Contacts of the helix formed by residues 224 - 244 (chain A) in PDB entry 4H3H
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 GLN 224 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG 5.9 0.9 - - - -
220A HIS 5.3 3.6 - - - +
222A TYR 3.4 16.7 + - - +
223A ILE* 1.3 73.7 - - - +
225A TYR* 1.3 66.8 + - - +
226A ASN* 4.5 3.4 - - + +
227A VAL* 3.2 32.1 + - + +
228A LEU* 3.2 23.4 + - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PRO* 4.6 12.8 - - - +
213A LEU* 3.3 59.1 - - + +
214A ASP* 4.5 5.1 - - - -
216A ILE* 3.6 29.1 - - + +
217A PRO 4.6 2.4 + - - +
218A ARG* 3.7 63.3 + - - +
223A ILE 3.6 4.8 + - - -
224A GLN* 1.3 70.9 - - - +
226A ASN* 1.3 71.4 + - - +
228A LEU* 3.3 4.4 + - - +
229A TRP* 2.9 37.3 + + + +
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Residues in contact with ASN 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG* 3.9 12.1 + - - -
224A GLN* 3.2 4.1 - - + +
225A TYR* 1.3 94.2 - - - +
227A VAL* 1.3 67.9 + - + +
229A TRP* 3.5 7.2 + - - +
230A GLU* 3.2 28.6 + - + +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLN* 3.2 40.6 + - + +
226A ASN* 1.3 81.1 - - + +
228A LEU* 1.3 59.8 + - + +
230A GLU* 3.2 7.4 + - - +
231A GLU* 3.0 47.7 + - + +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A TYR* 4.0 11.9 - - - +
141A LEU* 3.8 8.5 - - + -
158A TRP* 4.5 15.0 - - + +
194A LEU* 3.7 33.5 - - + +
213A LEU* 4.2 7.9 - - + -
216A ILE* 3.5 23.8 - - + -
223A ILE* 3.4 30.7 - - + -
224A GLN 3.2 11.7 + - - +
225A TYR 3.7 6.1 - - - +
227A VAL* 1.3 77.5 - - + +
229A TRP* 1.3 66.9 + - - +
231A GLU* 3.2 19.8 + - - +
232A GLY 2.9 18.9 + - - -
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Residues in contact with TRP 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU 3.6 13.7 - - - -
195A SER* 3.8 19.5 - - - -
196A PRO* 4.2 1.8 - - + -
213A LEU* 3.9 20.7 - - + +
225A TYR* 2.9 25.0 + + + +
226A ASN* 3.6 9.6 - - - +
228A LEU* 1.3 76.5 - - - +
230A GLU* 1.3 73.0 + - - +
232A GLY 3.3 1.4 + - - -
233A LYS* 3.1 50.7 + - + +
269A MET* 3.1 35.7 - - + -
270A PHE* 4.0 17.5 - + - -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 3.2 16.2 + - + +
227A VAL* 3.2 8.9 + - - +
228A LEU 3.2 0.2 - - - -
229A TRP* 1.3 87.4 - - + +
231A GLU* 1.3 56.8 - - - +
233A LYS* 2.7 44.3 + - - +
234A ALA* 2.9 30.2 + - - +
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A TYR* 4.7 5.7 + - - -
162A SER* 4.4 14.3 + - - -
190A LEU* 5.2 2.6 - - + +
194A LEU* 4.0 11.0 - - + +
227A VAL* 3.0 36.7 + - + +
228A LEU* 3.2 23.7 + - - +
230A GLU* 1.3 74.2 - - + +
232A GLY* 1.3 58.7 + - - +
234A ALA* 3.7 6.1 - - + +
235A ALA* 2.8 30.5 + - - +
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.8 13.6 - - - +
194A LEU* 3.9 24.8 - - - +
228A LEU 2.9 13.2 + - - -
229A TRP* 3.3 3.8 + - - -
231A GLU* 1.3 75.4 - - - +
233A LYS* 1.3 58.9 + - - +
235A ALA* 3.3 6.9 + - - +
236A LEU* 3.0 27.7 + - - +
270A PHE* 5.3 6.5 - - - -
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Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TRP* 3.1 59.0 + - + +
230A GLU* 2.7 42.3 + - - +
232A GLY* 1.3 77.8 - - - +
234A ALA* 1.3 56.3 + - - +
236A LEU* 3.1 9.7 + - - +
237A GLU* 2.9 28.0 + - - +
270A PHE* 4.7 10.3 - - + -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLU 2.9 18.6 + - - +
231A GLU* 3.9 7.4 - - + +
233A LYS* 1.3 76.8 - - - +
235A ALA* 1.3 61.6 + - - +
237A GLU* 3.3 8.4 + - - +
238A GLN* 3.0 29.8 + - + +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 4.5 10.7 - - + +
187A VAL* 3.9 12.4 - - + +
190A LEU* 4.0 24.5 - - + -
