Contacts of the helix formed by residues 247 - 259 (chain L) in PDB entry 2FIE
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 247 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121L ASP* 3.8 16.3 + - - -
122L GLY* 4.0 9.5 - - - -
130L VAL* 4.6 3.1 - - - -
131L SER 3.4 25.2 + - - -
132L VAL* 4.2 4.0 - - - -
245L VAL* 3.4 13.6 - - - -
246L GLY* 1.3 81.5 - - - +
248L MET* 1.3 66.8 + - - +
249L VAL* 4.0 7.1 + - - +
250L ALA* 3.2 7.8 + - - +
251L ASP* 3.1 25.1 + - - +
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Residues in contact with MET 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ASP* 3.2 20.1 + - - +
135L ILE* 4.3 2.0 - - + -
246L GLY 4.2 0.6 + - - -
247L SER* 1.3 71.3 - - - +
249L VAL* 1.3 64.8 + - - +
251L ASP* 4.9 3.1 - - - -
252L VAL* 2.9 36.5 + - + +
262L PHE* 4.2 14.6 - - + -
275L LEU* 3.5 37.9 - - + -
280L GLU* 3.9 33.4 - - - +
281L CYS* 4.7 4.0 - - - +
284L MET* 3.5 40.6 - - + -
316L VAL* 5.1 2.0 - - + -
318L LEU* 4.8 5.8 - - + -
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Residues in contact with VAL 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121L ASP* 3.9 6.3 + - + -
133L GLY* 3.4 35.9 - - - +
134L THR 4.1 0.7 - - - +
135L ILE* 3.8 25.1 - - + -
164L TYR* 3.5 22.6 - - + -
165L ALA 3.4 20.6 - - - +
166L LEU* 3.7 17.3 - - + -
247L SER* 3.4 3.4 - - - +
248L MET* 1.3 75.0 - - - +
250L ALA* 1.3 66.9 + - - +
252L VAL* 3.9 0.5 - - - +
253L HIS* 2.9 24.4 + - - +
284L MET* 3.6 8.0 - - + +
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Residues in contact with ALA 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H CYS 5.6 1.4 - - - +
131L SER* 4.6 16.4 - - - -
166L LEU* 4.2 12.6 - - + +
245L VAL* 3.8 28.5 - - + -
247L SER* 3.2 15.4 + - - +
248L MET 3.2 0.6 - - - -
249L VAL* 1.3 78.4 - - - +
251L ASP* 1.3 65.5 + - - +
253L HIS* 2.8 15.6 + - - +
254L ARG* 3.0 15.0 + - - +
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Residues in contact with ASP 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210L SER* 3.6 12.7 + - - +
244L TYR* 3.9 8.9 - - - -
245L VAL* 2.8 19.4 + - - +
246L GLY 3.1 18.7 + - - -
247L SER 3.1 19.0 + - - +
248L MET 4.2 0.9 - - - +
250L ALA* 1.3 78.4 - - - +
252L VAL* 1.3 61.4 + - - +
254L ARG* 2.6 39.7 + - - +
255L THR* 2.8 27.5 + - - -
262L PHE* 3.8 23.6 - - + -
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Residues in contact with VAL 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164L TYR* 4.9 6.7 - - + +
248L MET* 2.9 47.4 + - + +
251L ASP* 1.3 75.7 - - - +
253L HIS* 1.3 64.2 + - - +
255L THR* 3.2 9.3 + - - -
256L LEU* 3.1 20.0 + - + +
262L PHE* 4.0 20.0 - - + -
284L MET* 3.5 33.2 - - + +
287L VAL* 6.3 0.7 - - + -
288L MET* 4.1 10.5 - - + +
318L LEU* 4.2 16.4 - - + -
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Residues in contact with HIS 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ASP 4.7 2.0 + - - -
128H CYS* 3.9 20.2 - - - +
129H LEU* 4.5 4.6 - - + +
164L TYR* 2.6 36.7 + + + +
166L LEU* 3.8 27.1 - - + -
172L MET* 4.2 20.6 - - + -
174L VAL* 4.0 16.2 - - + -
183L CYS* 4.7 5.4 - - - -
