Contacts of the helix formed by residues 209 - 228 (chain A) in PDB entry 4GL5
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 ASP 209 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 1.3 74.1 - - - +
210A GLU* 1.3 69.7 + - - +
211A SER* 3.5 18.9 + - - -
212A ALA* 2.9 30.1 + - + +
213A ILE* 3.0 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A HIS* 2.6 40.3 + - - -
193A ARG* 3.6 25.9 - - + +
196A LEU* 3.9 10.3 - - + -
197A ASP* 4.1 19.8 - - + +
208A LEU* 3.4 24.5 + - + +
209A ASP* 1.3 70.1 + - - +
211A SER* 1.3 67.4 + - - +
212A ALA 2.9 1.4 + - - -
213A ILE 3.0 11.3 + - - -
214A VAL* 3.0 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU* 5.5 3.6 + - - -
193A ARG* 3.6 36.7 + - - +
209A ASP* 3.5 15.6 + - - -
210A GLU* 1.3 79.2 - - - +
212A ALA* 1.3 58.0 + - - +
214A VAL* 3.8 4.7 + - - +
215A VAL* 3.2 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 2.9 26.7 + - + +
210A GLU 2.9 2.0 + - - -
211A SER* 1.3 76.9 - - - +
213A ILE* 1.3 67.7 + - + +
215A VAL* 3.2 17.2 - - - +
216A LYS* 3.2 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.8 26.0 - - + -
208A LEU* 3.7 19.5 - - + -
209A ASP* 3.0 22.4 + - + +
210A GLU 3.0 2.0 + - - -
212A ALA* 1.3 75.0 - - + +
214A VAL* 1.3 56.3 + - - +
216A LYS* 3.0 11.0 + - + +
217A ILE* 2.7 48.1 + - + +
251A LEU* 4.2 9.9 - - + -
254A ALA* 3.8 28.7 - - + +
255A ILE* 5.5 5.4 - - + -
258A LEU* 4.6 12.8 - - + -
304A LEU* 6.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A THR* 4.8 14.6 - - + -
192A ARG* 3.7 36.1 - - + +
193A ARG* 3.8 32.5 - - + +
196A LEU* 4.0 15.9 - - + -
210A GLU 3.0 18.3 + - - +
211A SER 3.9 5.8 - - - +
213A ILE* 1.3 76.9 - - - +
215A VAL* 1.3 64.2 + - + +
217A ILE* 3.1 11.8 + - + +
218A GLN* 3.0 28.7 + - - +
308A PRO* 5.9 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER 3.2 15.9 - - - +
212A ALA* 3.2 20.2 - - - +
214A VAL* 1.3 74.1 - - + +
216A LYS* 1.3 62.7 + - + +
218A GLN* 3.4 19.7 - - + +
219A GLY* 3.2 17.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ALA* 3.2 29.2 - - - +
213A ILE* 3.0 11.4 + - + +
215A VAL* 1.3 75.2 - - + +
217A ILE* 1.3 65.6 + - - +
218A GLN 3.1 1.6 - - - -
219A GLY* 2.9 4.7 + - - +
220A TYR* 2.8 22.9 + - - +
247A SER 4.6 2.4 - - - +
250A ASP* 4.0 38.9 + - + +
251A LEU* 3.9 23.0 - - + +
254A ALA* 4.3 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.7 32.1 - - + -
213A ILE* 2.7 27.4 + - + +
214A VAL* 3.5 9.4 - - - +
216A LYS* 1.3 70.9 - - - +
218A GLN* 1.3 59.5 + - + +
220A TYR* 3.3 6.9 + - - +
221A PHE* 2.9 26.2 + - - +
251A LEU* 3.7 19.0 - - + +
304A LEU* 4.8 1.3 - - + -
305A ILE* 3.8 37.7 - - + +
308A PRO* 4.1 21.8 - - + -
309A ASP* 4.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 3.1 33.1 - - - +
214A VAL* 3.0 15.7 + - - +
215A VAL* 3.4 30.6 - - - +
216A LYS 3.1 0.2 - - - -
217A ILE* 1.3 78.3 - - + +
219A GLY* 1.3 51.1 + - - +
221A PHE* 3.0 8.3 + - - +
222A ASP* 2.7 46.7 + - - +
309A ASP* 5.5 0.7 - - - -
483A GLU* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A VAL 3.2 7.6 + - - -
216A LYS* 2.9 8.7 + - - -
218A GLN* 1.3 77.0 - - - +
220A TYR* 1.3 55.8 + - - +
222A ASP* 3.4 9.3 + - - +
223A ALA* 3.0 29.8 + - - +
244A TYR* 5.6 0.2 - - - -
247A SER* 3.6 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 2.6 35.0 + - + +
