Contacts of the helix formed by residues 246 - 259 (chain F) in PDB entry 1XSK
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 THR 246 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F GLY* 4.4 1.1 - - - -
244F GLY 3.3 0.8 - - - -
245F PRO* 1.3 90.8 - - + +
247F PRO* 1.3 75.7 - - + +
248F LYS 3.8 1.6 + - - -
249F ALA* 2.8 24.1 + - - +
250F VAL* 3.0 16.2 + - - +
596F PRO* 4.7 15.0 - - + -
3003F SO4 2.5 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 247 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F MET* 3.4 25.0 - - + +
202F THR 4.6 6.5 - - - +
203F ASN* 5.3 2.2 - - - -
205F GLY* 4.8 4.7 - - - +
245F PRO 4.6 1.3 - - - +
246F THR* 1.3 88.2 - - - +
248F LYS* 1.3 61.2 + - - +
250F VAL* 3.3 8.6 + - + +
251F LEU* 3.1 29.2 + - - +
592F MET* 3.8 32.3 - - + +
593F MET* 4.0 20.9 - - + +
596F PRO* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F THR* 3.1 1.8 + - - -
247F PRO* 1.3 79.9 - - - +
249F ALA* 1.3 57.6 + - - +
251F LEU* 3.6 7.2 + - - +
252F ASP* 3.1 26.2 + - - +
583F ARG* 3.7 14.8 + - - +
585F THR* 4.1 24.2 + - + +
589F ARG* 3.8 9.0 - - - +
593F MET* 3.8 30.9 + - + +
594F GLU* 3.0 40.8 + - - +
612F ASP* 3.5 14.6 + - - -
3003F SO4 3.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F ASP 4.4 0.2 - - - -
244F GLY* 3.3 28.9 - - - +
245F PRO* 4.7 1.8 - - + -
246F THR* 2.8 20.2 + - - +
248F LYS* 1.3 76.2 - - - +
250F VAL* 1.3 66.7 + - - +
252F ASP* 3.2 5.5 + - - +
253F ARG* 3.1 28.4 + - - +
583F ARG* 4.0 9.4 - - - +
3003F SO4 4.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F PHE* 4.0 17.3 - - + -
201F MET* 4.4 7.4 - - + -
205F GLY 3.4 31.0 - - - +
206F TYR* 3.7 7.2 - - - +
207F GLY* 3.6 26.9 - - - +
242F ILE* 4.0 11.3 - - + +
243F ASP 4.0 7.4 - - - +
244F GLY* 3.5 6.7 - - - +
246F THR 3.0 14.9 + - - +
247F PRO* 3.3 9.6 + - + +
249F ALA* 1.3 75.0 - - - +
251F LEU* 1.3 59.2 + - - +
253F ARG* 3.0 6.2 + - - +
254F TYR* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F PHE* 4.1 14.4 - - + -
201F MET* 3.8 22.4 - - + -
247F PRO 3.1 15.3 + - - +
248F LYS* 3.9 6.3 - - - +
250F VAL* 1.3 78.7 - - - +
252F ASP* 1.3 50.2 + - - +
254F TYR* 3.8 6.1 - - + -
255F THR* 2.6 40.5 + - + +
501F GLY 3.8 18.4 - - - +
502F LEU* 3.9 15.5 - - - +
504F GLY* 4.2 14.4 - - - +
583F ARG 3.5 2.7 - - - +
584F GLY 4.1 12.3 - - - +
585F THR* 5.2 0.9 - - - +
586F PRO* 4.0 19.3 - - + -
593F MET* 4.0 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LYS 3.1 15.0 + - - +
249F ALA* 3.4 12.3 - - - +
250F VAL 3.1 0.4 - - - -
251F LEU* 1.3 76.5 - - - +
253F ARG* 1.3 60.3 + - + +
256F ARG* 3.1 20.9 + - - +
260F ARG* 2.9 34.5 + - - -
582F ALA 4.4 0.3 - - - +