249L VAL 2.9 18.3 + - - +
250L ALA 2.8 4.9 + - - +
252L VAL* 1.3 78.9 - - - +
254L ARG* 1.3 61.0 + - - +
256L LEU* 3.2 6.1 + - + +
257L VAL* 3.0 49.6 + - + +
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Residues in contact with ARG 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H ASN* 5.3 4.8 - - - +
128H CYS* 4.0 26.7 + - + +
244H TYR 5.1 0.2 + - - -
245H VAL 5.3 2.4 + - - -
208L ILE* 4.4 27.5 - - - +
210L SER* 3.5 28.7 + - - -
243L ARG* 3.5 29.8 - - - +
244L TYR 4.1 1.6 - - - +
245L VAL* 3.8 16.2 - - - +
250L ALA 3.0 10.7 + - - +
251L ASP* 2.6 42.9 + - - +
253L HIS* 1.3 77.1 - - - +
255L THR* 1.3 60.8 + - - +
258L TYR* 2.7 52.3 + - + +
259L GLY 5.9 0.7 - - - -
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Residues in contact with THR 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE* 3.3 5.4 - - + +
210L SER* 5.4 0.5 - - - -
251L ASP 2.8 19.1 + - - -
252L VAL* 3.4 11.0 - - - -
253L HIS 3.2 0.2 - - - -
254L ARG* 1.3 86.8 + - - +
256L LEU* 1.3 57.3 + - - +
259L GLY* 2.8 33.9 + - - +
260L GLY* 3.5 31.0 - - - +
261L ILE 4.2 3.3 + - - +
262L PHE* 4.0 15.9 + - - +
288L MET* 4.7 4.3 - - - -
318L LEU* 4.3 6.5 - - + +
319L GLY* 3.6 20.0 - - - +
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Residues in contact with LEU 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164L TYR* 3.7 19.7 - - + +
174L VAL* 4.4 11.0 - - + -
181L VAL* 4.5 7.4 - - + -
183L CYS* 5.2 2.9 - - - -
200L VAL* 4.4 16.6 - - + +
201L LYS 4.7 3.1 - - - +
202L ILE* 3.8 25.4 - - + +
203L LYS 5.0 0.7 + - - -
252L VAL* 3.1 8.3 + - + +
253L HIS* 3.2 16.6 + - + +
255L THR* 1.3 79.2 - - - +
257L VAL* 1.3 63.5 + - + +
259L GLY 4.0 0.7 + - - -
287L VAL* 4.2 17.0 - - + -
288L MET* 3.3 28.5 - - + +
291L ALA* 3.6 28.9 - - + -
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Residues in contact with VAL 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ASP* 4.0 28.7 - - + +
128H CYS* 4.4 2.2 - - + -
183L CYS* 6.1 1.6 - - - -
203L LYS* 5.5 4.0 - - - +
253L HIS* 3.0 47.6 + - + +
254L ARG 4.0 1.8 - - - +
256L LEU* 1.3 81.9 - - + +
258L TYR* 1.3 76.7 + - + +
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Residues in contact with TYR 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H SER 2.9 26.2 + - - -
125H ASN* 3.2 24.0 - - - -
127H ASP* 3.7 17.3 - - + +
128H CYS* 3.3 45.5 - - + -
203L LYS* 3.6 30.5 + - - +
206L GLY* 4.5 2.4 - - - -
207L LYS 5.2 0.7 + - - -
208L ILE* 4.9 13.2 - - + -
254L ARG* 2.7 29.2 + - + +
257L VAL* 1.3 77.3 - - + +
259L GLY* 1.3 67.0 + - - +
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Residues in contact with GLY 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE* 4.2 8.3 - - - -
203L LYS* 4.2 11.2 - - - +
206L GLY* 3.7 7.4 - - - -
207L LYS 4.5 2.3 + - - -
208L ILE* 4.6 7.8 - - - +
254L ARG* 5.9 1.0 - - - -
255L THR* 2.8 25.1 + - - -
256L LEU 4.0 1.0 + - - -
257L VAL 3.5 2.2 - - - -
258L TYR* 1.3 90.0 - - - +
260L GLY* 1.3 58.3 + - - -
320L SER* 3.6 10.1 - - - -
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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