Contacts of the helix formed by residues 291 - 307 (chain F) in PDB entry 1FFT
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 ILE 291 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287F VAL 3.8 17.2 + - - +
288F TYR* 3.8 9.6 - - + +
289F ILE 3.3 0.2 - - - -
290F LEU* 1.3 80.0 - - - +
292F LEU* 1.3 68.6 + - + +
293F PRO* 3.3 2.2 - - - -
294F VAL* 3.2 20.6 + - + +
295F PHE* 2.8 34.1 - - + -
387F PHE* 5.4 4.0 - - + -
391F PHE* 3.2 37.9 - - + -
423F VAL 4.1 2.5 - - - +
427F GLY 4.0 7.6 - - - +
428F VAL* 3.6 24.0 - - + -
1002F HEO 4.0 15.7 - - + -
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Residues in contact with LEU 292 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F ALA* 3.4 10.3 - - + +
234F CYS* 4.0 9.0 - - + -
235F ALA* 3.5 21.8 - - + +
238F LEU* 3.5 31.4 - - + -
288F TYR* 2.8 26.5 + - + +
291F ILE* 1.3 76.6 - - + +
293F PRO* 1.3 72.7 - - + +
295F PHE* 2.8 40.5 + - + +
320F THR* 5.0 12.6 - - + +
323F ILE* 3.7 31.4 - - + -
324F THR* 4.3 6.7 - - - +
362F LYS* 6.1 0.4 - - - -
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Residues in contact with PRO 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F PHE* 4.4 10.5 - - + -
119F VAL* 3.4 26.2 - - + -
123F MET* 4.4 9.2 - - + -
228F PHE* 3.6 19.9 - - + -
231F ALA* 4.1 11.4 - - + +
232F SER* 4.8 1.1 - - - +
235F ALA* 3.4 13.2 - - + -
289F ILE 3.0 25.8 - - - +
290F LEU 4.5 0.4 - - - -
291F ILE 3.5 2.9 - - - +
292F LEU* 1.3 95.2 - - + +
294F VAL* 1.3 52.3 + - - +
296F GLY* 2.6 31.0 + - - -
297F VAL 3.3 4.0 + - - -
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Residues in contact with VAL 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F PHE* 3.4 30.2 - - + -
290F LEU 3.6 4.3 - - - +
291F ILE* 3.3 36.1 - - + +
293F PRO* 1.3 73.9 - - - +
295F PHE* 1.3 54.0 + - + +
297F VAL* 3.2 6.9 + - + -
298F PHE* 2.6 43.6 + - + +
387F PHE* 5.4 8.5 - - + -
427F GLY 4.4 8.5 - - - +
428F VAL* 4.7 5.6 - - + +
431F GLY* 3.4 34.3 - - - +
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Residues in contact with PHE 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F VAL* 4.4 2.5 - - + -
231F ALA* 4.4 6.7 - - + -
291F ILE* 2.8 46.9 - - + -
292F LEU* 2.8 35.8 + - + +
294F VAL* 1.3 78.9 - - - +
296F GLY* 1.3 56.1 + - - +
298F PHE* 3.3 6.6 + - - +
299F SER* 2.8 35.8 + - - +
320F THR* 6.5 0.2 - - + -
323F ILE* 4.9 7.9 - - + -
359F THR* 5.5 7.2 - - + -
362F LYS* 3.4 45.8 - - + +
366F TRP* 3.6 24.3 - + + -
387F PHE* 5.1 8.3 - + - -
391F PHE* 4.9 16.8 - + - -
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Residues in contact with GLY 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F VAL* 3.6 9.0 - - - -
228F PHE* 3.3 34.3 - - - -
231F ALA* 4.0 3.3 - - - +
292F LEU 3.8 0.6 + - - -
293F PRO 2.6 16.4 + - - -
295F PHE* 1.3 72.7 - - - +
297F VAL* 1.3 63.9 + - - +
299F SER* 2.8 20.8 + - - -
300F GLU* 3.3 8.0 + - - +
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Residues in contact with VAL 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F PHE* 4.9 2.0 - - + -
122F LEU* 3.3 22.9 - - + -
228F PHE* 3.1 34.2 - - + -
293F PRO 3.3 2.9 + - - +
294F VAL* 3.2 14.3 + - + +
296F GLY* 1.3 71.9 - - - +
298F PHE* 1.3 64.4 + - - +
300F GLU* 3.6 2.7 + - - +
301F ILE* 3.2 28.3 + - + +
431F GLY* 4.7 5.4 - - - +
434F ALA* 5.4 0.9 - - + -
435F GLY* 3.4 35.4 - - - +
438F TYR* 5.4 0.2 - - - -
439F TRP* 3.5 18.4 - - + -
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Residues in contact with PHE 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F VAL* 2.6 26.9 + - + +
295F PHE* 3.5 4.7 - - - +
297F VAL* 1.3 75.9 - - - +
299F SER* 1.3 62.5 + - - +
301F ILE* 3.3 5.6 + - - +
302F ALA* 3.0 24.9 + - + +
366F TRP* 3.2 57.7 - + + -
384F THR* 3.0 45.3 - - + -
387F PHE* 3.2 40.8 - + + -
388F ILE* 3.2 19.5 - - + -
434F ALA* 6.1 5.4 - - + -
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Residues in contact with SER 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227F VAL* 2.8 40.4 - - - +
