Contacts of the helix formed by residues 247 - 258 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121C ASP* 4.8 3.4 - - - -
122C GLY* 4.2 21.8 - - - -
125C ASN* 5.4 1.1 - - - -
130C VAL* 4.5 8.7 - - - +
131C SER 3.2 26.3 + - - -
132C VAL* 4.8 1.4 - - - -
245C VAL 3.6 2.2 - - - -
246C GLY* 1.3 79.7 - - - +
248C MET* 1.3 66.8 + - - +
249C VAL* 3.2 3.4 + - - +
250C ALA* 3.0 25.8 + - - +
251C ASP* 3.1 12.9 + - - +
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Residues in contact with MET 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ASP* 3.8 13.8 + - - +
135C ILE* 4.2 7.9 - - - -
246C GLY 4.2 0.4 - - - -
247C SER* 1.3 70.2 - - - +
249C VAL* 1.3 57.8 + - - +
250C ALA 3.2 0.2 + - - -
251C ASP* 3.3 5.9 + - - -
252C VAL* 2.8 45.3 + - + +
262C PHE* 4.6 12.6 - - + -
275C LEU* 3.5 35.7 - - + -
280C GLU* 3.6 49.8 - - - +
281C CYS* 4.2 5.8 - - - +
284C MET* 3.8 22.0 - - + -
316C ILE* 4.8 7.0 - - + -
318C LEU* 5.4 0.4 - - + -
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Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ASP* 3.6 23.1 + - + +
132C VAL 5.0 0.2 - - - -
133C GLY* 4.2 14.1 - - - +
135C ILE* 3.6 28.0 - - + -
164C TYR* 3.5 29.9 - - + -
165C ALA 3.9 9.0 - - - +
166C LEU* 3.8 23.5 - - + +
247C SER* 3.1 4.7 + - - +
248C MET* 1.3 74.7 - - - +
250C ALA* 1.3 57.8 + - - +
253C HIS* 3.0 30.8 + - - +
284C MET* 4.1 7.9 - - + -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C SER* 4.2 16.6 - - - +
166C LEU* 4.3 11.0 - - + +
245C VAL* 3.7 26.1 - - + +
247C SER* 3.0 20.7 + - - +
249C VAL* 1.3 79.8 - - - +
251C ASP* 1.3 58.6 + - - +
253C HIS* 3.5 3.4 + - - +
254C ARG* 3.1 28.8 + - - +
128D CYS 5.2 2.8 - - - +
130D VAL* 4.7 8.0 - - + +
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Residues in contact with ASP 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C SER* 3.8 6.1 - - - -
244C TYR* 3.6 15.4 - - - -
245C VAL* 3.0 18.5 + - - +
246C GLY* 3.1 22.2 + - - -
247C SER 3.1 12.5 + - - +
248C MET 3.9 1.6 - - - +
250C ALA* 1.3 75.7 - - - +
252C VAL* 1.3 60.3 + - - +
254C ARG* 2.9 36.3 + - - +
255C THR* 3.0 31.0 + - - -
262C PHE* 3.7 23.4 - - + -
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TYR* 4.5 4.9 - - + +
248C MET* 2.8 39.7 + - + +
251C ASP* 1.3 68.2 - - - +
253C HIS* 1.3 61.2 + - - +
255C THR* 3.6 6.1 - - - -
256C LEU* 2.9 26.2 + - - +
262C PHE* 4.0 13.2 - - + -
284C MET* 3.9 36.3 - - + +
287C VAL* 5.9 1.1 - - + -
288C MET* 3.6 22.4 - - + -
318C LEU* 3.8 22.9 - - + -
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Residues in contact with HIS 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 2.7 35.1 + + + +
166C LEU* 3.9 17.9 - - + +
172C MET* 4.0 29.9 - - + -
174C VAL* 4.0 11.2 - - + -
183C CYS* 4.8 4.5 - - - -
249C VAL 3.0 21.7 + - - +
250C ALA 3.8 3.6 - - - +
252C VAL* 1.3 77.2 - - - +
254C ARG* 1.3 62.6 + - - +
256C LEU* 3.3 2.7 + - + +
257C VAL* 3.1 45.0 + - + +
127D ASP 4.4 6.5 + - - -
128D CYS 3.3 27.7 + - - -
129D LEU* 4.5 1.8 - - + +
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE* 4.3 13.3 - - + +
210C SER* 2.7 38.2 + - - -
243C ARG* 3.4 38.5 + - - +
245C VAL* 3.7 16.2 - - - +
250C ALA 3.1 13.2 + - - +
251C ASP* 2.9 36.9 + - - +
253C HIS* 1.3 76.1 - - - +
255C THR* 1.3 58.3 + - - +
257C VAL 3.1 1.4 + - - -
258C TYR* 2.8 46.0 + - + +
259C GLY 5.3 0.7 - - - +
128D CYS* 4.2 32.8 - - + +
130D VAL* 5.5 9.1 - - + +
245D VAL 5.8 0.2 + - - -
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ILE* 3.9 4.5 - - + +
210C SER* 5.2 0.3 - - - -
251C ASP 3.0 18.0 + - - -
252C VAL* 3.6 9.4 - - - -
254C ARG* 1.3 80.1 + - - +
256C LEU* 1.3 58.1 + - - +
259C GLY* 2.8 37.0 + - - +
260C GLY* 4.1 14.8 - - - +
261C ILE 4.4 3.5 + - - +
262C PHE* 3.8 15.9 + - - +
288C MET* 4.2 8.3 - - + -
318C LEU* 4.2 8.1 - - + +
319C GLY* 3.7 30.3 - - - +
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Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C TYR* 3.8 17.5 - - - +
174C VAL* 4.2 18.4 - - + -
181C VAL* 4.5 2.9 - - + -
183C CYS* 4.4 9.0 - - - -
200C VAL* 4.2 23.8 - - + +
201C LYS 5.0 1.7 - - - +
202C ILE* 4.0 22.3 - - + +
203C LYS 4.9 0.9 + - - -
252C VAL 2.9 17.1 + - - +
253C HIS* 3.6 7.9 - - - +
254C ARG 3.3 0.2 - - - -
255C THR* 1.3 78.4 - - - +
257C VAL* 1.3 65.5 + - + +
259C GLY 4.2 1.0 + - - -
287C VAL* 4.4 9.2 - - + -
288C MET* 3.9 21.0 - - + +
291C ALA* 3.6 31.0 - - + -
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C CYS* 5.6 4.0 - - - -
200C VAL* 6.1 2.0 - - + -
203C LYS* 5.5 4.4 - - - +
253C HIS* 3.1 41.4 + - + +
254C ARG* 3.1 3.8 + - - +
256C LEU* 1.3 84.8 - - + +
258C TYR* 1.3 62.3 + - + +
127D ASP* 4.0 21.1 - - + +
128D CYS* 4.0 20.9 - - - -
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Residues in contact with TYR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C LYS* 3.8 33.8 + - - +
206C GLY* 4.9 1.7 - - - -
207C LYS* 5.2 10.6 + - + +
208C ILE* 3.3 40.9 - - + +
254C ARG* 2.8 23.5 + - + +
257C VAL* 1.3 76.4 - - + +
259C GLY* 1.3 64.9 + - - +
128D CYS* 4.0 23.1 - - - -
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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