Contacts of the helix formed by residues 356 - 369 (chain A) 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 ALA 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A THR 4.6 0.6 + - - -
353A MET 4.0 14.0 + - - +
354A ILE 2.5 6.9 + - - -
355A ILE* 1.3 70.5 - - - +
357A ILE* 1.3 56.9 + - - +
358A PRO* 3.0 2.5 - - - -
359A THR* 2.4 33.7 + - - -
360A GLY 2.9 10.2 + - - -
399A VAL* 4.9 3.1 - - + -
1002A HEO 3.2 54.6 - - + +
100B ILE* 4.1 3.4 - - + -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ILE* 3.4 30.3 - - + +
356A ALA* 1.3 77.4 - - - +
358A PRO* 1.3 68.4 - - + +
360A GLY* 3.4 2.5 + - - +
361A VAL* 3.2 25.6 + - + +
1002A HEO 5.5 0.2 - - - -
93B TRP* 5.7 9.4 - - + +
96B PRO* 4.8 13.4 - - + +
97B ILE* 3.9 47.8 - - + +
100B ILE* 4.5 13.2 - - + -
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Residues in contact with PRO 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ALA* 4.4 5.2 - - + +
322A CYS* 5.1 10.8 - - + -
323A ILE* 3.6 33.8 - - + +
326A LEU* 5.1 12.1 - - + -
354A ILE* 3.1 13.9 - - + +
355A ILE* 3.1 20.2 - - + +
356A ALA 3.1 5.4 - - - -
357A ILE* 1.3 95.9 - - + +
359A THR* 1.3 59.6 + - - +
361A VAL* 3.4 21.8 - - + +
362A LYS* 3.7 11.3 - - - +
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PHE* 5.4 8.1 - - + -
323A ILE* 5.3 2.5 - - + -
355A ILE 2.7 21.3 + - - -
356A ALA* 2.4 23.7 + - - -
358A PRO* 1.3 72.2 - - - +
360A GLY* 1.3 64.8 + - - +
361A VAL 3.4 0.3 + - - -
362A LYS* 3.5 9.0 + - - +
363A ILE* 3.5 21.1 + - + +
391A PHE* 3.8 24.9 - - + -
1002A HEO 3.3 44.2 + - + +
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ALA 2.9 10.7 + - - -
357A ILE* 3.4 3.5 + - - -
359A THR* 1.3 75.1 - - - +
361A VAL* 1.3 69.9 + - - +
363A ILE* 3.2 5.2 + - - -
364A PHE* 2.9 46.1 + - - -
1002A HEO 3.3 15.6 - - - +
60B LEU* 6.5 0.4 - - - -
96B PRO* 6.0 2.7 - - - -
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER* 3.8 20.0 - - - +
316A LEU* 3.3 21.5 - - + +
319A ALA* 3.9 18.6 - - + -
357A ILE* 3.2 22.0 + - + +
358A PRO* 3.4 14.8 - - + +
360A GLY* 1.3 78.7 - - - +
362A LYS* 1.3 65.0 + - - +
364A PHE* 3.8 1.6 - - - +
365A ASN* 2.7 28.6 + - - +
93B TRP* 3.5 29.8 - - + -
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Residues in contact with LYS 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 6.1 0.4 - - - -
295A PHE* 3.4 35.2 - - + +
316A LEU* 3.0 34.9 + - + +
319A ALA* 3.3 17.3 - - + -
320A THR* 2.6 33.9 + - - +
323A ILE* 3.7 17.0 - - + -
358A PRO 3.7 11.9 - - - +
359A THR* 3.7 6.5 - - + +
361A VAL* 1.3 80.4 - - - +
363A ILE* 1.3 69.1 + - + +
365A ASN* 3.0 3.3 + - - +
366A TRP* 2.9 46.2 + - + -
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Residues in contact with ILE 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A THR* 3.5 13.4 + - + +
360A GLY* 3.2 8.9 + - - +
362A LYS* 1.3 75.4 - - + +
364A PHE* 1.3 63.1 + - + +
366A TRP* 2.6 52.4 + - + +
367A LEU* 3.1 23.9 + - + +
