Contacts of the helix formed by residues 216 - 227 (chain A) in PDB entry 2FK8
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 SER 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.8 3.4 - - - -
180A SER* 3.4 19.9 + - - -
181A TYR* 4.7 6.7 - - - -
182A HIS* 4.9 6.7 - - - -
185A GLU* 5.1 4.0 - - - -
215A PRO* 1.3 75.9 - - - +
217A THR* 1.3 65.2 + - - +
218A GLU* 3.6 10.6 + - - +
219A MET* 3.1 43.2 + - - +
220A MET* 3.2 13.5 + - - +
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Residues in contact with THR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 3.4 23.6 - - - +
180A SER 4.4 0.6 + - - -
181A TYR* 6.0 1.4 - - - -
216A SER* 1.3 71.1 - - - +
218A GLU* 1.3 62.5 + - - +
220A MET* 3.2 7.2 + - - +
221A VAL* 3.0 24.8 + - + +
234A PRO* 3.8 30.7 - - + -
288A ASP* 4.7 3.5 + - - -
290A SER* 2.7 30.4 + - - +
292A VAL* 4.8 2.0 - - + -
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Residues in contact with GLU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 5.7 2.6 - - - +
216A SER* 3.1 10.5 + - - +
217A THR* 1.3 77.1 - - - +
219A MET* 1.3 57.9 + - + +
221A VAL* 3.4 5.6 + - - +
222A GLU* 2.9 68.3 + - + +
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A HIS* 3.4 50.9 - - + +
156A TYR* 3.6 19.5 - - + -
215A PRO* 4.0 3.4 - - + -
216A SER* 3.1 36.1 + - - +
218A GLU* 1.3 74.2 - - + +
220A MET* 1.3 64.0 + - - +
222A GLU* 4.8 3.6 - - - -
223A HIS* 3.0 48.8 + - + +
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Residues in contact with MET 220 (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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148A PHE* 3.7 22.7 - - + -
160A PHE* 3.7 8.4 - - - -
175A VAL* 3.8 27.1 - - + +
177A SER* 3.8 25.8 - - - -
179A VAL* 3.6 27.8 - - - -
215A PRO* 3.9 4.7 - - + +
216A SER 3.2 9.4 + - - +
217A THR* 3.4 7.6 - - - +
219A MET* 1.3 76.8 - - - +
221A VAL* 1.3 60.6 + - - +
224A GLY 3.4 6.9 + - - -
290A SER* 4.3 7.2 - - - +
292A VAL* 3.6 27.6 - - + -
294A TYR* 2.8 32.6 + - - +
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Residues in contact with VAL 221 (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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217A THR* 3.0 23.5 + - + +
218A GLU* 3.8 5.4 - - - +
220A MET* 1.3 74.4 - - - +
222A GLU* 1.3 62.0 + - + +
224A GLY* 3.2 2.6 + - - -
225A GLU* 3.0 47.4 + - - +
231A VAL* 3.8 30.2 - - + +
234A PRO* 3.6 31.4 - - + -
292A VAL* 4.3 4.0 - - + -
294A TYR* 4.7 0.2 - - - -
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Residues in contact with GLU 222 (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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218A GLU* 2.9 56.7 + - + +
219A MET* 4.3 3.3 - - - +
221A VAL* 1.3 77.3 - - + +
223A HIS* 1.3 59.3 + - + +
225A GLU* 3.3 15.8 + - - +
226A LYS* 2.9 30.4 + - - +
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Residues in contact with HIS 223 (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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153A HIS 4.9 4.0 + - - -
156A TYR* 3.6 34.5 - + + +
157A ASP* 2.6 38.1 + - - +
160A PHE* 3.5 26.6 - - + +
219A MET* 3.0 41.6 + - + +
222A GLU* 1.3 75.3 - - + +
224A GLY* 1.3 65.0 + - - +
226A LYS* 3.5 11.4 + - + +
227A ALA* 3.3 21.1 + - - +
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Residues in contact with GLY 224 (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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160A PHE* 3.8 13.8 - - - -
220A MET 3.4 5.5 + - - -
221A VAL 3.2 7.1 + - - -
223A HIS* 1.3 77.7 - - - +
225A GLU* 1.3 61.8 + - - +
227A ALA* 3.2 12.1 + - - +
228A GLY 3.2 0.7 + - - -
229A PHE* 3.1 26.0 + - - -
231A VAL* 4.5 0.4 - - - -
294A TYR* 3.8 24.9 - - - -
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Residues in contact with GLU 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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221A VAL* 3.0 36.1 + - - +
222A GLU* 3.7 17.3 - - - +
224A GLY* 1.3 77.0 - - - +
226A LYS* 1.3 57.7 + - - +
228A GLY* 2.8 22.2 + - - -
229A PHE 3.6 15.0 - - - +
231A VAL* 3.9 24.3 + - + +
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Residues in contact with LYS 226 (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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157A ASP* 3.1 39.4 + - - +
222A GLU 2.9 21.2 + - - +
223A HIS* 3.6 11.4 - - + +
224A GLY 3.3 0.2 - - - -
225A GLU* 1.3 73.1 - - - +
227A ALA* 1.3 59.8 + - - +
228A GLY* 3.4 1.2 + - - -
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Residues in contact with ALA 227 (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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157A ASP 5.4 1.1 - - - +
160A PHE* 3.7 43.1 - - + +
161A LYS* 4.1 7.2 - - + +
164A PHE* 3.4 24.2 - - + +
223A HIS 3.3 1.9 + - - +
224A GLY 3.2 10.3 + - - +
225A GLU 3.2 0.4 - - - -
226A LYS* 1.3 77.1 - - - +
228A GLY* 1.3 57.4 + - - +
229A PHE* 3.7 5.4 - - + -
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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