127A MET* 3.5 28.6 - - + +
216A LYS 2.8 11.2 + - - +
217A ILE 3.5 9.0 - - - +
218A GLN 3.2 0.2 - - - -
219A GLY* 1.3 72.4 - - - +
221A PHE* 1.3 61.3 + - - +
223A ALA* 3.2 5.3 + - - +
224A TRP* 2.9 35.9 + + + +
247A SER* 4.4 5.4 + - - +
248A VAL* 4.1 31.9 - - + -
251A LEU* 3.7 26.5 - - + -
252A LYS* 5.2 0.2 - - - -
298A GLN* 3.2 19.9 + - - -
301A LEU* 3.8 18.8 - - + -
305A ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE 2.9 10.7 + - - +
218A GLN* 3.6 8.1 - - - +
220A TYR* 1.3 76.4 - - - +
222A ASP* 1.3 69.9 + - - +
223A ALA 3.0 0.3 + - - -
224A TRP* 3.2 29.1 + + - +
225A GLN* 2.8 51.5 + - + +
309A ASP* 3.4 28.0 - - - +
477A LEU* 4.2 20.6 - - + -
478A SER* 3.5 22.0 - - - -
480A HIS* 4.3 8.3 - + - -
601A G29 3.7 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLN* 2.7 33.3 + - - +
219A GLY* 3.4 13.2 - - - +
221A PHE* 1.3 76.1 - - - +
223A ALA* 1.3 56.6 + - - +
225A GLN* 3.6 17.4 + - - +
226A ALA* 3.0 26.3 + - - +
244A TYR* 4.4 8.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.3 4.7 - - + -
219A GLY 3.0 17.7 + - - +
220A TYR* 3.5 4.3 - - - +
221A PHE 3.1 0.4 - - - -
222A ASP* 1.3 71.9 - - - +
224A TRP* 1.3 66.7 + - - +
225A GLN 3.1 1.3 - - - -
226A ALA* 2.8 12.8 + - - +
227A LEU* 2.9 17.3 + - + +
244A TYR* 3.7 45.9 - - + +
247A SER* 4.7 0.9 - - - -
248A VAL* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.5 32.8 - - + +
127A MET* 3.6 22.6 - - + -
133A ILE* 3.8 14.4 - - + -
134A PHE* 3.4 42.5 - + - -
220A TYR* 2.9 23.3 + + + +
221A PHE* 3.5 22.2 - + - +
223A ALA* 1.3 70.7 - - - +
225A GLN* 1.3 63.0 + - - +
227A LEU* 4.0 0.7 - - - +
228A LEU* 3.1 37.6 + - + +
305A ILE* 3.9 13.7 - - + -
477A LEU* 3.7 17.8 - - + +
601A G29 3.3 48.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.6 8.5 - - - +
221A PHE* 2.8 35.0 + - + +
222A ASP* 3.6 19.6 + - - +
224A TRP* 1.3 75.8 - - - +
226A ALA* 1.3 62.9 + - - +
228A LEU* 4.0 8.4 + - - +
229A ILE* 5.4 0.5 + - - +
474A ILE* 4.4 3.7 - - - +
476A ASP* 3.2 40.2 + - - +
477A LEU* 3.5 33.6 + - + +
480A HIS* 3.2 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASP 3.0 15.0 + - - +
223A ALA 2.8 9.3 + - - +
225A GLN* 1.3 80.3 - - - +
227A LEU* 1.3 59.0 + - - +
228A LEU 3.8 0.3 + - - -
229A ILE* 4.7 2.3 + - - +
230A LYS* 3.2 33.5 + - - +
244A TYR* 3.5 40.6 - - + +
476A ASP* 5.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 3.8 2.6 - - - -
121A GLY* 3.6 27.5 - - - +
124A CYS* 3.8 33.4 - - + -
125A ILE* 4.3 11.7 - - + -
223A ALA* 2.9 17.9 + - + +
224A TRP 4.6 0.9 - - - +
226A ALA* 1.3 78.5 - - + +
228A LEU* 1.3 67.5 + - - +
229A ILE 3.1 4.2 + - - -
230A LYS* 3.5 11.3 + - - -
234A PHE* 3.8 26.7 - - + -
235A PHE* 4.3 9.5 - - + -
241A TYR* 4.3 5.2 - - + -
244A TYR* 3.7 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 5.0 5.6 - - + -
116A PHE 3.6 22.7 - - - +
117A GLY* 3.5 1.5 - - - -
118A SER* 2.8 28.4 + - - +
121A GLY* 5.3 3.4 - - - -
122A LEU* 3.8 23.3 - - + +
125A ILE* 5.1 0.9 - - + -
134A PHE* 3.9 11.4 - - + -
224A TRP* 3.1 43.4 + - + +
225A GLN* 4.0 8.7 + - - +
226A ALA 3.5 1.8 - - - -
227A LEU* 1.3 76.9 - - - +
229A ILE* 1.3 67.0 + - + +
374A MET* 3.8 25.6 - - + -
477A LEU* 4.6 9.9 - - + -
----------------------------------------------------------
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