Contacts of the helix formed by residues 221 - 235 (chain B) in PDB entry 3SRF
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
----------------------------------------------------------
115B GLY 5.3 3.6 + - - -
116B PRO* 6.2 1.1 - - - -
218B PRO* 4.1 22.6 + - - -
219B ALA 4.0 1.2 - - - -
220B VAL* 1.3 75.7 - - - +
222B GLU* 1.3 69.6 + - - +
223B LYS* 3.6 9.2 + - - +
224B ASP* 3.0 33.7 + - - -
225B ILE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO* 5.1 5.4 - - - +
221B SER* 1.3 81.5 - - - +
223B LYS* 1.3 76.6 + - + +
225B ILE* 3.7 17.1 + - + +
226B GLN* 3.6 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 3.8 11.8 + - - -
76B SER 5.9 0.4 - - - -
80B HIS* 6.1 0.6 - - - -
114B LYS* 3.7 33.9 - - + +
221B SER* 3.1 8.5 - - - +
222B GLU* 1.3 91.9 + - + +
224B ASP* 1.3 66.1 + - - +
226B GLN* 3.3 8.4 + - - +
227B ASP* 3.1 47.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 4.0 11.7 + - - +
114B LYS* 3.5 17.0 + - - +
115B GLY* 3.3 39.3 + - - -
219B ALA 3.9 5.4 - - - +
220B VAL* 4.0 10.1 - - + -
221B SER* 3.0 37.6 + - - +
223B LYS* 1.3 75.0 - - - +
225B ILE* 1.3 60.3 + - - +
227B ASP* 3.2 11.4 + - - +
228B LEU* 3.0 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B VAL* 4.1 17.9 - - + +
221B SER 2.9 20.3 + - - +
222B GLU* 3.7 18.8 - - + +
223B LYS 3.2 0.2 - - - -
224B ASP* 1.3 75.5 - - - +
226B GLN* 1.3 64.5 + - - +
228B LEU* 3.2 4.1 + - - +
229B LYS* 3.0 51.8 + - - +
252B GLU* 5.3 4.0 - - - +
256B VAL* 4.2 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS* 3.2 24.4 - - + +
222B GLU 3.6 13.1 + - - +
223B LYS* 3.3 9.3 + - - +
225B ILE* 1.3 86.9 - - - +
227B ASP* 1.3 61.3 + - - +
229B LYS* 4.0 19.5 - - - +
230B PHE* 3.1 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 3.2 36.8 - - + +
80B HIS* 2.9 24.0 + - - -
111B LEU* 3.3 20.1 - - + +
113B THR* 5.4 2.5 - - + -
114B LYS 4.6 1.7 + - - -
223B LYS* 3.1 40.3 + - - +
224B ASP* 3.2 22.6 + - - +
226B GLN* 1.3 77.8 - - - +
228B LEU* 1.3 57.2 + - + +
230B PHE* 3.5 4.4 - - - +
231B GLY 3.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 4.3 3.8 - - + -
113B THR* 4.1 16.8 - - + -
220B VAL* 4.2 17.9 - - + -
224B ASP* 3.0 20.2 + - + +
225B ILE 3.2 4.0 + - - +
227B ASP* 1.3 75.0 - - - +
229B LYS* 1.3 65.6 + - - +
230B PHE 3.2 0.4 - - - -
231B GLY* 3.0 12.4 + - - +
232B VAL* 3.1 19.0 + - - +
239B VAL* 3.8 40.2 - - + -
253B VAL* 3.9 25.6 - - + +
256B VAL* 4.0 25.4 - - + -
257B LEU* 4.2 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ILE* 3.0 39.3 + - + +
226B GLN* 4.0 21.5 - - - +
228B LEU* 1.3 74.9 - - - +
230B PHE* 1.3 62.8 + - - +
232B VAL* 3.1 20.0 + - - +
233B GLU* 3.2 15.5 + - - +
256B VAL* 4.9 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.1 21.3 - + - -
80B HIS* 3.1 58.6 - + + +
83B HIS* 4.4 8.7 - - + -
84B ALA* 3.7 15.9 - - + -
87B ILE* 4.8 2.9 - - + -
111B LEU* 5.3 0.2 - - + -
226B GLN 3.1 16.9 + - - +
227B ASP 3.5 5.4 - - - +
228B LEU 3.2 0.2 - - - -
229B LYS* 1.3 80.0 - - - +
231B GLY* 1.3 61.1 + - - +
233B GLU* 3.7 20.8 + - - +
234B GLN* 3.1 65.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.7 21.5 - - - +
227B ASP 3.1 7.7 + - - -
228B LEU* 3.0 9.8 + - - -
230B PHE* 1.3 78.1 - - - +
232B VAL* 1.3 58.7 + - - +
235B ASP 3.1 3.6 + - - -
236B VAL* 2.9 47.7 + - - +
257B LEU* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU 3.3 16.6 - - - +
229B LYS* 3.1 10.8 + - - +
231B GLY* 1.3 76.9 - - - +
233B GLU* 1.3 58.8 + - - +
235B ASP* 3.1 19.9 + - - +
256B VAL 5.4 0.9 - - - +
257B LEU* 3.8 33.4 - - + +
260B LYS* 3.6 39.7 - - + +
261B GLY* 3.8 12.6 - - - +
264B ILE* 4.2 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS 3.2 11.0 + - - +
230B PHE* 3.8 30.1 - - + +
232B VAL* 1.3 75.4 - - - +
234B GLN* 1.3 66.3 + - + +
235B ASP* 3.1 8.3 + - - +
260B LYS* 6.1 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 3.9 15.1 - - - +
87B ILE* 3.4 41.8 - - + +
91B ARG* 2.7 39.0 + - - +
230B PHE* 3.1 62.1 + - + +
231B GLY 4.0 3.8 - - - +
233B GLU* 1.3 80.3 + - + +
235B ASP* 1.3 57.6 + - - +
236B VAL* 4.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 3.0 15.1 + - - +
231B GLY 3.1 0.6 + - - -
232B VAL* 3.1 17.1 + - - +
233B GLU 3.1 3.1 - - - +
234B GLN* 1.3 83.0 - - - +
236B VAL* 1.3 71.6 + - - +
237B ASP* 3.8 7.8 + - - +
264B ILE* 5.6 2.3 - - - +
457B GLN* 4.4 13.0 + - - -
460B ARG* 4.1 17.5 + - - -
----------------------------------------------------------
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