Contacts of the helix formed by residues 293 - 310 (chain F) in PDB entry 1SXG
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 293 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F ILE* 3.7 17.5 - - + -
291F VAL* 3.5 18.7 - - + +
292F GLN* 1.3 78.7 - - + +
294F MET* 1.3 53.2 + - - +
295F TYR* 3.2 3.4 - - - -
296F ASP* 3.0 24.2 + - + +
297F ILE* 2.7 43.6 + - + +
321F LEU* 4.2 10.8 - - + -
322F PRO 3.7 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 294 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F ILE 4.0 1.3 - - - +
74F PHE* 3.3 48.5 - - + +
77F GLU* 3.4 38.8 - - + +
78F LEU* 3.4 27.0 - - + +
275F ASP 3.6 17.0 - - - +
276F ASN 4.5 4.3 - - - +
277F THR* 3.2 31.4 - - + -
292F GLN* 2.4 31.8 + - - +
293F PRO* 1.3 65.6 - - - +
295F TYR* 1.3 61.3 + - - +
297F ILE* 3.5 9.8 + - - +
298F GLY 3.1 16.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 295 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F GLU* 4.0 21.7 + - - +
80F ARG* 3.5 42.8 - - + +
81F GLY* 3.5 31.2 + - - -
84F ASP* 3.4 27.9 + - - +
85F ILE* 5.2 3.6 - - - +
293F PRO 3.2 1.0 - - - -
294F MET* 1.3 77.9 - - - +
296F ASP* 1.3 79.6 + - - +
298F GLY 3.1 2.8 + - - -
299F ALA* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 296 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F PRO* 3.0 24.6 + - + +
295F TYR* 1.3 92.9 - - - +
297F ILE* 1.3 54.8 + - - +
299F ALA* 3.2 5.0 + - - +
300F VAL* 2.7 42.6 + - + +
321F LEU* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F LEU* 3.6 16.8 - - + -
145F ALA* 4.3 0.7 - - + -
146F ALA* 3.9 18.2 - - + +
157F VAL* 3.7 29.4 - - + +
158F THR* 4.6 9.0 - - - -
159F ILE* 4.3 13.0 - - + -
292F GLN* 3.8 36.3 - - + +
293F PRO* 2.7 25.8 + - + +
294F MET* 3.6 7.6 - - - +
296F ASP* 1.3 72.5 - - - +
298F GLY* 1.3 64.8 + - - +
301F ALA* 3.1 20.1 + - - +
321F LEU* 3.7 19.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 298 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F LEU* 3.5 24.2 - - - -
81F GLY 3.9 5.6 - - - -
82F ILE* 3.9 14.9 - - - +
294F MET 3.1 5.5 + - - -
295F TYR 3.1 6.5 + - - -
297F ILE* 1.3 79.0 - - - +
299F ALA* 1.3 63.8 + - - +
301F ALA* 2.9 16.1 + - - +
302F MET* 2.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F GLY 3.6 16.4 - - - +
85F ILE* 3.6 25.8 - - + +
295F TYR* 2.9 33.2 + - + +
296F ASP* 3.5 9.2 - - - +
298F GLY* 1.3 70.6 - - - +
300F VAL* 1.3 56.9 + - + +
302F MET 3.5 0.3 + - - -
303F ARG* 2.9 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 300 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F VAL* 3.9 22.7 - - + -
296F ASP* 2.7 28.5 + - + +
299F ALA* 1.3 70.5 - - + +
301F ALA* 1.3 60.8 + - - +
303F ARG* 3.3 21.6 - - + +
304F LEU* 2.8 27.3 + - + +
319F VAL* 3.9 26.0 - - + -
321F LEU* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ILE* 5.6 0.2 - - + -
121F ILE* 4.5 7.9 - - + -
143F VAL* 3.8 20.0 - - + +
145F ALA* 4.4 12.3 - - + -
157F VAL* 3.4 22.0 - - + +
297F ILE 3.1 13.2 + - - +
298F GLY* 2.9 10.1 + - - +
300F VAL* 1.3 74.4 - - - +
302F MET* 1.3 55.6 + - - +
303F ARG 3.0 1.3 - - - -
304F LEU* 3.0 7.1 + - - +
