Contacts of the helix formed by residues 247 - 258 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D ASP* 3.7 19.0 + - - -
122D GLY* 4.7 6.3 - - - -
125D ASN* 4.4 10.8 - - - -
131D SER 2.9 29.9 + - - -
132D VAL* 4.0 1.7 - - - -
245D VAL* 3.4 8.9 - - - -
246D GLY* 1.3 80.9 - - - +
248D MET* 1.3 64.2 + - - +
249D VAL* 4.0 5.4 + - - +
250D ALA* 3.2 7.8 + - - +
251D ASP* 3.0 23.6 + - - +
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Residues in contact with MET 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 3.3 15.4 + - - +
135D ILE* 4.2 8.1 - - + -
246D GLY 4.1 0.6 - - - -
247D SER* 1.3 71.1 - - - +
249D VAL* 1.3 57.7 + - - +
251D ASP* 4.4 5.4 - - - -
252D VAL* 2.8 46.7 + - + +
262D PHE* 4.2 19.5 - - + -
275D LEU* 3.7 32.1 - - + -
280D GLU* 3.4 47.1 - - - +
281D CYS* 4.4 5.6 - - - +
284D MET* 3.7 21.8 - - + -
316D ILE* 4.8 5.2 - - + -
318D LEU* 4.9 4.0 - - + -
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ASP* 3.6 16.1 + - + +
133D GLY* 4.0 14.6 - - - +
135D ILE* 3.6 35.4 - - + -
164D TYR* 3.5 28.2 - - + -
165D ALA 3.8 14.8 - - - +
166D LEU* 3.8 17.0 - - + -
247D SER* 3.2 5.0 - - - +
248D MET* 1.3 75.0 - - - +
250D ALA* 1.3 59.6 + - - +
252D VAL* 4.2 0.9 - - - +
253D HIS* 3.0 32.9 + - - +
284D MET* 4.0 6.5 - - + -
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C CYS 5.1 2.9 - - - +
130C VAL* 6.2 3.6 - - + -
131D SER* 3.9 21.5 - - - +
166D LEU* 4.0 12.9 - - + +
245D VAL* 3.8 28.2 - - + +
247D SER* 3.2 12.3 + - - +
249D VAL* 1.3 78.9 - - - +
251D ASP* 1.3 57.5 + - - +
253D HIS* 3.8 2.5 - - - +
254D ARG* 3.1 31.5 + - - +
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Residues in contact with ASP 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D SER* 3.1 12.0 + - - +
244D TYR* 4.1 5.3 - - - -
245D VAL* 3.0 15.5 + - - -
246D GLY* 2.9 27.9 + - - -
247D SER 3.0 15.7 + - - +
248D MET 3.8 1.8 - - - +
250D ALA* 1.3 77.6 - - - +
252D VAL* 1.3 56.6 + - - +
254D ARG* 2.6 37.8 + - - +
255D THR* 2.6 31.8 + - - -
262D PHE* 3.5 27.1 - - + -
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Residues in contact with VAL 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TYR* 5.2 5.2 - - + +
248D MET* 2.8 44.5 + - + +
249D VAL 4.2 1.1 - - - +
251D ASP* 1.3 70.7 - - - +
253D HIS* 1.3 55.7 + - - +
255D THR* 3.0 10.1 + - - -
256D LEU* 2.8 26.9 + - - +
262D PHE* 4.4 8.3 - - + -
284D MET* 4.0 37.9 - - + -
287D VAL* 6.0 0.4 - - + -
288D MET* 3.7 23.1 - - + +
318D LEU* 3.9 20.2 - - + -
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Residues in contact with HIS 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP 4.9 1.8 + - - -
128C CYS 3.8 17.2 - - - -
129C LEU* 4.1 13.9 - - + +
164D TYR* 2.7 35.7 + + + +
166D LEU* 3.5 26.9 - - + -
172D MET* 4.0 18.7 - - + -
174D VAL* 3.9 18.6 - - + -
183D CYS* 4.9 3.6 - - - -
249D VAL 3.0 20.5 + - - +
250D ALA 3.8 3.6 - - - +
252D VAL* 1.3 76.3 - - - +
254D ARG* 1.3 61.4 + - - +
256D LEU* 3.0 4.5 + - + +
257D VAL* 2.9 49.0 + - + +
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Residues in contact with ARG 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ASN* 5.6 2.7 - - - +
128C CYS* 4.0 30.7 + - + +
130C VAL* 5.3 5.4 - - + -
208D ILE* 4.4 20.3 - - - +
210D SER* 3.5 24.0 + - - -
243D ARG* 3.5 39.6 + - - +
245D VAL* 4.0 12.1 - - - +
250D ALA 3.1 15.3 + - - +
251D ASP* 2.6 46.3 + - - +
253D HIS* 1.3 75.3 - - - +
255D THR* 1.4 62.9 + - - +
257D VAL* 4.4 5.2 - - - -
258D TYR* 2.9 36.7 + - + +
259D GLY 3.7 2.3 + - - +
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ILE* 3.6 7.6 - - + +
251D ASP 2.6 22.1 + - - -
252D VAL* 3.0 14.7 + - - -
254D ARG* 1.4 83.8 + - - +
256D LEU* 1.3 58.5 + - - +
259D GLY* 3.1 30.8 + - - +
260D GLY 3.7 30.5 - - - +
261D ILE* 3.9 9.1 + - - +
262D PHE* 4.1 10.6 + - + +
288D MET* 5.1 1.6 - - + -
318D LEU* 4.2 5.8 - - + +
319D GLY* 3.8 18.8 - - - -
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D TYR* 3.5 21.1 - - - +
174D VAL* 4.3 13.2 - - + -
181D VAL* 4.6 5.4 - - + -
183D CYS* 4.9 4.7 - - - -
200D VAL* 4.3 20.1 - - + +
201D LYS 4.8 2.1 - - - +
202D ILE* 3.8 26.9 - - + +
203D LYS 4.8 1.2 + - - -
252D VAL 2.8 11.0 + - - +
253D HIS* 3.0 13.9 + - + +
255D THR* 1.3 78.0 - - - +
257D VAL* 1.3 68.2 + - + +
259D GLY 4.3 1.0 + - - -
287D VAL* 4.2 16.6 - - + -
288D MET* 4.0 15.4 - - + +
291D ALA* 3.5 31.9 - - + -
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ASP* 3.8 25.6 - - + +
128C CYS* 4.2 17.0 - - - -
183D CYS* 5.7 5.2 - - - -
203D LYS* 5.5 4.7 - - - +
253D HIS* 2.9 47.4 + - + +
254D ARG* 3.9 3.8 - - - +
256D LEU* 1.3 85.7 - - + +
258D TYR* 1.3 60.8 - - - +
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Residues in contact with TYR 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ASN* 5.9 1.8 - - - -
128C CYS* 4.1 25.1 - - - -
203D LYS* 3.4 42.9 + - - +
206D GLY* 4.7 2.3 - - - -
207D LYS* 5.0 16.8 + - + +
208D ILE* 3.8 36.5 - - + +
254D ARG* 2.9 22.1 + - + +
257D VAL* 1.3 74.2 - - + +
259D GLY* 1.3 60.7 + - - +
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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