583F ARG* 2.7 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLN* 3.4 7.9 + - - +
62F GLU* 3.2 52.6 + - - -
63F GLY* 3.8 17.1 - - - -
64F ILE* 3.9 7.3 - - + +
107F ASN* 5.9 0.8 + - - -
242F ILE* 3.5 17.7 - - + -
243F ASP* 2.7 40.7 + - - +
244F GLY* 2.8 20.6 + - - -
249F ALA* 3.1 12.9 + - - +
250F VAL 3.0 3.2 + - - +
252F ASP* 1.3 80.3 - - + +
254F TYR* 1.3 58.6 + - - +
256F ARG* 3.3 7.1 + - - +
257F PHE* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F ILE* 3.4 24.4 - - - +
199F PHE* 3.6 50.0 - + + -
209F LEU* 4.2 9.9 - - + -
242F ILE* 4.0 17.4 - - + +
250F VAL 2.8 18.8 + - - +
251F LEU* 4.1 7.6 - - + +
253F ARG* 1.3 69.5 - - - +
255F THR* 1.3 64.9 + - + +
257F PHE* 3.1 5.8 + + - +
258F THR* 2.7 64.3 + - + -
470F VAL* 3.9 14.0 - - - +
473F GLN* 4.4 7.0 + - - -
503F SER 3.3 22.5 + - - -
504F GLY* 4.0 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F LEU* 2.6 25.5 + - - +
254F TYR* 1.3 78.6 - - + +
256F ARG* 1.3 56.9 + - - +
258F THR* 4.3 2.0 - - - -
259F GLY* 2.8 49.3 + - - +
260F ARG* 2.7 34.9 + - - +
261F PRO* 3.8 3.8 - - + -
473F GLN* 4.9 1.1 - - - +
504F GLY* 3.7 33.0 - - - +
584F GLY* 3.5 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 256 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLN* 3.2 31.8 - - - +
85F ASN* 3.4 16.3 + - - +
87F LEU* 6.4 0.7 - - - -
252F ASP* 3.1 25.2 + - - +
253F ARG* 3.6 9.2 - - - +
254F TYR 3.2 0.2 - - - -
255F THR* 1.3 78.7 + - - +
257F PHE* 1.3 61.6 + - - +
260F ARG* 3.3 34.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 257 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 3.6 28.9 - - + -
61F GLN* 3.5 16.1 + - - +
64F ILE* 3.9 13.2 - - + -
84F LEU* 3.6 25.6 - - + -
85F ASN* 2.8 59.9 + - - -
86F ILE* 4.1 1.6 - - + -
209F LEU* 3.8 14.4 - - + -
240F PHE* 3.8 38.6 - + + -
242F ILE* 4.6 7.6 - - + -
253F ARG 2.9 18.1 + - - +
254F TYR* 3.4 3.6 - - - +
256F ARG* 1.3 78.3 - - - +
258F THR* 1.3 69.3 + - + +
259F GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 258 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PRO* 4.2 15.4 - - - +
84F LEU* 4.1 6.7 - - + +
85F ASN* 4.4 3.6 - - - -
209F LEU* 4.1 7.0 - - + -
254F TYR* 2.7 54.0 + - + +
257F PHE* 1.3 89.3 - - + +
259F GLY* 1.3 55.4 + - - +
470F VAL* 3.9 22.2 - - + -
471F GLY* 3.4 19.9 - - - -
473F GLN* 2.9 20.1 + - - -
474F LYS* 4.4 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F ASN* 4.2 8.5 - - - +
255F THR* 2.8 28.7 + - - +
257F PHE 3.7 1.2 - - - -
258F THR* 1.3 76.8 + - - +
260F ARG* 1.3 62.3 + - - -
473F GLN* 3.2 22.8 + - - +
474F LYS* 3.7 22.4 - - - -
----------------------------------------------------------
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