Contacts of the helix formed by residues 218 - 232 (chain A) in PDB entry 4R54
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 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLN* 4.1 16.2 - - + -
209A ILE 3.1 28.5 + - - +
211A VAL 3.4 10.3 - - - +
212A PHE* 3.6 32.5 - - + +
213A THR* 3.9 1.8 - - - -
217A TYR* 1.3 77.4 - - - +
219A TYR* 1.3 65.8 + - - +
220A GLU* 3.8 1.0 - - - +
221A GLU* 2.9 41.7 + - - +
222A MET* 3.0 22.7 + - - +
243A CYS* 4.8 0.3 - - - +
306B ARG* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 3.6 22.9 - - - +
211A VAL* 2.9 44.8 + - + +
212A PHE 4.1 5.6 - - - -
213A THR* 3.5 30.1 - - + +
218A THR* 1.3 73.7 - - - +
220A GLU* 1.3 56.7 + - - +
222A MET* 3.8 3.1 - - + +
223A LYS* 2.9 45.2 + - + +
226A LYS* 5.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 2.8 42.3 + - - +
129A SER* 3.4 6.4 + - - -
155A GLN* 3.4 16.1 + - - +
209A ILE* 3.2 47.7 + - + +
210A ASP* 3.8 2.7 - - + +
218A THR* 3.1 2.6 + - - +
219A TYR* 1.3 76.3 - - - +
221A GLU* 1.3 62.8 + - - +
223A LYS* 3.3 19.5 + - - +
224A MET* 3.2 23.4 + - - +
243A CYS* 3.6 21.1 - - + -
404A ACT 3.8 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.3 16.5 - - + +
218A THR* 2.9 35.7 + - - +
220A GLU* 1.3 77.4 - - - +
222A MET* 1.3 62.6 + - - +
224A MET* 3.3 6.2 + - - +
225A THR* 3.2 23.0 + - - -
241A ALA* 3.4 30.1 + - + +
242A THR* 3.5 2.7 - - - -
243A CYS* 3.0 41.7 + - - +
306B ARG* 2.9 36.6 + - - -
308B ARG* 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A THR* 4.1 19.1 - - + +
215A ASN* 3.4 26.0 - - - +
217A TYR* 3.7 19.5 - - + -
218A THR 3.0 19.0 + - - +
219A TYR* 4.0 6.7 - - + +
221A GLU* 1.3 75.0 - - - +
223A LYS* 1.3 58.5 + - - +
225A THR* 3.3 11.8 + - + -
226A LYS* 2.8 58.1 + - + +
311B LEU* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 4.0 9.9 - - - -
99A ARG* 3.6 12.1 - - - +
127A ASN* 4.6 6.5 - - + -
130A THR* 4.3 0.2 - - - -
210A ASP* 3.2 26.6 + - - -
219A TYR* 2.9 36.5 + - + +
220A GLU* 3.3 25.3 + - - +
221A GLU 3.4 0.2 - - - -
222A MET* 1.3 75.0 - - - +
224A MET* 1.3 58.1 + - - +
226A LYS* 4.5 9.6 - - - +
227A GLU* 2.8 52.2 + - - +
405A 3JM 2.7 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 4.5 2.7 - - - +
129A SER* 3.8 19.1 - - - +
130A THR* 3.5 18.4 + - - +
133A MET* 3.9 20.9 - - + -
151A VAL* 3.7 23.1 - - + -
153A THR* 3.8 11.4 - - + -
220A GLU* 3.2 11.4 + - - +
221A GLU 3.5 7.9 - - - +
222A MET 3.2 0.2 - - - -
223A LYS* 1.3 76.2 - - - +
225A THR* 1.3 59.5 + - - +
228A THR* 2.7 34.6 + - - -
239A VAL* 4.4 3.6 - - + -
241A ALA* 4.0 11.2 - - + -
243A CYS* 3.6 28.3 - - - -
254A GLU* 3.8 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 6.0 0.3 - - - -
221A GLU 3.2 11.6 + - - -
222A MET* 3.5 18.2 - - + -
224A MET* 1.3 80.0 - - - +
226A LYS* 1.3 65.6 + - + +
