298L CYS* 1.3 79.7 - - + +
300L TYR* 1.3 61.9 + - - +
301L PHE 3.3 2.0 - - - -
302L ASP* 2.9 41.0 + - - +
----------------------------------------------------------
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