Contacts of the helix formed by residues 227 - 238 (chain F) in PDB entry 4HHM
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 ASN 227 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ASP* 3.1 37.6 + - + +
221F GLU* 5.5 0.3 - - - +
226F LEU* 1.3 73.9 - - - +
228F PHE* 1.3 63.7 + - - +
229F PRO* 2.8 36.6 - - - +
230F HIS* 2.9 43.5 + - + +
231F GLY* 3.0 18.5 + - - -
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Residues in contact with PHE 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ILE* 4.6 0.9 - - + -
216F PRO* 3.6 26.7 - - + -
217F GLU 3.4 18.8 - - - -
218F VAL* 3.2 46.7 - - + +
221F GLU* 3.5 25.8 - - + -
222F GLN* 4.2 18.0 + - + +
226F LEU 3.4 6.2 + - - -
227F ASN* 1.3 70.6 - - - +
229F PRO* 1.3 66.9 - - + +
231F GLY* 3.1 2.1 + - - -
232F ILE* 2.8 57.2 + - + +
244F ILE* 4.0 7.6 - - + -
267F ALA* 5.6 2.4 - - + +
271F LEU* 3.6 24.7 - - + -
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Residues in contact with PRO 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E VAL* 5.5 0.2 - - - -
227F ASN* 2.8 19.1 - - - +
228F PHE* 1.3 90.1 - - + +
230F HIS* 1.3 60.8 + - + +
232F ILE* 4.3 6.7 - - + -
233F ALA* 3.0 24.3 + - - +
267F ALA* 3.5 34.8 - - + +
270F TRP* 3.9 25.8 - - + +
271F LEU* 3.9 15.0 - - + +
274F LEU* 3.3 15.6 - - + +
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Residues in contact with HIS 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E GLY 5.3 0.7 - - - -
143E ALA* 4.8 18.9 - - + +
145E SER 5.3 4.0 + - - -
146E GLY* 5.7 4.4 + - - -
149E LYS* 5.3 5.1 + - + +
151E VAL* 3.5 33.0 - - + +
190E ASP* 3.8 31.0 + - + +
191E ILE 5.1 3.8 + - - +
192E LEU* 4.4 14.5 - - + +
194E PRO* 6.5 1.3 - - + -
227F ASN* 2.9 43.1 + - + +
228F PHE 3.2 0.2 - - - -
229F PRO* 1.3 77.6 - - + +
231F GLY* 1.3 66.9 + - - +
233F ALA* 3.1 16.3 + - - +
234F GLN* 3.1 12.6 + - - +
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Residues in contact with GLY 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E HIS* 4.8 13.7 - - - -
196F ILE* 3.6 26.9 - - - +
221F GLU* 5.6 1.3 - - - -
227F ASN 3.0 14.0 + - - -
228F PHE* 3.6 3.1 - - - -
230F HIS* 1.3 73.8 - - - +
232F ILE* 1.3 64.7 + - - +
234F GLN* 3.2 9.1 + - - +
235F ALA* 3.1 17.2 + - - +
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Residues in contact with ILE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ILE* 3.9 0.4 - - + +
216F PRO* 3.7 25.1 - - + -
228F PHE* 2.8 59.8 + - + +
229F PRO* 3.7 5.2 - - + +
231F GLY* 1.3 70.3 - - - +
233F ALA* 1.3 57.5 + - - +
235F ALA* 2.9 7.6 + - - +
236F LEU* 2.9 38.3 + - + +
241F LEU* 4.1 17.0 - - + -
244F ILE* 3.7 12.8 - - + -
271F LEU* 4.1 7.9 - - + -
274F LEU* 3.5 19.7 - - + -
275F LEU* 4.2 9.6 - - + -
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Residues in contact with ALA 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E VAL* 3.4 28.9 - - + -
152E ARG* 3.5 16.9 - - + +
155E LEU* 4.6 1.3 - - - -
229F PRO 3.0 15.6 + - - +
230F HIS 3.1 12.8 - - - +
232F ILE* 1.3 78.2 - - - +
234F GLN* 1.3 55.2 + - - +
236F LEU* 3.4 3.9 + - - +
237F TRP* 2.8 29.8 + - - +
274F LEU* 3.9 15.0 - - + -
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Residues in contact with GLN 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E VAL* 5.5 0.4 - - + -
155E LEU* 3.7 26.4 - - + +
193E LEU* 3.9 15.4 + - - +
194E PRO* 5.0 0.2 - - - +
198E HIS* 3.1 57.5 + - + +
201E ALA* 3.7 18.4 - - - +
202E PHE* 3.9 8.7 - - - +
196F ILE* 5.7 0.7 - - + -
200F LEU* 4.5 10.5 - - + +
230F HIS 3.1 10.8 + - - +
231F GLY* 3.2 8.9 + - - +
233F ALA* 1.3 76.6 - - - +
235F ALA* 1.3 57.7 + - - +
237F TRP* 3.2 9.2 + - + +
238F ALA* 2.9 30.2 + - + +
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Residues in contact with ALA 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ILE* 4.3 7.0 - - + -
200F LEU* 4.2 12.0 - - - +
214F VAL* 4.1 24.5 - - + -
216F PRO* 5.0 0.9 - - + -
231F GLY 3.1 11.3 + - - +
232F ILE* 2.9 14.3 + - - +
234F GLN* 1.3 77.1 - - - +
236F LEU* 1.3 60.9 + - - +
238F ALA* 3.3 2.1 + - - -
239F GLY 3.1 3.8 + - - -
240F LYS* 2.8 29.3 + - - +
241F LEU* 4.2 16.4 - - + +
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Residues in contact with LEU 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 3.9 21.2 + - - +
232F ILE* 2.9 33.2 + - + +
233F ALA* 3.7 4.0 - - - +
235F ALA* 1.3 73.8 - - - +
237F TRP* 1.3 61.7 + - - +
239F GLY* 2.9 20.4 + - - -
241F LEU* 3.4 33.0 - - + -
274F LEU* 3.8 27.4 - - + -
275F LEU* 4.6 3.8 - - + -
278F ALA* 4.3 17.0 - - + -
280F TRP* 3.9 17.9 - - + -
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Residues in contact with TRP 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ARG* 3.7 31.9 + - + +
155E LEU* 3.6 42.0 - - + -
156E ASP* 2.7 29.4 + - - -
159E LYS* 4.1 17.9 - - + -
202E PHE* 3.8 41.1 - + - -
205E ARG* 2.8 64.1 + - + +
233F ALA 2.8 18.5 + - - +
234F GLN* 3.4 12.3 - - + +
236F LEU* 1.3 78.6 - - - +
238F ALA* 1.3 61.5 + - + +
239F GLY 3.5 0.2 + - - -
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Residues in contact with ALA 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E ARG* 4.1 24.3 - - + +
200F LEU* 4.8 9.2 - - + -
234F GLN* 2.9 16.6 + - + +
235F ALA* 3.9 1.8 - - - +
236F LEU 3.1 0.2 - - - -
237F TRP* 1.3 78.6 - - + +
239F GLY* 1.3 63.5 + - - +
240F LYS* 3.4 27.9 - - + +
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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
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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