Contacts of the helix formed by residues 358 - 377 (chain F) in PDB entry 3IFS
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 THR 358 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F GLU* 4.0 22.0 + - + +
339F LEU 3.1 14.1 - - - +
340F THR* 4.2 11.2 - - - +
341F ILE* 4.2 2.5 - - - -
356F GLY 5.0 2.0 - - - +
357F GLU* 1.3 80.5 + - - +
359F VAL* 1.3 64.0 + - - +
360F ASP* 3.5 5.5 + - - +
361F PHE* 3.0 39.9 + - - +
362F VAL* 3.4 10.2 + - - +
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Residues in contact with VAL 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 3.7 20.1 - - + +
123E SER* 3.8 17.0 - - - -
126E MSE 3.4 29.2 - - + -
154E LEU* 4.5 7.9 - - + -
158E ILE* 3.8 23.3 - - + -
339F LEU* 2.8 32.7 + - + +
341F ILE* 4.3 12.1 - - + -
358F THR* 1.3 70.8 - - - +
360F ASP* 1.3 63.7 + - - +
362F VAL* 3.1 11.6 + - - +
363F ASN* 3.1 16.8 + - - +
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Residues in contact with ASP 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE 5.0 1.0 - - - +
122E SER* 6.2 0.2 - - - -
123E SER* 4.1 12.5 + - - +
275F GLU* 4.4 4.7 - - - +
331F LYS* 5.6 0.9 + - - -
332F VAL 5.3 3.1 - - - +
333F GLY 4.6 8.1 - - - +
335F SER* 3.7 27.6 + - - -
338F GLU* 3.6 22.5 + - - +
339F LEU 4.8 0.2 + - - -
358F THR* 3.1 3.1 + - - +
359F VAL* 1.3 77.6 - - - +
361F PHE* 1.3 66.0 + - - +
363F ASN* 3.1 20.6 + - - +
364F THR* 2.8 37.0 + - - -
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Residues in contact with PHE 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E LEU 4.4 3.6 - - - -
433E LEU* 3.9 39.5 - - + -
354F LEU* 4.3 2.5 - - + -
357F GLU* 3.8 42.0 - - + +
358F THR* 3.0 27.8 + - - +
360F ASP* 1.3 75.5 - - - +
362F VAL* 1.3 63.8 + - + +
364F THR* 3.2 8.2 + - - -
365F LYS* 3.0 62.5 + - + +
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Residues in contact with VAL 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 3.9 20.4 - - + -
150E THR* 4.2 23.6 - - + -
154E LEU* 4.3 8.1 - - + -
429E MSE 5.0 2.4 - - - +
433E LEU* 3.8 29.8 - - + +
341F ILE* 3.8 22.2 - - + -
354F LEU* 4.2 9.6 - - + -
358F THR 3.7 12.6 - - - +
359F VAL 3.1 8.0 + - - +
361F PHE* 1.3 79.5 - - + +
363F ASN* 1.3 64.2 + - - +
365F LYS* 3.3 2.4 + - - +
366F ALA* 2.9 22.2 + - - +
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Residues in contact with ASN 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 3.3 47.7 + - - +
122E SER* 4.8 0.2 - - - +
274F TYR* 3.1 53.4 + - - +
275F GLU* 4.2 7.7 + - - +
308F SER 4.9 1.4 + - - -
331F LYS* 5.9 0.2 - - - -
359F VAL 3.1 6.1 + - - +
360F ASP* 3.1 23.4 + - - +
362F VAL* 1.3 75.4 - - - +
364F THR* 1.3 62.3 + - - +
366F ALA* 3.3 2.4 + - - +
367F TYR* 3.0 22.7 + - - +
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Residues in contact with THR 364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F LYS* 3.9 27.2 + - - +
360F ASP* 2.8 25.0 + - - -
361F PHE* 3.5 11.1 - - - -
363F ASN* 1.3 76.6 - - - +
365F LYS* 1.3 65.7 + - - +
367F TYR* 3.2 8.1 + - + +
368F GLU* 3.0 49.1 + - + +
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Residues in contact with LYS 365 (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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429E MSE 4.2 6.5 - - - +
432E LEU* 4.0 32.4 - - + +
433E LEU* 3.7 33.2 - - + -
446E GLU* 5.8 1.8 + - - -
361F PHE* 3.0 51.2 + - + +
362F VAL 3.9 0.2 - - - +
364F THR* 1.3 81.0 - - - +
366F ALA* 1.3 60.6 + - - +
368F GLU* 2.9 29.8 + - - +
369F GLY* 3.0 27.0 + - - -
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Residues in contact with ALA 366 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 3.8 17.3 - - + -
425E TYR* 5.8 2.0 - - + -
429E MSE 3.6 31.5 - - - +
274F TYR* 4.3 9.9 - - + -
308F SER* 5.2 4.3 - - - -
311F LEU* 5.8 0.4 - - + -
362F VAL 2.9 17.8 + - - +
363F ASN 3.5 5.8 - - - +
365F LYS* 1.3 76.0 - - - +
367F TYR* 1.3 56.7 + - - +
370F THR* 2.5 40.8 + - - +
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Residues in contact with TYR 367 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F TYR* 3.4 40.3 + + + -
329F VAL* 3.7 23.3 - - + -
331F LYS* 3.3 41.5 - - + +
363F ASN 3.0 12.6 + - - +
364F THR* 3.2 13.2 + - + +
366F ALA* 1.3 76.9 - - - +
368F GLU* 1.3 82.1 + - + +
370F THR* 3.8 1.4 - - - -
371F LEU* 2.9 46.4 + - + +
383F ILE* 3.3 36.7 - - - +
385F ASN* 5.0 0.5 + - - -
