Contacts of the helix formed by residues 215 - 230 (chain A) in PDB entry 1U1H
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 GLU 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ASP 4.1 1.4 + - - -
214A LEU* 1.3 78.5 - - - +
216A GLY* 1.3 65.5 + - - +
217A GLN* 2.6 38.3 + - - +
218A LYS* 3.2 56.1 + - + +
219A LEU* 3.3 11.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU* 1.3 74.1 - - - +
217A GLN* 1.3 66.4 + - - +
219A LEU* 3.5 11.4 + - - +
220A GLN* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU* 5.4 0.7 - - - +
215A GLU* 2.6 44.6 + - - +
216A GLY* 1.3 82.1 - - - +
218A LYS* 1.3 59.9 + - + +
220A GLN* 3.3 19.8 - - - +
221A ALA* 3.5 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 4.3 23.9 - - + +
176A GLU* 5.5 7.6 - - - +
178A LEU* 3.9 23.5 - - + +
214A LEU* 4.1 27.6 - - + +
215A GLU* 3.2 40.1 + - + +
217A GLN* 1.3 74.7 - - + +
219A LEU* 1.3 61.2 + - - +
220A GLN 3.0 1.8 - - - -
221A ALA* 2.7 27.7 + - - +
222A PHE* 3.5 9.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 4.0 22.0 - - + -
214A LEU* 4.1 29.1 - - + +
215A GLU 3.3 9.6 + - - +
216A GLY* 3.9 11.7 - - - +
218A LYS* 1.3 76.3 - - - +
220A GLN* 1.3 63.9 + - - +
222A PHE* 2.9 25.4 + - - +
223A THR 3.4 3.3 + - - -
250A GLU* 3.9 15.5 - - + +
251A ALA* 3.7 44.0 - - + +
254A THR* 3.5 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLY 3.1 13.6 + - - +
217A GLN* 3.3 15.3 - - - +
218A LYS 3.0 0.6 - - - -
219A LEU* 1.3 77.4 - - - +
221A ALA* 1.3 61.4 + - - +
223A THR* 3.2 25.9 + - - +
224A GLY* 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 4.5 5.6 - - + -
178A LEU* 3.7 34.3 - - + -
181A LEU* 3.9 15.4 - - + +
217A GLN 3.5 4.2 + - - +
218A LYS 2.7 21.5 + - - +
220A GLN* 1.3 70.9 - - - +
222A PHE* 1.3 64.7 + - - +
224A GLY* 3.5 1.4 + - - -
225A ALA* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 3.2 48.0 - - + -
160A SER* 4.4 1.3 - - - -
163A LEU* 4.2 9.4 - - + -
207A GLU* 3.6 18.8 - - + -
209A VAL* 4.5 3.8 - - + -
210A LEU* 3.4 49.1 - - + -
214A LEU* 3.8 22.9 - - + -
218A LYS 3.5 14.1 - - - -
219A LEU* 2.9 14.4 + - - +
221A ALA* 1.3 77.1 - - - +
223A THR* 1.3 64.6 + - - +
225A ALA* 2.9 13.3 + - - +
226A TYR* 2.9 23.1 + + + -
254A THR* 4.0 11.2 - - + -
258A LEU* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A LEU 3.4 2.5 + - - -
220A GLN* 3.2 29.7 + - - +
222A PHE* 1.3 77.4 - - - +
224A GLY* 1.3 62.6 + - - +
226A TYR* 3.6 1.7 + - - +
227A ALA* 3.0 25.7 + - + +
254A THR* 3.4 22.9 + - - +
257A SER* 5.7 3.9 + - - +
258A LEU* 4.0 12.2 - - + +
259A LYS* 5.4 9.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A LEU* 5.8 0.2 - - - -
185A LEU* 5.6 0.2 - - - -
220A GLN* 3.0 18.2 + - - -
221A ALA* 4.0 2.0 - - - -
223A THR* 1.3 78.0 - - - +
225A ALA* 1.3 57.5 + - - +
227A ALA* 3.2 6.6 + - - +
228A GLU* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 4.9 2.9 - - + -
159A VAL* 4.6 6.3 - - + -
181A LEU* 4.3 23.8 - - + +
185A LEU* 4.1 18.1 - - + +
221A ALA 3.0 14.0 + - - +
222A PHE* 2.9 11.5 + - - +
224A GLY* 1.3 75.1 - - - +
226A TYR* 1.3 69.0 + - + +
228A GLU* 3.2 5.4 + - - +
229A LEU* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 4.1 9.0 - - + +
159A VAL* 4.3 11.2 - - + -
205A LEU* 3.7 29.6 - - + +
207A GLU* 2.5 41.5 + - + +
222A PHE* 2.9 22.8 + + - +
223A THR 4.3 1.6 - - - +
225A ALA* 1.3 77.1 - - + +
227A ALA* 1.3 61.0 + - - +
229A LEU* 3.5 12.0 - - + +
230A GLU 2.8 24.6 + - - -
233A LEU* 4.5 8.5 - - + -
240A VAL* 3.9 19.2 - - + +
258A LEU* 4.0 20.2 - - + -
259A LYS* 3.4 33.1 - - - +
261A VAL* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A THR* 3.0 22.2 + - + +
224A GLY* 3.6 7.2 - - - +
225A ALA 3.2 0.2 - - - -
226A TYR* 1.3 78.8 - - - +
228A GLU* 1.3 61.7 + - - +
229A LEU 3.4 0.7 + - - -
230A GLU* 3.5 14.7 + - - +
231A SER 4.8 1.0 + - - -
259A LYS* 3.8 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU* 4.0 21.1 - - + -
189A LYS* 2.9 42.8 + - - +
224A GLY 2.9 16.7 + - - +
225A ALA 3.5 4.9 - - - +
227A ALA* 1.3 77.6 - - - +
229A LEU* 1.3 56.8 + - - +
230A GLU 3.6 0.2 - - - -
231A SER* 5.1 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PRO* 4.4 23.6 - - + -
185A LEU* 3.7 32.3 - - + +
188A TYR* 4.9 8.3 - - + -
189A LYS* 4.2 21.1 - - + +
192A ILE* 4.8 14.1 - - + -
205A LEU* 5.9 4.0 - - + -
225A ALA 3.0 15.2 + - - +
226A TYR* 3.2 15.2 + - + +
227A ALA 3.2 0.4 - - - -
228A GLU* 1.3 83.4 - - - +
230A GLU* 1.3 65.4 + - - +
231A SER 3.4 2.0 - - - -
232A THR* 2.9 19.1 + - - -
233A LEU* 3.0 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A TYR 2.8 12.7 + - - +
227A ALA 3.5 14.8 + - - +
229A LEU* 1.3 76.0 - - - +
231A SER* 1.3 65.3 + - - +
233A LEU* 3.0 19.9 + - - +
234A SER* 3.1 11.4 + - - -
259A LYS* 3.6 39.2 - - + +
260A GLY* 4.0 13.8 + - - +
----------------------------------------------------------
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