Contacts of the helix formed by residues 286 - 304 (chain A) in PDB entry 1ESE
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 ASP 286 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 3.7 15.5 - - - +
270A GLN* 2.8 34.4 + - - +
280A TRP* 4.4 0.9 - - - -
285A ASN* 1.3 76.2 - - + +
287A LYS* 1.3 57.0 + - - +
289A ARG* 3.2 22.3 + - - +
290A ASP* 2.9 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.3 17.3 - - - +
258A ALA 4.1 10.9 + - - -
259A ASP* 3.3 35.0 + - - +
260A ARG 3.2 16.6 + - - +
261A GLY* 3.8 5.2 - - - -
285A ASN* 3.2 7.4 + - - +
286A ASP* 1.3 74.7 - - - +
288A GLY* 1.3 70.0 + - - +
290A ASP* 2.9 20.9 + - - +
291A ILE* 3.0 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 5.8 2.3 - - - +
249A THR* 6.3 0.9 - - - -
261A GLY* 3.2 30.7 - - - -
262A ILE* 5.5 1.1 - - - -
284A PRO* 4.0 9.4 - - - -
285A ASN* 3.1 7.7 + - - -
287A LYS* 1.3 84.9 - - - +
289A ARG* 1.3 58.8 + - - +
291A ILE* 3.4 15.5 + - - +
292A GLN* 3.5 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ASN* 3.5 29.4 - - - +
21A ILE* 3.7 23.2 - - + +
39A GLU* 2.6 48.3 + - - +
41A TYR* 3.8 13.6 - - + +
44A VAL* 3.9 18.6 - - - +
284A PRO* 4.1 0.6 - - - +
285A ASN 2.4 30.6 + - - +
286A ASP* 3.3 27.3 + - - +
288A GLY* 1.3 68.4 - - - +
290A ASP* 1.3 88.1 + - - +
292A GLN* 3.7 9.8 - - - +
293A ALA* 2.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.9 5.8 - - - +
286A ASP* 2.9 20.4 + - - +
287A LYS* 2.9 13.2 + - + +
289A ARG* 1.3 105.2 + - - +
291A ILE* 1.3 57.0 - - + +
293A ALA* 3.4 5.8 + - - +
294A LYS* 3.0 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.8 4.0 - - + -
248A GLY 5.1 4.7 - - - +
249A THR* 3.8 24.7 - - + -
252A ASN* 3.6 37.9 - - + +
287A LYS* 3.3 30.5 - - + +
288A GLY* 3.6 10.5 - - - +
289A ARG 3.3 0.2 - - - -
290A ASP* 1.3 73.9 - - + +
292A GLN* 1.3 58.1 + - + +
293A ALA 3.1 1.3 - - - -
294A LYS* 3.4 5.5 - - - +
295A GLN* 2.8 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 292 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 2.8 30.5 + - - +
18A ASN* 2.8 28.1 + - - +
41A TYR* 3.4 26.7 - - + +
184A VAL* 5.9 0.2 - - - +
187A PRO* 4.6 8.0 - - + +
245A LEU* 3.8 33.8 - - + +
284A PRO* 3.8 19.6 - - - +
288A GLY 3.5 10.5 + - - +
289A ARG* 3.7 9.8 - - - +
291A ILE* 1.3 76.3 - - + +
293A ALA* 1.3 66.3 - - - +
295A GLN* 4.0 0.2 - - - +
296A VAL* 3.1 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.8 17.0 - - - +
44A VAL* 3.3 38.1 - - + -
45A ALA* 3.7 8.9 - - - +
48A SER* 6.0 0.9 - - - +
289A ARG 2.8 21.7 + - - +
290A ASP 3.5 6.1 - - - +
291A ILE 3.1 0.4 - - - -
292A GLN* 1.3 79.3 - - - +
294A LYS* 1.3 55.9 + - - +
297A ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 5.5 4.2 - - - +
290A ASP 3.0 16.7 + - - +
291A ILE* 3.4 10.8 - - - +
292A GLN 3.2 0.2 - - - -
293A ALA* 1.3 73.4 - - - +
295A GLN* 1.3 71.7 + - - +
297A ALA* 3.2 6.1 + - - +
298A ASP* 2.8 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 4.0 10.0 - - + +
244A ASP 5.8 0.4 - - - +
245A LEU* 3.5 27.6 - - + -