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Residues in contact with GLU 368 (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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432E LEU* 3.8 13.8 - - + +
449E LEU* 4.0 32.3 - - + +
364F THR* 3.0 26.8 + - - +
365F LYS* 2.9 37.5 + - - +
366F ALA 3.4 0.2 - - - -
367F TYR* 1.3 95.8 - - + +
369F GLY* 1.3 61.1 + - - +
371F LEU* 3.3 5.9 + - - +
372F LEU* 3.2 28.3 + - - +
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Residues in contact with GLY 369 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E TYR 4.5 3.4 - - - -
428E ASN* 3.1 34.0 + - - +
429E MSE 4.3 4.3 - - - -
432E LEU* 3.6 10.9 - - - +
445E LEU* 5.1 0.2 - - - -
365F LYS 3.0 15.1 + - - -
368F GLU* 1.3 76.4 - - - +
370F THR* 1.3 56.5 + - - +
372F LEU* 3.5 1.7 + - - -
373F ALA* 2.9 26.6 + - - +
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Residues in contact with THR 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E TYR* 3.5 30.9 + - + +
274F TYR* 3.4 19.7 + - - +
307F PHE* 4.4 2.0 - - + -
311F LEU* 3.6 18.9 - - + +
366F ALA* 2.5 23.8 + - - -
369F GLY* 1.3 75.4 - - - +
371F LEU* 1.3 55.2 + - - +
373F ALA* 3.7 0.2 - - - +
374F HIS* 2.7 66.9 + - + +
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Residues in contact with LEU 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E LEU* 5.7 3.4 - - + -
11F LYS* 3.9 24.2 - - + -
329F VAL* 4.9 3.6 - - + -
367F TYR* 2.9 34.4 + - + +
368F GLU* 3.7 6.1 - - - +
369F GLY 3.3 0.2 - - - -
370F THR* 1.3 78.2 - - - +
372F LEU* 1.3 69.3 + - + +
374F HIS* 4.1 1.2 - - - +
375F SER* 2.7 46.2 + - - +
381F ASN* 3.6 35.7 + - + +
383F ILE* 3.8 32.8 - - + -
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Residues in contact with LEU 372 (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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428E ASN* 4.0 9.2 - - - +
432E LEU* 5.0 0.2 - - + -
445E LEU* 3.9 33.0 - - + +
448E ARG* 3.6 39.3 - - + +
449E LEU* 3.8 35.0 - - + -
11F LYS* 5.4 6.5 - - + -
368F GLU 3.2 16.7 + - - +
369F GLY* 3.9 3.4 - - - +
371F LEU* 1.3 87.4 - - + +
373F ALA* 1.3 60.8 + - - +
375F SER* 3.7 3.7 - - - +
376F ASP* 3.0 36.9 + - - +
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Residues in contact with ALA 373 (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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424E ALA* 3.8 7.2 - - + -
425E TYR* 3.6 29.2 - - + +
428E ASN* 3.4 13.4 - - - +
319F GLN* 3.1 19.6 + - - +
369F GLY 2.9 19.5 + - - +
370F THR 3.7 3.1 - - - +
372F LEU* 1.3 76.3 - - - +
374F HIS* 1.3 62.5 + - + +
376F ASP* 3.2 7.3 + - - +
377F GLY 3.0 16.8 + - - -
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Residues in contact with HIS 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425E TYR* 5.3 3.5 - - + +
307F PHE* 3.8 10.7 - + - -
311F LEU* 3.8 12.0 - - + +
315F GLY 4.6 4.8 + - - -
318F VAL* 3.4 29.9 - - + +
319F GLN* 3.3 24.4 - - - +
327F GLU* 2.7 35.0 + - - +
370F THR* 2.7 47.9 + - + +
371F LEU* 5.3 0.2 - - - -
373F ALA* 1.3 73.2 - - + +
375F SER* 1.3 62.6 + - - +
377F GLY* 3.0 11.1 + - - +
378F GLY 3.2 0.5 + - - -
379F VAL* 3.0 26.8 + - + +
381F ASN* 3.7 10.6 + - - +
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Residues in contact with SER 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E ARG* 4.7 5.4 - - - -
11F LYS 4.2 10.8 + - - -
14F SER* 5.7 1.6 - - - -
15F PHE* 3.3 26.2 - - - -
371F LEU* 2.7 35.1 + - - +
372F LEU* 3.7 8.1 - - - -
373F ALA 3.3 0.2 - - - -
374F HIS* 1.3 74.4 - - - +
376F ASP* 1.3 61.8 + - - +
378F GLY* 3.0 16.3 + - - -
379F VAL 3.4 15.8 + - - -
381F ASN* 4.1 7.4 + - - +
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Residues in contact with ASP 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428E ASN* 5.2 2.6 + - - -
448E ARG* 2.8 41.4 + - - -
319F GLN* 4.7 0.7 - - - +
372F LEU 3.0 19.9 + - - +
373F ALA* 3.7 6.6 - - - +
375F SER* 1.3 76.9 - - - +
377F GLY* 1.3 59.1 + - - +
378F GLY 3.2 1.2 + - - -
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Residues in contact with GLY 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E GLN* 5.6 1.4 + - - -
319F GLN* 3.6 26.5 - - - +
323F ARG* 2.8 31.5 + - - -
373F ALA 3.0 5.9 + - - -
374F HIS 3.0 10.2 + - - -
376F ASP* 1.3 76.8 - - - +
378F GLY* 1.3 56.7 + - - +
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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
------------------------------------------------------------
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