Contacts of the helix formed by residues 222 - 236 (chain A) in PDB entry 1FOK
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLN* 5.0 6.6 + - - +
191A GLY 3.7 15.3 - - - -
193A THR* 3.5 6.8 + - - -
221A GLY* 1.3 69.1 - - - -
223A SER* 1.3 61.9 + - - +
225A LYS* 3.2 12.4 + - - +
226A TYR* 3.3 25.2 + - - -
935C C 4.0 5.0 - - - -
936C A 2.7 54.5 + - - +
937C T 4.3 10.6 - - - +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLY* 3.8 25.8 + - - -
184A LEU* 3.9 10.7 + - - +
187A SER* 5.1 0.9 + - - -
192A PHE* 2.9 42.3 + - - +
193A THR 3.4 10.1 + - - -
194A SER* 4.6 2.2 - - - -
221A GLY 3.2 1.0 - - - -
222A SER* 1.3 75.0 - - - +
224A ASP* 1.3 66.5 + - - +
226A TYR* 3.4 13.5 + - - +
227A ALA* 3.0 22.9 + - - +
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Residues in contact with ASP 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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177A LYS* 3.2 32.0 - - + +
178A PHE* 3.6 14.1 - - - -
181A GLY* 3.9 2.4 - - - -
194A SER* 2.7 20.8 + - - -
195A LEU* 2.9 24.4 + - - +
220A GLU* 3.9 12.8 - - + -
221A GLY* 2.9 30.8 + - - +
223A SER* 1.3 76.9 - - - +
225A LYS* 1.3 64.4 + - - +
227A ALA* 3.2 2.3 + - - +
228A ARG* 2.9 25.1 + - - +
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Residues in contact with LYS 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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12A GLN* 3.3 38.8 + - + +
220A GLU* 4.0 9.5 + - - +
221A GLY 3.0 5.1 + - - -
222A SER* 3.4 9.9 - - - +
224A ASP* 1.3 78.1 - - - +
226A TYR* 1.3 63.5 + - + +
228A ARG* 3.2 29.6 - - - +
229A MET* 2.8 54.1 + - - +
904B G 2.7 48.9 + - - -
937C T 3.8 20.9 - - + -
938C C 4.3 1.8 - - - +
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Residues in contact with TYR 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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10A TRP* 3.5 44.4 + + + +
11A VAL 3.6 34.8 - - - -
12A GLN* 4.0 17.2 + - + +
112A ARG* 4.8 0.3 + - - -
184A LEU* 3.6 15.0 - - + -
191A GLY 4.1 16.7 + - - -
192A PHE* 4.2 13.9 - + - -
222A SER* 3.3 20.7 + - - -
223A SER* 3.6 13.0 - - - +
224A ASP 3.4 0.2 - - - -
225A LYS* 1.3 77.6 - - + +
227A ALA* 1.3 57.9 + - - +
229A MET* 3.3 4.4 + - - -
230A ILE* 2.8 39.3 + - + +
298A THR* 4.4 2.3 + - - +
935C C 4.2 25.8 + - - -
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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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165A ILE* 4.9 5.1 - - - +
177A LYS* 3.6 23.6 - - - +
180A LEU* 3.9 21.6 - - + +
181A GLY* 3.9 11.0 - - - +
184A LEU* 3.6 11.1 - - + +
223A SER 3.0 13.6 + - - +
224A ASP 3.5 7.9 - - - +
226A TYR* 1.3 75.5 - - - +
228A ARG* 1.3 65.6 + - - +
230A ILE* 4.0 0.9 - - - +
231A GLY* 2.9 22.9 + - - -
265A PHE* 4.5 0.9 - - - -
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Residues in contact with ARG 228 (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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177A LYS* 3.9 13.8 - - + +
220A GLU* 3.3 27.2 + - - +
224A ASP 2.9 17.1 + - - +
225A LYS* 3.2 43.3 - - - +
227A ALA* 1.3 72.7 - - - +
229A MET* 1.3 68.7 + - - +
231A GLY* 3.4 1.6 + - - -
232A GLY* 2.8 29.6 + - - -
242A GLN* 4.9 2.1 + - - -
263A HIS* 3.6 36.6 - - + -
265A PHE* 3.7 16.2 - - + -
902B C 3.8 17.5 + - - +
903B G 2.5 48.2 + - - -
904B G 3.4 2.2 + - - -
939C C 4.1 1.0 - - - +
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Residues in contact with MET 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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11A VAL 4.4 7.0 - - - +
12A GLN 3.3 19.3 - - - +
13A ASN 4.0 6.3 - - - +
14A PRO 4.3 16.4 - - - +