191A ILE* 3.7 16.8 - - + -
231A GLU 2.8 22.5 + - - +
232A GLY* 3.5 6.3 - - - +
234A ALA* 1.3 73.4 - - - +
236A LEU* 1.3 61.5 + - - +
238A GLN* 3.4 9.5 + - - +
239A LEU* 3.1 20.8 + - - +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.7 22.8 - - + +
232A GLY 3.0 13.5 + - - +
233A LYS* 3.1 9.8 + - - +
235A ALA* 1.3 74.4 - - - +
237A GLU* 1.3 62.8 + - - +
239A LEU* 3.2 5.0 + - + +
240A LEU* 3.0 40.1 + - + +
260A LEU* 4.0 26.5 - - + -
263A ILE* 4.5 7.6 - - + -
270A PHE* 3.5 47.8 - - + -
273A GLU* 4.3 17.3 - - + -
274A VAL* 5.8 1.6 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LYS 2.9 12.9 + - - +
234A ALA* 3.3 11.4 + - - +
236A LEU* 1.3 75.1 - - - +
238A GLN* 1.3 67.8 + - - +
240A LEU* 3.2 18.2 + - - +
241A LYS* 2.9 64.8 + - + +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 4.3 20.4 - - + +
170A LEU* 5.9 2.8 - - - +
172A LEU* 4.6 17.3 - - + +
173A ASP* 5.7 0.5 - - - +
187A VAL* 5.9 0.2 - - + -
234A ALA* 3.0 19.1 + - + +
235A ALA* 3.6 11.2 - - - +
237A GLU* 1.3 80.8 - - - +
239A LEU* 1.3 58.6 + - - +
241A LYS* 3.5 16.3 + - - +
242A PHE* 2.9 29.0 + - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 4.9 6.4 - - + +
184A ILE* 4.1 26.0 - - + -
187A VAL* 4.4 12.8 - - + -
188A GLU 5.1 2.2 - - - +
191A ILE* 3.9 20.9 - - + -
235A ALA 3.1 11.5 + - - +
236A LEU* 3.2 8.9 + - + +
238A GLN* 1.3 80.2 - - - +
240A LEU* 1.3 58.8 + - - +
242A PHE* 3.3 15.2 + - + +
243A MET* 3.0 33.4 + - - +
256A ALA* 4.1 14.4 - - + -
259A SER* 4.6 11.2 - - - -
260A LEU* 3.9 27.1 - - + -
263A ILE* 4.2 7.9 - - + -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.0 36.8 + - + +
237A GLU* 3.7 20.6 - - - +
239A LEU* 1.3 75.2 - - - +
241A LYS* 1.3 62.4 + - - +
243A MET* 3.3 19.4 + - - +
244A VAL* 3.6 13.9 + - - +
260A LEU* 4.0 22.7 - - + -
273A GLU* 4.2 28.9 - - + +
274A VAL* 6.1 0.2 - - + -
277A ALA* 3.8 28.0 - - + -
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLU* 2.9 47.7 + - + +
238A GLN* 3.6 15.7 - - - +
240A LEU* 1.3 73.2 - - - +
242A PHE* 1.3 65.7 + - - +
243A MET 3.2 0.7 + - - -
244A VAL* 3.2 22.1 + - - +
245A HIS* 3.3 9.9 + - - +
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.4 44.0 - - + -
173A ASP* 5.3 3.8 - - - -
180A ARG* 4.4 8.3 - - + -
184A ILE* 3.7 28.0 - - + -
238A GLN 2.9 18.1 + - - +
239A LEU* 3.3 20.2 + - + +
241A LYS* 1.3 74.3 - - - +
243A MET* 1.3 69.3 + - + +
245A HIS* 3.1 30.8 + - + +
248A ILE* 3.6 31.0 - - + +
252A ASN* 3.8 28.0 - - + -
256A ALA* 4.8 0.4 - - + -
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LEU* 3.0 21.4 + - - +
240A LEU* 3.5 12.3 - - - +
241A LYS 3.1 0.6 - - - -
242A PHE* 1.3 79.8 - - + +
244A VAL* 1.3 61.2 + - + +
245A HIS 3.3 1.3 + - - -
248A ILE* 3.8 23.8 - - + +
253A LEU* 4.0 17.4 - - + +
256A ALA* 3.6 32.5 - - + -
257A LEU* 3.8 29.8 - - + +
260A LEU* 3.5 33.7 - - + -
277A ALA* 4.8 10.1 - - + +
281A LEU* 5.4 5.9 - - + +
286A PRO* 5.1 3.5 - - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LEU 3.6 11.6 + - - +
241A LYS* 3.2 17.2 + - - +
243A MET* 1.3 81.4 - - + +
245A HIS* 1.3 65.4 + - - +
246A PRO* 3.3 6.4 - - - +
277A ALA* 6.1 0.7 - - - +
280A THR* 4.0 27.6 - - + -
281A LEU* 5.7 2.2 - - - +
286A PRO* 6.4 0.4 - - - -
332D GLN* 3.8 12.6 + - - +
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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
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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) + - + + + + + -
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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