295F PHE 2.8 15.2 + - - -
296F GLY 2.8 7.5 + - - -
298F PHE* 1.3 71.9 - - - +
300F GLU* 1.3 57.4 + - - -
302F ALA* 3.3 3.5 + - - +
303F ALA* 2.9 31.4 + - - +
310F LEU* 3.1 32.5 - - - +
366F TRP* 3.2 15.0 + - - +
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Residues in contact with GLU 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLN* 4.4 9.8 + - - +
226F PRO* 4.3 1.4 - - - +
227F VAL* 3.2 21.1 + - + +
228F PHE* 2.9 47.5 + - - +
296F GLY 3.3 5.5 + - - +
297F VAL* 4.2 4.0 - - - +
299F SER* 1.3 73.5 - - - +
301F ILE* 1.3 67.5 + - - +
302F ALA 3.1 1.3 - - - -
303F ALA* 4.5 4.7 - - - +
304F THR* 2.8 32.7 + - - +
438F TYR* 3.8 23.6 - - + +
439F TRP* 3.9 15.2 - - - -
538F THR* 4.6 17.5 - - + -
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Residues in contact with ILE 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F VAL* 3.2 22.7 + - + +
298F PHE* 3.8 3.1 - - - +
300F GLU* 1.3 76.5 - - - +
302F ALA* 1.3 63.5 + - - +
305F PHE* 3.9 13.7 + - - +
380F ALA* 3.5 32.3 - - + +
381F MET* 3.7 8.3 - - - +
384F THR* 3.0 21.5 - - - +
434F ALA* 3.0 42.4 - - + +
435F GLY* 3.3 13.7 - - - +
438F TYR* 3.5 29.6 - - + -
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Residues in contact with ALA 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F PHE* 3.0 21.2 + - + +
299F SER* 3.4 11.0 - - - +
301F ILE* 1.3 80.1 - - - +
303F ALA* 1.3 68.3 + - - +
306F SER* 3.1 28.2 + - - +
310F LEU* 4.9 0.7 - - + -
366F TRP* 4.9 10.3 - - + +
369F THR* 5.3 4.3 - - + -
370F MET* 6.4 2.2 - - + -
381F MET* 3.7 13.4 - - + +
384F THR* 3.9 17.0 + - + -
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Residues in contact with ALA 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F SER 2.9 16.8 + - - +
300F GLU* 4.1 4.3 - - - +
302F ALA* 1.3 76.7 - - - +
304F THR* 1.3 67.8 + - - +
306F SER* 3.5 0.4 + - - -
307F ARG* 2.9 15.6 + - - -
308F LYS 3.2 29.7 + - - +
309F ARG* 4.7 1.3 - - - -
310F LEU* 4.3 17.9 - - + +
369F THR* 4.4 6.2 - - - +
535F GLY* 5.1 3.3 - - - +
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Residues in contact with THR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F GLU* 2.8 18.1 + - - +
301F ILE 4.3 0.7 - - - -
303F ALA* 1.3 81.3 - - - +
305F PHE* 1.3 81.8 + - + +
307F ARG* 2.8 24.9 + - - +
438F TYR* 2.5 35.5 + - + -
532F ASP* 4.0 12.3 - - + -
533F PRO* 4.7 6.1 - - + +
535F GLY* 4.1 8.6 + - - -
536F GLY* 3.4 30.4 - - - +
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Residues in contact with PHE 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F ILE 3.9 6.0 + - - +
302F ALA 3.5 1.6 + - - -
304F THR* 1.3 89.1 - - + +
306F SER* 1.3 65.1 + - - +
307F ARG* 3.1 3.7 + - - +
374F ARG 3.7 0.9 - - - +
375F ILE* 3.4 0.5 - - - -
376F VAL* 2.7 53.1 + - + +
378F HIS* 3.5 36.6 - + + -
380F ALA* 4.1 20.2 - - + -
381F MET* 3.8 28.5 - - + -
437F THR* 6.0 1.1 - - + -
438F TYR* 4.3 11.7 - + - -
447F LYS* 5.1 3.6 - - - -
532F ASP* 3.2 37.7 - - + -
533F PRO* 5.1 8.1 - - + -
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Residues in contact with SER 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302F ALA* 3.1 14.4 + - - +
303F ALA* 4.2 3.4 - - - -
305F PHE* 1.3 72.4 - - - +
307F ARG* 1.3 64.7 + - - +
308F LYS* 4.5 2.3 - - - +
369F THR* 4.2 17.4 - - - +
370F MET* 4.3 5.1 - - - +
373F GLY 3.2 8.0 - - - +
374F ARG 2.3 28.1 - - - +
375F ILE* 2.9 38.9 - - - +
381F MET* 3.1 17.5 - - - +
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Residues in contact with ARG 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F ALA 2.9 3.6 + - - -
304F THR 2.8 21.4 + - - +
305F PHE* 3.7 4.5 - - - +
306F SER* 1.3 79.9 - - - +
308F LYS* 1.3 60.4 + - - +
374F ARG* 3.5 45.3 + - - +
376F VAL* 4.0 24.3 - - - +
533F PRO* 4.3 27.8 - - + +
534F TRP* 4.5 28.2 - - + +
535F GLY* 4.9 10.1 - - - -
73G ASN* 6.3 1.0 - - - +
78G TYR* 5.0 3.8 - - - -
79G SER* 2.9 38.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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