15A GLY* 4.6 8.3 - - - -
225A LYS* 2.8 47.5 + - - +
226A TYR* 3.5 7.0 - - - +
228A ARG* 1.3 94.7 - - - +
230A ILE* 1.3 62.0 + - + +
231A GLY 3.0 1.1 - - - -
232A GLY* 2.8 19.2 + - - -
233A TRP* 3.0 27.0 + - + +
902B C 5.8 0.9 - - + -
903B G 3.9 22.0 - - + +
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Residues in contact with ILE 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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10A TRP* 4.7 9.9 - - + -
11A VAL 5.9 2.0 - - - +
159A TYR* 4.0 11.7 - - + +
161A PRO* 3.8 33.2 - - + +
162A ALA* 3.7 30.3 - - + -
165A ILE* 3.9 16.8 - - + -
184A LEU* 4.7 6.3 - - + -
226A TYR* 2.8 26.3 + - + +
229A MET* 1.3 72.7 - - + +
231A GLY* 1.3 61.4 + - - +
233A TRP* 3.5 27.4 + - + +
234A LEU* 3.1 26.1 + - + +
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Residues in contact with GLY 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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165A ILE* 4.7 13.6 - - - +
180A LEU* 5.7 0.2 - - - -
227A ALA 2.9 17.5 + - - -
228A ARG 3.5 3.1 - - - -
230A ILE* 1.3 79.5 - - - +
232A GLY* 1.3 55.4 + - - +
234A LEU* 3.8 4.4 + - - -
235A ASP* 3.2 24.9 + - - +
240A VAL* 3.5 10.9 - - - +
265A PHE* 3.7 21.0 - - - -
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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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228A ARG 2.8 11.3 + - - -
229A MET* 2.8 12.5 + - - -
231A GLY* 1.3 76.9 - - - +
233A TRP* 1.3 64.3 + - - -
235A ASP* 3.3 7.4 + - - +
236A LYS* 3.1 33.7 + - - +
242A GLN* 4.5 11.4 - - - -
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Residues in contact with TRP 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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11A VAL* 3.5 33.4 - - + -
14A PRO 3.3 23.5 + - - -
15A GLY* 4.3 10.1 - - - -
17A PHE* 4.1 17.2 - + + -
113A TRP* 3.4 63.0 - + - -
117A LEU* 4.7 1.1 - - + -
156A ILE* 4.5 15.7 - - + -
159A TYR* 3.6 27.6 - + - -
229A MET* 3.0 27.3 + - + +
230A ILE* 3.7 24.2 - - + +
231A GLY 3.5 0.2 - - - -
232A GLY* 1.3 73.5 - - - +
234A LEU* 1.3 68.6 + - + +
236A LYS* 2.9 16.8 + - - +
237A LEU* 2.9 21.1 + - + +
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Residues in contact with LEU 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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156A ILE* 4.2 28.0 - - + -
162A ALA* 3.9 19.3 - - + +
165A ILE* 3.7 29.8 - - + -
166A LEU* 4.2 12.8 - - + -
230A ILE* 3.1 23.2 + - + +
231A GLY* 4.0 1.8 - - - +
233A TRP* 1.3 75.3 - - + +
235A ASP* 1.3 60.0 + - - +
237A LEU* 3.5 4.3 + - + -
238A GLY 3.1 2.9 + - - -
239A LEU* 2.8 55.3 + - + -
240A VAL* 3.2 18.6 + - + +
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Residues in contact with ASP 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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231A GLY 3.2 16.1 + - - +
232A GLY* 3.4 12.1 - - - +
233A TRP 3.0 0.8 - - - -
234A LEU* 1.3 76.1 - - - +
236A LYS* 1.3 64.5 + - - +
238A GLY* 2.7 22.7 + - - -
240A VAL* 3.4 19.3 - - + +
241A LYS* 3.5 13.5 + - - +
242A GLN* 2.8 39.8 + - + +
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Residues in contact with LYS 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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15A GLY* 3.0 26.7 + - - -
17A PHE* 4.0 24.7 - - + -
18A GLU* 4.3 14.6 - - - +
149A LYS* 5.5 1.7 - - - -
232A GLY* 3.1 19.0 + - - +
233A TRP* 2.9 13.4 + - - +
235A ASP* 1.3 77.9 - - + +
237A LEU* 1.3 61.1 + - - +
238A GLY* 3.3 1.0 + - - -
903B G 3.4 30.0 + - - -
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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