Contacts of the helix formed by residues 220 - 229 (chain F) in PDB entry 5FHK
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 LEU 220 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99F TYR* 5.8 0.6 - - - -
100F ASN* 3.5 29.1 + - - +
191F GLY* 3.7 28.0 - - - +
192F HIS 3.7 9.3 + - - +
193F PRO* 3.9 15.3 - - + -
194F LEU* 4.1 10.1 - - + -
219F ALA* 1.3 69.6 - - - +
221F ASN* 1.3 66.3 + - - +
222F VAL 3.2 2.7 - - - -
223F VAL* 3.1 18.1 + - + +
224F ARG* 3.4 9.5 + - - +
234F THR* 5.3 0.4 - - - +
235F LEU 4.1 11.7 - - - +
236F MET* 4.0 23.6 - - + +
237F PRO* 4.0 24.0 - - + -
240F MET* 4.1 15.9 - - + -
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Residues in contact with ASN 221 (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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103C LYS* 3.1 56.1 + - - +
221C ASN* 6.1 2.5 - - - +
99F TYR* 5.5 1.1 + - - -
100F ASN* 4.9 4.3 + - - +
219F ALA* 3.4 21.3 - - - +
220F LEU* 1.3 78.8 - - - +
222F VAL* 1.3 73.7 + - - +
223F VAL 3.7 0.2 + - - -
224F ARG* 3.8 12.6 + - - +
225F SER 4.0 4.0 + - - -
240F MET* 4.8 10.8 - - + +
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Residues in contact with VAL 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 3.9 26.7 - - + -
103C LYS* 4.3 12.3 - - + +
107C MET* 3.5 25.8 - - + +
124C LEU* 4.0 10.5 - - + -
126C THR* 4.9 5.8 - - + -
215F PHE* 3.7 3.9 - - + -
217F ALA* 3.6 22.0 - - + -
219F ALA* 3.5 17.9 - - + +
221F ASN* 1.3 93.7 + - - +
223F VAL* 1.3 66.1 + - - +
224F ARG 3.3 0.4 - - - -
225F SER* 3.3 17.6 - - - -
226F ALA 3.5 4.0 + - - -
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Residues in contact with VAL 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189F LEU* 3.7 23.3 - - + +
190F LYS 3.8 6.7 - - - +
191F GLY* 3.6 25.1 - - - +
215F PHE* 4.1 15.9 - - + -
217F ALA* 4.4 2.0 - - + -
219F ALA 3.6 17.7 - - - +
220F LEU* 3.1 12.4 + - + +
222F VAL* 1.3 76.1 - - - +
224F ARG* 1.3 64.8 + - - +
226F ALA* 3.2 3.3 + - - +
227F CYS* 3.0 20.6 + - - +
234F THR* 3.0 31.2 - - + +
236F MET* 4.9 0.9 - - - -
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Residues in contact with ARG 224 (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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103C LYS* 4.8 16.0 - - - +
220F LEU 3.4 7.8 + - - +
221F ASN* 4.1 10.1 + - - +
222F VAL 3.3 0.6 - - - -
223F VAL* 1.3 75.7 - - - +
225F SER* 1.3 85.9 + - - +
227F CYS* 3.1 7.2 + - + +
228F SER* 2.5 69.5 + - - +
234F THR* 5.4 0.9 - - - -
236F MET* 4.7 13.5 - - + -
240F MET* 5.7 0.7 - - + -
241F ILE* 4.1 19.3 - - + -
244F TYR* 3.6 43.1 + - - -
250F LEU* 4.6 6.7 - - + -
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Residues in contact with SER 225 (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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103C LYS* 4.7 9.3 + - - +
107C MET* 3.8 18.4 - - - +
108C PRO* 5.3 1.0 - - - +
111C ASN* 3.4 18.1 + - - -
221F ASN 4.0 2.5 + - - -
222F VAL* 3.3 17.6 + - - -
224F ARG* 1.3 96.8 + - - +
226F ALA* 1.3 62.8 + - - +
228F SER* 3.1 4.6 + - - -
229F GLU* 3.0 28.6 + - - +
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Residues in contact with ALA 226 (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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111C ASN* 3.2 22.6 + - - +
114C MET* 4.6 0.2 - - + -
189F LEU* 3.7 14.4 - - + -
215F PHE* 3.8 27.8 - - + -
222F VAL 3.5 3.0 + - - +
223F VAL 3.2 9.9 + - - +
225F SER* 1.3 77.5 - - - +
227F CYS* 1.3 63.0 + - - +
229F GLU* 3.2 8.5 + - - -
231F LEU* 3.3 33.2 + - + +
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Residues in contact with CYS 227 (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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165F VAL* 3.5 27.1 - - - -
166F ALA* 3.6 7.6 - - - -
167F SER* 3.5 13.2 + - - -
189F LEU* 3.5 13.2 - - + +
223F VAL 3.0 12.4 + - - +
224F ARG* 3.5 10.8 - - + +
226F ALA* 1.3 77.0 - - - +
228F SER* 1.3 58.1 + - - +
230F GLY* 2.9 18.7 + - - -
231F LEU 4.2 0.4 + - - +
232F GLY 3.7 8.1 - - - +
234F THR* 3.8 19.3 - - + -
250F LEU* 3.6 22.9 - - + -
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Residues in contact with SER 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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167F SER* 3.9 10.2 - - - -
169F GLU* 4.6 4.0 - - - +
224F ARG* 2.5 49.0 + - - +
225F SER* 3.1 4.5 + - - -
227F CYS* 1.3 73.3 - - - +
229F GLU* 1.3 69.6 + - - +
230F GLY 3.1 1.1 + - - -
244F TYR* 5.4 3.1 - - - -
249F SER* 5.3 5.1 + - - +
250F LEU* 4.4 17.1 - - - +
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Residues in contact with GLU 229 (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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108C PRO* 6.4 1.1 - - - -
111C ASN* 3.4 35.4 - - + +
115C SER* 5.8 2.5 - - - -
169F GLU* 5.6 2.3 - - - +
225F SER* 3.0 16.7 + - - +
226F ALA 3.2 6.9 + - - +
227F CYS 3.2 0.6 - - - -
228F SER* 1.3 85.8 - - - +
230F GLY* 1.3 61.8 + - - +
231F LEU* 3.5 9.0 - - + +
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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