Contacts of the helix formed by residues 221 - 235 (chain B) in PDB entry 3STJ
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 SER 221 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 3.7 10.3 - - - +
130B ALA 2.7 24.5 + - - -
132B SER* 3.2 13.9 + - - -
198B LEU* 3.3 30.1 + - - +
199B ILE* 2.9 18.8 + - - -
200B GLY* 4.0 3.1 - - - +
220B PRO* 1.4 71.1 - - - +
222B ASN* 1.3 57.9 + - - +
224B ALA* 3.9 5.6 - - - +
225B ARG* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA 3.4 2.2 + - - -
131B ASP* 2.8 24.4 + - - +
132B SER* 3.1 30.7 + - - +
133B ASP* 3.2 22.7 - - - +
220B PRO* 5.5 0.4 - - + -
221B SER* 1.3 75.0 - - - +
223B MET* 1.3 58.7 + - - +
225B ARG* 3.1 37.4 + - - +
226B THR* 2.8 33.3 + - - -
304B ARG* 6.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER* 5.0 7.2 - - - -
172B LEU* 5.2 6.1 - - - +
174B ASN* 3.6 39.7 - - + +
219B ILE* 4.0 17.5 - - + -
220B PRO* 3.1 21.5 + - + +
222B ASN* 1.3 76.1 - - - +
224B ALA* 1.4 64.7 + - - +
226B THR* 3.8 1.2 - - - -
227B LEU* 3.1 40.7 + - + +
303B SER* 3.8 18.6 - - - +
304B ARG* 4.6 6.1 - - + +
307B THR* 3.7 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 3.8 25.3 - - + +
113B ILE* 3.8 24.9 - - + -
198B LEU* 5.6 1.3 - - + -
201B ILE* 3.9 14.8 - - + -
219B ILE* 4.2 2.4 - - + +
220B PRO 3.0 15.4 + - - +
221B SER* 3.9 6.7 - - - +
223B MET* 1.4 74.5 - - - +
225B ARG* 1.4 52.9 + - - +
227B LEU* 3.5 1.4 + - - +
228B ALA* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.9 7.2 - - + -
78B LEU* 4.8 0.4 - - - +
129B ILE* 3.6 39.2 + - + +
130B ALA 3.4 17.6 + - - -
131B ASP* 4.4 3.2 - - - +
221B SER 2.8 21.7 + - - +
222B ASN* 3.1 47.6 + - - +
224B ALA* 1.4 69.2 - - - +
226B THR* 1.3 62.4 + - - +
228B ALA* 3.3 8.1 + - - +
229B GLN* 3.0 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN* 2.8 20.5 + - - +
223B MET 3.8 3.1 - - - -
225B ARG* 1.3 78.4 + - - +
227B LEU* 1.3 62.3 + - - +
229B GLN* 3.3 8.8 + - - +
230B GLN* 3.1 27.3 + - - +
307B THR* 3.4 31.9 - - + +
308B THR* 4.8 7.9 - - + +
309B GLU* 5.3 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 3.7 6.5 - - + +
111B SER* 3.3 29.2 - - - +
113B ILE* 4.0 22.7 - - + -
223B MET* 3.1 36.6 + - + +
224B ALA 3.9 3.1 - - - +
226B THR* 1.3 74.6 - - - +
228B ALA* 1.4 62.0 + - - +
230B GLN* 3.2 10.9 + - - +
231B LEU* 3.1 27.7 + - + +
237B ILE* 3.8 16.3 - - + +
239B ARG* 3.6 26.7 - - - +
307B THR* 4.2 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.1 24.2 - - + -
78B LEU* 4.3 7.4 - - + -
113B ILE* 4.9 0.6 - - - +
115B LEU* 4.2 17.3 - - + +
224B ALA 2.9 19.6 + - - +
225B ARG 3.4 5.6 - - - +
227B LEU* 1.4 74.8 - - - +
229B GLN* 1.4 56.3 + - - +
231B LEU* 3.1 13.8 + - - +
232B ILE* 2.9 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ARG* 3.0 19.1 + - + +
226B THR* 3.3 11.8 + - - +
228B ALA* 1.4 74.2 - - - +
230B GLN* 1.3 56.8 + - + +
232B ILE* 3.2 26.0 + - - +
233B ASP* 2.9 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 3.1 22.8 + - + +
227B LEU* 3.2 12.7 + - - +
229B GLN* 1.3 74.9 - - + +
231B LEU* 1.3 58.2 + - - +
233B ASP* 4.9 0.2 - - - -
234B PHE* 2.9 46.1 + - + -
236B GLU 3.0 18.7 - - - +
237B ILE* 3.5 15.4 - - - +
238B LYS 2.9 41.5 + - - +
239B ARG* 5.4 0.6 - - - +
307B THR 3.0 25.5 + - - +
309B GLU* 3.9 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.4 12.3 - - - +
106B GLY* 3.7 25.4 - - - +
107B SER* 3.5 30.5 - - - +
108B ASP 5.0 0.2 - - - +
113B ILE* 4.3 18.4 - - + +
115B LEU* 3.9 26.7 - - + +
227B LEU 3.1 20.4 + - - +
228B ALA* 3.1 6.5 + - - +
230B GLN* 1.3 75.2 - - - +
232B ILE* 1.4 60.0 + - - +
235B GLY* 3.0 23.9 + - - +
236B GLU* 3.8 28.0 - - - +
237B ILE* 4.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 6.2 0.9 - - + -
71B ASN* 6.1 0.9 - - - +
74B LYS* 5.5 6.1 - - - +
76B TYR* 3.9 40.6 + - + +
105B ILE* 4.6 3.7 - - - +
115B LEU* 3.4 24.0 - - + -
228B ALA* 2.9 22.8 + - + +
229B GLN* 3.2 33.8 + - - +
231B LEU* 1.4 76.5 - - - +
233B ASP* 1.4 74.8 + - - +
234B PHE 3.8 0.2 + - - -
235B GLY 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLN* 2.9 42.8 + - - +
232B ILE* 1.4 86.2 - - - +
234B PHE* 1.3 92.5 + - + +
309B GLU* 4.9 4.9 - - - +
229E GLN* 5.9 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLN* 2.9 34.4 + - + +
233B ASP* 1.3 100.7 - - + +
235B GLY* 1.3 59.3 + - - +
236B GLU* 3.0 32.0 + - + +
238B LYS* 4.0 35.7 - - + -
309B GLU* 3.9 34.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.8 16.5 - - - +
106B GLY* 3.6 16.8 - - - -
107B SER 4.7 0.7 + - - +
230B GLN 3.7 0.4 + - - -
231B LEU* 3.0 26.5 + - - -
232B ILE 4.8 0.4 + - - -
233B ASP 4.0 0.2 - - - -
234B PHE* 1.3 75.4 - - - +
236B GLU* 1.3 58.8 + - - +
----------------------------------------------------------
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