305F LEU* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL* 4.0 16.6 - - + -
82F ILE* 3.4 34.5 - - + +
85F ILE* 3.8 24.9 - - + +
86F ALA* 3.9 5.2 - - - +
91F TYR* 4.2 13.0 - - + -
93F ILE* 4.5 1.8 - - - -
121F ILE* 3.6 24.3 - - - +
298F GLY 2.9 13.9 + - - +
301F ALA* 1.3 75.5 - - - +
303F ARG* 1.3 57.0 + - - +
305F LEU* 3.3 8.3 + - + +
306F THR* 2.9 54.1 + - - +
309F MET* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F ILE* 4.2 26.8 - - + +
88F MET* 5.8 6.1 - - - +
89F TYR* 5.0 11.8 + - + +
299F ALA* 2.9 34.4 + - - +
300F VAL* 3.3 23.7 - - + +
302F MET* 1.3 76.2 - - - +
304F LEU* 1.3 58.4 + - - +
306F THR* 3.0 10.7 + - - -
307F LYS* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F VAL* 4.0 22.0 - - + -
155F PRO* 4.1 8.7 - - + -
156F SER 4.6 6.7 - - - +
157F VAL* 5.7 1.8 - - + -
300F VAL* 2.8 22.7 + - + +
301F ALA* 3.6 5.2 - - - +
303F ARG* 1.3 73.2 - - - +
305F LEU* 1.3 61.4 + - - +
307F LYS* 3.1 23.3 - - + +
308F TYR* 3.2 17.7 + - + -
314F VAL* 3.3 34.3 - - + -
316F SER 3.9 7.4 - - - +
317F SER 3.5 23.8 - - - +
319F VAL* 4.6 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL* 3.5 32.3 - - + -
119F GLY* 3.9 3.8 - - - -
120F ILE 3.7 20.2 - - - +
121F ILE* 3.5 14.4 - - + -
141F PRO* 3.7 38.8 - - + +
142F VAL 4.0 2.0 - - - +
143F VAL* 3.9 13.6 - - + +
301F ALA 2.7 20.3 + - - +
302F MET* 3.5 8.5 - - + +
304F LEU* 1.3 71.4 - - - +
306F THR* 1.3 54.5 + - - +
308F TYR* 3.0 7.2 + - + +
309F MET* 2.5 52.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F TYR* 3.6 46.0 - - + +
91F TYR* 4.1 11.4 - - + -
302F MET* 2.9 30.1 + - - +
303F ARG* 3.2 11.7 - - - +
305F LEU* 1.3 72.5 - - - +
307F LYS* 1.3 69.1 + - - +
309F MET* 3.8 10.1 - - - +
310F ASN* 2.8 41.5 + - - +
312F GLU* 5.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F ARG 2.8 12.9 + - - +
304F LEU* 3.1 20.4 - - + +
306F THR* 1.3 81.0 - - - +
308F TYR* 1.3 52.7 + - - +
310F ASN 3.7 0.2 + - - -
311F LYS 3.6 0.7 + - - -
312F GLU* 2.8 62.1 + - - +
313F THR* 2.4 37.9 + - - +
314F VAL* 3.2 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F PRO* 3.7 27.6 - - + +
142F VAL 5.2 3.4 - - - -
143F VAL* 5.5 1.3 - - + -
155F PRO* 3.3 43.6 - - + +
304F LEU* 3.2 23.5 + - + -
305F LEU* 3.0 9.3 + - + +
307F LYS* 1.3 76.2 - - - +
309F MET* 1.3 57.5 - - - +
310F ASN 3.1 1.8 - - - -
311F LYS* 2.3 34.3 + - - +
312F GLU 4.5 6.5 - - - -
314F VAL* 3.3 42.1 - - + +
317F SER* 3.9 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL* 3.6 22.0 - - + -
91F TYR* 3.0 51.7 + - + +
118F ASP* 3.1 45.9 - - + +
119F GLY* 3.5 1.8 - - - -
141F PRO* 3.9 10.6 - - + +
302F MET* 3.9 14.8 - - + -
305F LEU* 2.5 45.4 + - + +
306F THR* 3.6 6.1 - - - +
308F TYR* 1.3 72.1 - - - +
310F ASN* 1.3 57.8 + - - +
311F LYS* 3.4 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F TYR* 5.2 4.9 - - - -
91F TYR* 3.8 16.3 + - - -
306F THR* 2.8 35.4 + - - +
309F MET* 1.3 70.5 - - - +
311F LYS* 1.3 72.3 + - - +
312F GLU* 2.4 37.5 + - + +
----------------------------------------------------------
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