Contacts of the helix formed by residues 195 - 204 (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 THR 195 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E THR* 4.6 1.3 - - + -
198E HIS* 3.3 13.6 - - - -
226E LEU* 4.4 15.0 - - + -
182F PRO* 3.5 12.3 - - - +
193F LEU 3.3 1.2 + - - -
194F PRO* 1.3 93.1 - - + +
196F ILE* 1.3 66.5 + - - +
197F GLY 3.1 9.4 + - - -
198F HIS* 2.8 41.9 + - + +
199F ALA 3.0 9.4 + - - -
221F GLU* 3.6 13.7 - - - -
224F ALA* 5.0 2.9 - - + -
226F LEU* 4.0 18.2 - - + -
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Residues in contact with ILE 196 (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* 4.6 6.1 - - + +
182F PRO* 3.8 11.6 - - + +
195F THR* 1.3 72.0 - - - +
197F GLY* 1.3 64.1 + - - +
199F ALA* 3.4 1.1 + - - +
200F LEU* 2.9 45.4 + - + +
214F VAL* 4.4 7.9 - - + -
216F PRO* 3.6 33.4 - - + -
221F GLU* 3.2 32.6 + - + +
228F PHE* 4.6 1.3 - - + -
231F GLY* 3.6 39.9 - - - +
232F ILE* 3.9 4.3 - - + +
234F GLN* 5.7 0.4 - - + -
235F ALA* 4.3 9.0 - - + -
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Residues in contact with GLY 197 (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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197E GLY 2.9 20.6 - - - +
198E HIS* 3.5 35.5 + - - -
201E ALA* 3.8 0.6 - - - +
195F THR* 3.0 7.5 + - - -
196F ILE* 1.3 82.1 - - - +
198F HIS* 1.3 56.3 + - - +
200F LEU* 3.7 7.8 - - - +
201F ALA* 3.1 19.8 + - - +
234F GLN* 5.1 0.2 - - - -
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Residues in contact with HIS 198 (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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195E THR* 3.1 31.0 - - - -
196E ILE* 4.4 8.0 - - + +
197E GLY* 3.4 21.4 + - - -
221E GLU* 4.8 1.2 + - - -
226E LEU* 4.2 7.3 - - + +
231E GLY* 4.8 13.7 - - - -
234E GLN* 3.1 34.7 + - + +
193F LEU* 3.8 17.8 - - - +
194F PRO* 3.7 27.3 - - + +
195F THR* 2.8 36.2 + - + +
197F GLY* 1.3 69.2 - - - +
199F ALA* 1.3 59.7 + - - +
201F ALA* 3.6 1.5 - - - +
202F PHE* 3.0 24.9 + - - +
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Residues in contact with ALA 199 (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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180F ILE* 4.2 18.4 - - + -
182F PRO* 3.6 30.1 - - + -
193F LEU* 4.3 15.4 - - + +
195F THR 3.0 4.9 + - - -
196F ILE 3.9 1.3 - - - +
198F HIS* 1.3 73.1 - - - +
200F LEU* 1.3 67.1 + - - +
202F PHE* 3.2 3.1 + - - +
203F ILE* 3.0 29.6 + - - +
214F VAL* 3.7 15.9 - - + -
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Residues in contact with LEU 200 (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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201E ALA* 3.7 19.1 - - + -
196F ILE* 2.9 42.2 + - + +
197F GLY* 3.7 4.5 - - - +
199F ALA* 1.3 79.4 - - - +
201F ALA* 1.3 60.3 + - - +
203F ILE* 3.6 6.8 + - + +
204F GLU* 3.5 25.5 + - - +
214F VAL* 3.9 15.3 - - + -
234F GLN* 4.5 15.5 - - + +
235F ALA* 4.2 17.3 - - - +
238F ALA* 4.8 5.6 - - + -
240F LYS* 3.4 42.8 - - + -
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Residues in contact with ALA 201 (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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197E GLY 3.8 11.4 - - - +
200E LEU* 3.9 22.7 - - + -
201E ALA* 4.0 8.7 - - - +
204E GLU* 5.6 1.8 - - - +
234E GLN* 4.1 11.0 - - - +
237E TRP* 6.0 0.2 - - - -
197F GLY 3.1 18.0 + - - +
198F HIS* 3.6 8.1 - - - +
199F ALA 3.2 0.4 - - - -
200F LEU* 1.3 75.6 - - - +
202F PHE* 1.3 64.5 + - - +
204F GLU* 3.4 17.2 + - - +
205F ARG* 4.0 10.0 + - - +
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Residues in contact with PHE 202 (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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234E GLN* 4.0 5.8 - - - +
237E TRP* 3.7 32.5 - + - -
155F LEU* 3.9 15.7 - - + -
158F MET* 3.1 36.6 - - + -
159F LYS* 3.4 24.5 - - + -
162F PHE* 3.8 17.3 - + - -
180F ILE* 3.9 14.8 - - + -
193F LEU* 3.8 24.0 - - + -
198F HIS 3.0 17.7 + - - +
199F ALA 3.5 4.0 - - - +
201F ALA* 1.3 74.2 - - - +
203F ILE* 1.3 70.0 + - - +
205F ARG* 3.0 19.1 + - - +
206F LEU* 3.9 16.9 - - + +
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Residues in contact with ILE 203 (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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180F ILE* 4.0 20.0 - - + -
199F ALA 3.0 17.0 + - - +
200F LEU* 3.8 8.1 - - - +
201F ALA 3.4 0.2 - - - -
202F PHE* 1.3 75.9 - - - +
204F GLU* 1.3 61.1 + - - +
206F LEU* 2.9 33.0 + - + +
209F PRO* 3.7 23.0 - - + +
212F TYR* 3.7 32.1 - - + +
213F GLY* 3.4 34.5 - - - +
214F VAL* 4.2 10.1 - - + -
240F LYS* 4.0 14.8 - - - +
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Residues in contact with GLU 204 (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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201E ALA* 5.4 2.7 - - - +
204E GLU* 4.0 42.8 - - + +
205E ARG* 6.5 0.7 - - - -
200F LEU 3.5 15.7 + - - +
201F ALA* 3.4 11.1 + - - +
202F PHE 3.2 1.0 + - - -
203F ILE* 1.3 83.6 - - - +
205F ARG* 1.3 60.3 + - + +
206F LEU 3.3 2.7 + - - +
209F PRO* 4.3 19.6 - - - +
240F LYS* 4.5 14.7 + - - +
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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