Contacts of the helix formed by residues 213 - 228 (chain F) in PDB entry 1SHZ
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 GLU 213 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F VAL* 3.7 25.9 - - - +
211F ASP* 2.6 18.3 + - - +
212F GLU* 1.3 76.6 - - - +
214F LYS* 1.3 64.0 + - - +
215F SER 3.0 3.9 + - - -
216F ALA* 3.1 18.1 + - + +
217F ALA* 3.1 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F GLU* 4.5 19.5 + - - +
72F PRO* 5.7 6.7 - - + -
109F VAL* 3.5 35.0 - - + +
110F LEU* 4.8 3.4 - - + -
209F SER* 2.9 35.0 + - - -
210F THR* 5.2 4.2 - - - +
211F ASP* 2.6 33.3 + - + +
213F GLU* 1.3 74.1 - - - +
215F SER* 1.3 56.7 + - - +
217F ALA* 3.5 1.7 + - - +
218F VAL* 3.1 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F GLN* 3.7 27.2 + - - +
206F HIS* 5.8 0.2 - - - -
208F ILE* 4.0 18.1 - - - +
209F SER* 4.7 9.3 - - - +
211F ASP 3.3 7.6 + - - -
212F GLU* 3.4 20.5 + - - -
214F LYS* 1.3 77.3 - - - +
216F ALA* 1.3 73.6 + - - +
218F VAL* 3.1 5.2 + - - +
219F VAL* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205F GLN* 4.9 9.0 - - - +
212F GLU 4.7 5.2 - - - +
213F GLU* 3.1 14.8 + - + +
215F SER* 1.3 81.9 + - - +
217F ALA* 1.3 58.0 + - - +
219F VAL* 3.4 7.8 + - - +
220F ASN* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F VAL* 3.4 41.5 - - + -
110F LEU* 4.5 9.3 - - + +
213F GLU* 3.1 12.3 + - - +
214F LYS 3.6 3.1 - - - +
215F SER 3.1 0.2 - - - -
216F ALA* 1.3 77.4 - - - +
218F VAL* 1.3 63.2 + - - +
220F ASN* 3.4 8.6 + - - +
221F ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 218 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ALA* 5.5 4.9 - - + -
72F PRO* 3.6 32.8 - - + -
76F LEU* 4.2 14.4 - - + -
110F LEU* 3.8 12.6 - - + -
208F ILE* 4.2 28.5 - - + -
214F LYS* 3.1 20.3 + - + +
215F SER 3.4 7.9 - - - +
217F ALA* 1.3 77.9 - - - +
219F VAL* 1.3 62.5 + - - +
221F ALA* 3.3 4.0 + - - +
222F ILE* 3.1 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LEU* 5.8 2.9 - - + +
201F LEU* 4.9 7.0 - - + -
202F GLU* 3.8 35.9 - - + +
205F GLN* 3.9 28.3 - - + +
208F ILE* 3.7 20.6 - - + -
215F SER 3.1 17.4 + - - +
216F ALA* 3.7 6.1 - - - +
217F ALA 3.3 0.2 - - - -
218F VAL* 1.3 74.1 - - - +
220F ASN* 1.3 64.9 + - - +
222F ILE* 3.1 11.2 + - + +
223F GLY* 2.9 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 220 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216F ALA* 2.7 30.4 + - - +
217F ALA* 3.9 6.4 - - - +
219F VAL* 1.3 79.0 - - - +
221F ALA* 1.3 59.2 + - - +
223F GLY* 3.0 16.4 + - - +
224F LEU* 3.2 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LEU* 3.8 27.9 - - + +
80F HIS* 2.9 41.1 + - + +
110F LEU* 3.9 13.5 - - + -
217F ALA 3.0 18.2 + - - +
218F VAL 3.4 7.0 - - - +
219F VAL 3.2 0.2 - - - -
220F ASN* 1.3 77.6 - - - +
222F ILE* 1.3 58.3 + - - +
224F LEU* 4.3 0.9 - - - -
225F TYR* 4.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F MET* 4.6 6.5 - - - -
63F LEU* 4.5 27.4 - - + +
67F ALA* 6.0 3.1 - - + -
76F LEU* 3.7 18.8 - - + -
79F LEU* 6.4 0.9 - - + -
198F LEU* 4.1 15.7 - - + -
201F LEU* 4.3 26.9 - - + -
218F VAL* 3.1 32.1 - - + +
219F VAL* 3.1 7.7 + - - +
221F ALA* 1.3 76.5 - - - +
223F GLY* 1.3 67.4 + - - +
224F LEU 3.3 0.4 - - - -
225F TYR* 4.2 3.3 - - + +
226F MET* 3.0 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 223 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LEU* 5.2 8.3 - - - +
219F VAL 2.9 13.7 + - - -
220F ASN* 3.0 6.6 + - - -
222F ILE* 1.3 78.6 - - - +
224F LEU* 1.3 57.0 + - - +
226F MET* 3.5 4.6 - - - +
227F ARG* 2.8 36.8 + - - +
231F VAL 4.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F HIS* 4.1 26.9 - - + +
83F MET* 4.1 17.7 - - + +
98F ASP* 5.6 9.4 - - + +
220F ASN* 3.2 25.6 + - + +
221F ALA* 5.6 0.2 - - - -
222F ILE 3.3 0.4 - - - -
223F GLY* 1.3 72.6 - - - +
225F TYR* 1.3 68.0 + - - +
227F ARG* 3.0 34.5 + - - +
228F HIS* 2.9 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 225 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F LYS* 2.6 38.6 + - - +
54F ARG* 5.8 0.2 - - - +
59F LEU* 3.6 26.7 - - + -
79F LEU* 3.1 56.8 - - + -
80F HIS* 4.6 3.6 - - + -
82F ASP* 3.9 16.9 + - + -
83F MET* 3.5 25.7 - - + -
221F ALA 4.1 9.8 + - - +
222F ILE* 3.7 6.8 + - + +
224F LEU* 1.3 79.8 - - - +
226F MET* 1.3 65.0 + - + +
228F HIS* 3.1 23.9 + + - +
229F LEU* 3.5 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F PRO* 3.7 13.0 - - + +
59F LEU* 4.7 18.4 - - - -
60F MET* 3.7 33.4 - - + +
63F LEU* 5.9 0.2 - - - -
194F ALA* 3.8 3.4 - - + -
198F LEU* 3.8 23.1 - - + -
222F ILE* 3.0 36.6 + - + +
223F GLY 3.5 3.6 - - - +
225F TYR* 1.3 74.7 - - + +
227F ARG* 1.3 60.8 + - - +
228F HIS 3.0 1.3 - - - -
229F LEU* 2.8 28.6 + - - +
230F GLY 3.2 0.2 + - - -
231F VAL* 3.0 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F MET* 5.9 1.4 - - - +
223F GLY* 2.8 16.4 + - - +
224F LEU* 3.3 44.1 + - - +
226F MET* 1.3 74.9 - - - +
228F HIS* 1.3 56.5 + - - +
230F GLY* 2.8 23.2 + - - -
231F VAL 3.5 13.9 + - - +
232F ARG* 4.6 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 228 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ASP* 5.1 4.5 - - - -
83F MET* 3.7 52.6 + - + -
224F LEU 2.9 11.8 + - - +
225F TYR* 3.1 27.8 - + - +
227F ARG* 1.3 77.0 - - - +
229F LEU* 1.3 70.6 - - + +
----------------------------------------------------------
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