Contacts of the helix formed by residues 218 - 232 (chain A) in PDB entry 1R4L
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 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR 5.5 0.2 - - - -
208A GLU* 4.9 7.1 + - - -
210A ASN* 5.8 0.4 - - - +
216A ASP* 4.5 8.2 + - - -
217A TYR* 1.3 95.8 - - - +
219A ARG* 1.3 66.1 + - - +
220A GLY 4.4 4.3 - - - -
221A GLN* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS 4.5 6.5 + - - -
196A TYR* 3.6 22.4 - - - +
197A GLU* 4.3 6.3 + - - -
201A ASP* 2.6 63.6 + - - +
204A ARG* 3.7 31.2 - - + +
205A GLY* 3.4 17.7 - - - +
208A GLU* 2.7 49.5 + - + +
218A SER* 1.3 71.1 - - - +
220A GLY* 1.3 61.2 - - - +
221A GLN 2.8 10.5 + - - -
222A LEU* 3.1 19.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 5.4 0.2 + - - -
204A ARG* 4.8 3.8 - - - -
218A SER* 4.4 3.0 - - - -
219A ARG* 1.3 78.1 - - - +
221A GLN* 1.3 62.4 + - - +
223A ILE* 3.6 23.4 - - - +
224A GLU* 3.8 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.3 30.5 - - + +
218A SER* 3.2 33.4 + - - +
219A ARG 2.8 1.2 + - - -
220A GLY* 1.3 73.4 - - - +
222A LEU* 1.3 57.2 + - - +
223A ILE 2.5 16.0 + - - -
224A GLU* 2.8 49.4 + - - +
225A ASP* 2.9 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.9 16.4 - - + +
207A TYR* 3.5 49.4 - - + -
217A TYR* 3.0 29.1 + - + +
218A SER 4.5 0.2 - - - +
219A ARG 3.1 12.4 + - - +
221A GLN* 1.3 75.3 - - - +
223A ILE* 1.3 67.8 + - - +
225A ASP* 3.5 1.4 + - + +
226A VAL* 3.0 30.9 + - + +
461A TRP* 3.7 31.6 - - + -
513A ILE* 4.5 9.9 - - + -
517A THR* 4.3 11.7 - - + -
579A MET* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.4 43.1 - - - +
220A GLY* 3.6 15.5 - - - +
221A GLN 2.5 5.9 + - - -
222A LEU* 1.3 72.6 - - - +
224A GLU* 1.3 56.1 + - + +
225A ASP 2.6 1.6 + - - -
226A VAL* 2.5 33.4 + - - +
227A GLU* 3.1 29.5 + - + +
458A LYS* 5.2 10.3 - - + +
461A TRP* 4.6 26.5 - - + -
465A LYS* 3.9 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLY 3.9 10.5 - - - +
221A GLN* 2.8 39.3 + - - +
223A ILE* 1.3 76.9 - - + +
225A ASP* 1.3 57.1 + - - +
227A GLU* 3.0 18.6 - - + +
228A HIS* 3.2 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.0 32.0 + - - +
221A GLN* 2.9 24.4 + - - +
222A LEU 3.7 2.7 - - - +
223A ILE 2.6 6.7 + - - -
224A GLU* 1.3 74.7 - - - +
226A VAL* 1.3 58.5 + - - +
228A HIS* 4.2 5.3 - - - +
229A THR* 2.9 26.7 + - - +
578A ASN* 3.1 35.4 + - - +
579A MET* 3.2 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.0 31.4 + - + +
223A ILE* 2.5 14.6 + - - +
225A ASP* 1.3 71.8 - - - +
227A GLU* 1.3 66.3 + - - +
229A THR* 2.8 20.8 - - - +
230A PHE* 2.8 14.0 + - - +
454A TYR* 4.6 19.3 - - + -
461A TRP* 4.9 5.2 - - + -
513A ILE* 4.4 23.3 - - + -
516A TYR* 3.5 41.5 - - + -
517A THR* 5.1 1.3 - - + -
579A MET* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.1 23.8 + - + +
224A GLU* 3.0 31.9 - - + +
226A VAL* 1.3 75.8 - - - +
228A HIS* 1.3 57.4 + - - +
230A PHE* 2.8 33.2 + - - +
231A GLU* 3.5 10.7 + - - +
454A TYR* 2.9 28.0 + - - -
458A LYS* 5.0 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU 3.2 14.0 + - - +
225A ASP* 4.2 6.7 - - - +
227A GLU* 1.3 78.3 - - - +
229A THR* 1.3 70.5 + - - +
230A PHE 2.9 1.6 + - - -
231A GLU* 3.0 27.5 + - + +
232A GLU* 3.8 24.6 + - + +
582A ARG* 5.2 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP 2.9 19.8 + - - +
226A VAL* 2.8 22.2 - - - +
228A HIS* 1.3 87.6 + - - +
230A PHE* 1.3 58.3 + - - +
231A GLU 3.4 0.4 + - - -
232A GLU* 4.0 4.2 + - - -
233A ILE* 3.3 20.8 + - - +
516A TYR* 2.6 31.5 + - + +
520A LEU* 2.8 29.4 - - - +
579A MET* 3.7 11.8 + - + -
581A VAL* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A VAL 2.8 12.4 + - - +
227A GLU* 2.8 17.3 + - - +
229A THR* 1.3 75.8 - - - +
231A GLU* 1.3 67.6 + - - +
233A ILE* 3.0 28.0 + - + +
234A LYS* 3.1 46.6 + - + +
237A TYR* 5.9 2.9 - + - -
450A LEU 4.7 1.8 - - - -
451A PRO* 4.0 28.7 - - + -
454A TYR* 3.2 43.3 - + + -
484A ILE* 3.8 23.8 - - + -
516A TYR* 3.7 14.1 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU 3.8 11.3 - - - +
228A HIS* 3.0 18.3 + - + +
230A PHE* 1.3 75.0 - - - +
232A GLU* 1.3 59.9 + - + +
233A ILE 2.6 15.3 + - - -
234A LYS* 2.8 35.7 + - - +
235A PRO* 3.1 12.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 3.8 23.7 + - + +
229A THR* 4.0 4.7 + - - +
230A PHE 3.5 0.6 - - - -
231A GLU* 1.3 81.1 - - + +
233A ILE* 1.3 59.2 + - - +
234A LYS 3.5 0.2 - - - -
235A PRO* 4.1 11.7 - - - +
236A LEU* 5.0 2.8 + - - +
581A VAL* 3.6 28.2 - - + +
582A ARG* 2.5 46.0 + - - -
585A LEU* 3.5 25.5 - - + +
----------------------------------------------------------
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