387A PHE* 3.8 17.5 - - + -
388A ILE* 4.3 18.4 - - + -
391A PHE* 4.7 10.3 - - + -
392A SER* 3.7 19.7 - - - +
1002A HEO 5.7 2.5 - - + -
60B LEU* 4.2 28.3 - - + -
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Residues in contact with PHE 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY* 2.9 37.4 + - - +
361A VAL* 3.8 2.2 - - - +
363A ILE* 1.3 84.6 - - + +
365A ASN* 1.3 62.9 + - - +
367A LEU* 3.1 40.2 + - + +
368A PHE* 3.1 17.2 + - + -
1002A HEO 4.9 4.9 - - + -
56B ILE* 4.6 18.8 - - + -
59B ILE* 5.7 4.0 - - + -
60B LEU* 4.9 14.6 - - + -
63B VAL* 5.3 6.5 - - + -
92B VAL* 3.3 57.9 - - + -
95B VAL* 6.4 0.2 - - + -
96B PRO* 4.3 13.2 - - + -
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Residues in contact with ASN 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A PHE* 3.2 38.1 + - - +
312A GLY* 2.8 43.4 + - - -
315A SER* 3.5 11.5 + - - -
316A LEU* 2.9 27.4 - - + +
361A VAL* 2.7 38.1 + - - +
362A LYS 3.2 5.4 - - - +
363A ILE 2.8 2.4 + - - -
364A PHE* 1.3 75.0 - - - +
366A TRP* 1.3 61.5 + - - +
368A PHE* 3.8 1.2 + - - -
369A THR* 3.2 5.4 + - - -
89B GLU* 5.6 3.2 - - - +
92B VAL* 5.7 0.7 - - - +
93B TRP* 4.8 4.9 - - - -
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Residues in contact with TRP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PHE* 3.6 28.7 - + + -
298A PHE* 3.3 39.5 - + + -
299A SER* 3.2 28.5 + - - +
302A ALA* 4.9 6.2 - - + +
310A LEU* 3.3 31.9 - - + +
316A LEU* 4.9 3.9 - - + +
362A LYS* 2.9 53.1 + - + -
363A ILE* 2.6 28.9 + - + +
365A ASN* 1.3 70.8 - - - +
367A LEU* 1.3 65.9 + - + +
369A THR* 2.9 21.9 + - - -
370A MET* 3.3 16.7 + - + +
387A PHE* 3.4 24.7 - + - -
388A ILE* 5.7 3.4 - - + -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ILE* 3.1 15.4 + - + +
364A PHE* 3.1 40.8 - - + +
366A TRP* 1.3 76.2 - - - +
368A PHE* 1.3 54.4 + - + +
370A MET* 2.4 54.5 + - + +
371A TYR* 3.0 11.3 + - - +
388A ILE* 4.1 13.2 - - + -
60B LEU* 5.7 3.8 - - + +
63B VAL* 3.4 41.7 - - + -
64B GLY* 4.0 17.3 - - - +
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Residues in contact with PHE 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LYS* 2.9 25.8 + - - -
311A PHE* 3.2 47.1 - + + +
364A PHE* 3.1 17.2 + - + -
365A ASN* 4.0 2.5 - - - +
367A LEU* 1.3 78.7 - - + +
369A THR* 1.3 56.6 + - - +
370A MET 3.0 0.2 - - - -
371A TYR* 3.6 29.4 + + + +
88B VAL* 3.0 51.1 - - + -
91B VAL* 4.1 18.4 - - + -
92B VAL* 4.9 7.4 - - + -
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ALA* 5.3 3.6 - - + -
303A ALA* 4.4 12.8 - - - +
306A SER* 4.2 9.6 - - - -
308A LYS* 3.3 49.9 - - - +
309A ARG 3.3 9.2 - - - +
310A LEU* 3.4 8.8 - - + -
311A PHE* 2.7 30.8 + - - -
365A ASN 3.2 5.9 + - - -
366A TRP* 2.9 18.4 + - - -
367A LEU 2.8 0.6 + - - -
368A PHE* 1.3 76.9 - - - +
370A MET* 1.3 59.1 + - + +
373A GLY 5.4 0.2 - - - +
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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