Contacts of the helix formed by residues 247 - 258 (chain B) in PDB entry 1FTA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ASP* 4.4 8.7 + - - -
122B GLY* 4.5 4.8 - - - -
125B ASN* 3.6 9.2 + - - +
131B SER 3.0 29.0 + - - -
132B VAL* 4.3 4.7 - - - -
245B VAL* 3.9 7.2 - - - -
246B GLY* 1.3 80.4 - - - +
248B MET* 1.3 68.2 + - - +
249B VAL* 4.3 3.8 + - - +
250B ALA* 3.1 17.0 + - - +
251B ASP* 3.0 24.8 + - - +
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Residues in contact with MET 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP* 3.2 14.3 + - - +
135B ILE* 3.5 26.9 - - - -
246B GLY 4.2 0.2 - - - -
247B SER* 1.3 70.5 - - - +
249B VAL* 1.3 58.3 + - - +
251B ASP* 3.0 7.8 + - - -
252B VAL* 2.8 43.6 + - + +
262B PHE* 4.4 18.2 - - + -
275B LEU* 4.0 29.8 - - + -
280B GLU* 3.3 39.9 - - + +
281B CYS* 4.0 6.1 - - - +
284B MET* 3.6 16.6 - - + -
316B ILE* 5.1 4.9 - - + -
318B LEU* 5.5 0.2 - - + -
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASP* 3.5 12.7 + - + +
132B VAL 4.8 0.4 - - - +
133B GLY* 4.0 14.1 - - - +
135B ILE* 3.4 36.8 - - + -
164B TYR* 3.5 28.0 - - + -
165B ALA 3.9 4.3 - - - +
166B LEU* 3.8 26.2 - - + +
247B SER* 3.3 3.7 - - - +
248B MET* 1.3 74.7 - - - +
250B ALA* 1.3 57.5 + - - +
252B VAL* 4.2 0.3 - - - +
253B HIS* 3.0 29.1 + - - +
284B MET* 3.6 11.4 - - + -
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A CYS 5.3 1.9 - - - +
131B SER* 3.9 27.6 - - - +
166B LEU* 3.9 13.6 - - + +
245B VAL* 3.7 22.0 - - + -
247B SER* 3.1 18.7 + - - +
249B VAL* 1.3 78.3 - - - +
251B ASP* 1.3 60.2 + - - +
253B HIS* 3.9 1.9 - - - +
254B ARG* 3.1 28.8 + - - +
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B SER* 3.5 8.1 + - - -
244B TYR* 4.2 5.1 - - - -
245B VAL* 3.0 27.3 + - - +
246B GLY* 3.0 23.0 + - - -
247B SER 3.0 22.5 + - - +
248B MET 3.7 2.5 - - - +
250B ALA* 1.3 74.9 - - - +
252B VAL* 1.3 58.5 + - - +
254B ARG* 2.9 29.4 + - - +
255B THR* 2.8 31.1 + - - -
262B PHE* 3.8 23.7 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 4.4 7.2 - - + +
248B MET* 2.8 39.0 + - + +
251B ASP* 1.3 70.3 - - - +
253B HIS* 1.3 59.4 + - - +
255B THR* 2.9 8.2 + - - -
256B LEU* 2.8 27.3 + - + +
262B PHE* 4.2 20.4 - - + -
284B MET* 3.5 43.1 - - + +
287B VAL* 5.7 1.8 - - + -
288B MET* 3.8 20.6 - - + -
318B LEU* 4.2 7.4 - - + -
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Residues in contact with HIS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP 4.9 1.8 + - - -
128A CYS 3.9 14.8 - - - -
129A LEU* 4.2 10.3 - - + +
164B TYR* 2.7 34.4 + + + +
166B LEU* 3.7 29.6 - - + -
172B MET* 3.6 33.1 - - + -
174B VAL* 3.7 12.3 - - + -
183B CYS* 4.4 3.4 - - - -
249B VAL 3.0 19.7 + - - +
250B ALA 3.4 1.1 + - - +
252B VAL* 1.3 74.5 - - - +
254B ARG* 1.3 63.0 + - - +
256B LEU* 3.0 5.1 + - + +
257B VAL* 2.9 46.6 + - + +
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Residues in contact with ARG 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 5.4 6.7 - - - -
128A CYS* 4.2 27.3 + - + +
130A VAL* 5.4 9.2 - - + +
245A VAL 5.3 2.8 + - - -
208B ILE* 4.2 19.8 - - - +
210B SER* 3.3 25.7 + - - -
243B ARG* 3.7 34.0 + - - +
245B VAL* 3.8 15.2 - - - +
250B ALA 3.1 12.7 + - - +
251B ASP* 2.9 40.5 + - - +
253B HIS* 1.3 75.6 - - - +
255B THR* 1.3 59.2 + - - +
257B VAL* 4.6 1.8 - - - -
258B TYR* 2.8 42.0 + - + +
259B GLY 4.2 0.8 - - - +
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Residues in contact with THR 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.4 5.6 - - + +
210B SER* 5.4 1.2 - - - -
251B ASP 2.8 20.8 + - - -
252B VAL* 2.9 10.6 + - - -
254B ARG* 1.3 79.9 + - - +
256B LEU* 1.3 58.6 + - - +
259B GLY* 2.7 35.0 + - - -
260B GLY* 3.7 33.6 - - - +
261B ILE* 4.1 3.7 + - - +
262B PHE* 4.0 13.5 + - - +
288B MET* 4.2 9.6 - - + -
318B LEU* 4.5 3.8 - - + +
319B GLY* 3.8 18.6 - - - -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B TYR* 3.4 20.9 - - - +
174B VAL* 3.9 25.6 - - + -
181B VAL* 4.5 6.1 - - + -
183B CYS* 4.6 7.6 - - - -
200B VAL* 4.4 19.5 - - + +
201B LYS 4.9 0.3 - - - +
202B ILE* 3.7 23.7 - - + +
203B LYS 5.0 0.3 + - - -
252B VAL* 2.8 13.1 + - + +
253B HIS* 3.0 11.2 + - + +
255B THR* 1.3 77.9 - - - +
257B VAL* 1.3 63.4 - - + +
287B VAL* 4.3 14.4 - - + -
288B MET* 4.2 13.2 - - + -
291B ALA* 3.7 30.1 - - + -
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 3.8 25.4 - - + +
128A CYS* 4.0 17.0 - - - -
172B MET* 5.8 0.9 - - - -
183B CYS* 5.3 6.3 - - - -
197B ASP* 6.1 0.4 - - - +
203B LYS* 5.1 7.6 + - - +
253B HIS* 2.9 43.8 + - + +
254B ARG* 4.2 2.5 - - - +
256B LEU* 1.3 83.4 - - + +
258B TYR* 1.3 63.8 + - + +
259B GLY 3.4 0.6 + - - -
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Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A CYS* 3.8 26.2 - - - -
203B LYS* 3.6 36.9 + - - +
206B GLY* 4.6 2.1 - - - -
207B LYS* 4.6 24.6 - - + +
208B ILE* 4.0 29.2 - - + -
254B ARG* 2.8 22.9 + - + +
257B VAL* 1.3 74.2 - - + +
259B GLY* 1.3 64.1 + - - +
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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