228A THR* 3.6 2.6 + - - -
229A LYS* 3.4 44.6 + - - +
239A VAL* 2.9 40.7 + - + +
240A SER* 4.3 2.9 - - - -
241A ALA 4.7 0.3 + - - -
311B LEU* 3.7 19.7 - - + +
312B ASP* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLN* 4.0 36.2 - - + +
219A TYR* 5.3 13.1 - - - -
222A MET* 2.8 48.1 + - + +
223A LYS* 4.3 7.3 - - - +
225A THR* 1.3 78.9 - - + +
227A GLU* 1.3 64.5 + - - +
229A LYS* 3.4 10.8 + - + +
230A LYS* 3.3 21.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
99A ARG* 2.9 37.4 + - - +
100A GLN* 3.5 17.4 + - - +
106A LEU* 3.9 17.5 - - + -
126A PRO* 3.6 3.8 - - - +
127A ASN* 2.9 24.2 + - - +
130A THR* 3.2 21.3 + - + -
223A LYS* 2.8 41.5 + - - +
226A LYS* 1.3 70.5 - - - +
228A THR* 1.3 60.2 - - - +
230A LYS* 3.3 1.9 + - - +
231A ILE* 2.9 38.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.1 3.7 - - - +
133A MET* 3.5 11.8 - - - +
134A MET* 3.4 37.5 - - + +
149A ILE* 4.0 10.8 - - + -
224A MET 2.7 24.8 + - - -
225A THR 3.7 4.7 - - - -
227A GLU* 1.3 76.0 - - - +
229A LYS* 1.3 58.8 + - - +
231A ILE* 3.9 0.7 - - - +
232A MET* 2.9 41.1 + - - +
237A ILE* 4.5 6.1 - - + -
239A VAL* 3.8 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 3.4 37.3 + - - +
226A LYS* 3.8 10.5 - - + +
227A GLU 3.3 0.8 - - - -
228A THR* 1.3 81.4 - - - +
230A LYS* 1.3 57.4 + - - +
232A MET* 5.1 0.7 - - - -
233A GLU* 2.8 22.7 + - - -
234A ASP 2.9 30.9 + - - +
235A ASP* 3.1 39.3 + - + +
236A SER 4.9 0.2 - - - -
237A ILE* 3.0 31.4 + - + +
238A ALA* 4.6 4.0 - - - +
239A VAL* 4.9 2.9 - - + +
312B ASP* 4.8 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ARG 2.7 30.1 + - - +
100A GLN* 4.0 13.8 - - - +
101A ASN 3.0 22.0 + - - +
102A PRO* 4.5 3.4 - - - +
104A VAL 2.9 28.4 + - - -
105A PRO* 5.1 0.9 - - - -
106A LEU* 3.8 24.5 - - + +
112A ASN* 4.9 2.1 + - - -
226A LYS 3.3 13.0 + - - +
227A GLU 3.3 4.1 + - - +
229A LYS* 1.3 78.0 - - - +
231A ILE* 1.3 64.8 + - - +
233A GLU* 3.2 18.9 + - - +
235A ASP* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 3.7 24.5 - - + +
108A VAL* 4.3 7.4 - - + -
111A VAL* 3.8 25.2 - - + +
112A ASN* 3.7 30.8 + - - +
126A PRO* 3.7 27.8 - - + -
130A THR* 3.7 23.3 - - + -
134A MET* 3.9 22.2 - - + -
227A GLU* 2.9 23.1 + - + +
228A THR 3.9 2.0 - - - +
230A LYS* 1.3 76.7 - - - +
232A MET* 1.3 61.6 + - - +
233A GLU* 3.2 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A VAL* 5.0 2.9 - - + -
134A MET* 3.7 30.7 - - + +
137A LEU* 4.0 6.3 - - + -
138A GLU* 3.8 41.7 - - + +
141A ARG* 3.8 36.0 + - - +
146A LEU* 3.8 21.8 - - + -
228A THR* 2.9 22.8 + - - +
229A LYS 4.5 0.7 - - - +
231A ILE* 1.3 76.6 - - + +
233A GLU* 1.3 72.4 + - - +
234A ASP* 3.1 5.6 + - - +
237A ILE* 3.9 25.8 - - + -
----------------------------------------------------------
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