291A ILE* 2.8 32.3 - - + +
292A GLN 4.0 0.4 - - - +
294A LYS* 1.3 113.1 - - - +
296A VAL* 1.3 59.5 + - - +
298A ASP* 3.4 14.9 + - - +
299A LYS* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 5.2 2.2 - - + -
41A TYR* 3.7 28.0 - - + -
45A ALA* 4.4 7.9 - - + -
100A VAL* 3.9 24.7 - - + -
182A VAL* 6.1 0.4 - - + -
184A VAL* 3.9 24.7 - - + -
243A VAL* 4.2 13.7 - - + -
245A LEU* 5.6 0.2 - - + -
292A GLN* 3.1 20.2 + - - +
293A ALA 4.0 2.9 - - - +
295A GLN* 1.3 71.3 - - - +
297A ALA* 1.3 68.4 + - - +
298A ASP 3.2 0.5 + - - -
299A LYS* 3.3 3.3 + - - +
300A ILE* 3.2 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 4.2 13.8 - - + +
48A SER* 4.5 12.6 - - - -
49A LEU* 3.6 34.6 - - + +
293A ALA 3.0 20.5 + - - +
294A LYS* 3.4 7.4 - - - +
296A VAL* 1.3 77.2 - - - +
298A ASP* 1.3 66.0 + - - +
300A ILE* 3.4 0.5 + - - +
301A GLU* 3.1 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 4.8 9.2 + - - -
294A LYS* 2.8 59.9 + - - +
295A GLN* 3.4 19.2 + - - +
296A VAL 3.2 0.4 + - - -
297A ALA* 1.3 77.1 - - - +
299A LYS* 1.3 56.0 + - - +
301A GLU* 3.0 25.7 + - - +
302A GLU* 3.1 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A VAL* 4.5 6.5 - - + -
241A ASP* 3.6 21.2 + - + +
242A PHE 3.5 23.5 + - - +
243A VAL* 3.8 31.0 - - + +
295A GLN 3.4 4.3 + - - +
296A VAL 3.3 4.1 + - - +
298A ASP* 1.3 72.4 - - - +
300A ILE* 1.3 65.0 + - + +
302A GLU* 3.1 45.4 + - - +
303A ILE* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 5.1 4.5 - - + -
45A ALA* 5.3 2.5 - - + -
49A LEU* 3.7 27.8 - - + -
56A LEU* 4.3 10.1 - - + -
98A LEU* 4.0 26.0 - - + -
100A VAL* 4.2 17.5 - - + -
182A VAL* 5.0 6.3 - - + -
296A VAL* 3.2 30.8 + - + +
297A ALA 3.7 6.5 - - - +
299A LYS* 1.3 76.8 - - + +
301A GLU* 1.3 64.1 + - - +
303A ILE* 3.6 7.4 + - - +
304A LEU* 2.9 56.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 4.3 11.3 - - + +
52A LYS* 3.1 51.4 + - - +
54A ILE* 4.3 15.9 - - + +
297A ALA 3.1 10.2 + - - +
298A ASP* 3.0 15.4 + - - +
300A ILE* 1.3 78.1 - - - +
302A GLU* 1.3 65.5 + - - +
304A LEU 3.2 8.7 + - - -
305A ASN* 3.1 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 4.0 8.3 - - - +
298A ASP 3.1 4.6 + - - +
299A LYS* 3.1 49.5 + - - +
301A GLU* 1.3 79.8 - - - +
303A ILE* 1.3 62.3 + - - +
305A ASN* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 5.1 4.0 - - + -
180A LYS* 3.9 43.6 + - + -
181A ARG 5.3 0.4 - - - +
182A VAL* 4.1 16.2 - - + -
241A ASP* 3.1 48.0 - - + +
299A LYS* 3.1 27.3 + - + +
300A ILE* 3.8 4.0 - - - +
302A GLU* 1.3 75.3 - - - +
304A LEU* 1.3 68.7 + - + +
305A ASN 3.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.5 17.3 - - + -
54A ILE* 3.6 38.4 - - + -
56A LEU* 4.3 8.3 - - + -
97A GLN* 5.8 2.0 - - - +
98A LEU* 4.5 13.7 - - + -
180A LYS* 5.0 8.5 - - + +
300A ILE* 2.9 48.0 + - + +
301A GLU 3.2 1.7 + - - +
303A ILE* 1.3 89.6 - - + +
305A ASN* 1.3 65.5 + - - +
----------------------------------------------------------
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