Contacts of the helix formed by residues 358 - 377 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A GLU* 3.9 25.9 + - + +
339A LEU 3.1 15.0 - - - +
340A THR* 4.0 13.9 - - - +
341A ILE* 4.3 2.5 - - - -
356A GLY 5.1 2.5 - - - +
357A GLU* 1.3 79.2 + - - +
359A VAL* 1.3 64.4 + - - +
360A ASP* 3.6 4.5 + - - +
361A PHE* 3.0 38.4 + - - +
362A VAL* 3.4 10.0 + - - +
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 2.8 26.3 + - + +
341A ILE* 4.2 10.1 - - + +
358A THR* 1.3 71.0 - - - +
360A ASP* 1.3 62.9 + - - +
362A VAL* 3.0 20.2 + - - +
363A ASN 3.0 9.5 + - - -
121B ILE* 3.6 32.8 - - + +
123B SER* 3.8 26.0 - - - +
126B MSE 4.2 9.6 - - + -
154B LEU* 4.2 11.7 - - + -
158B ILE* 3.8 28.3 - - + -
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Residues in contact with ASP 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLU* 4.4 5.5 - - - +
331A LYS* 5.7 1.2 + - - -
332A VAL 5.5 2.8 - - - +
333A GLY 4.9 6.6 - - - +
335A SER* 3.8 30.9 + - - -
338A GLU* 3.7 22.6 - - - +
339A LEU 5.7 0.2 - - - +
358A THR* 3.2 3.5 + - - +
359A VAL* 1.3 79.4 - - - +
361A PHE* 1.3 60.2 + - - +
363A ASN* 3.3 20.0 + - - +
364A THR* 2.9 37.9 + - - -
121B ILE 4.9 1.0 - - - +
122B SER* 6.2 0.2 - - - -
123B SER* 4.1 10.1 + - - +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.2 7.9 - - + -
357A GLU* 3.7 42.0 - - + +
358A THR* 3.0 27.2 + - - +
360A ASP* 1.3 75.7 - - - +
362A VAL* 1.3 68.0 + - + +
364A THR* 3.2 8.0 + - - -
365A LYS* 3.1 52.6 + - + +
432B LEU 4.4 9.2 - - - -
433B LEU* 3.8 28.9 - - + -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ILE* 3.8 21.8 - - + -
354A LEU* 4.3 10.3 - - + -
358A THR 3.7 12.6 - - - +
359A VAL 3.0 7.3 + - - +
361A PHE* 1.3 78.8 - - + +
363A ASN* 1.3 65.1 + - - +
365A LYS* 3.2 2.8 + - - +
366A ALA* 3.0 22.3 + - - +
121B ILE* 3.9 23.6 - - + -
150B THR* 4.3 19.3 - - + -
154B LEU* 4.5 7.4 - - + -
429B MSE 5.1 3.0 - - - +
433B LEU* 3.9 29.6 - - + -
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Residues in contact with ASN 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.1 48.5 + - - +
275A GLU* 4.1 9.5 + - - +
308A SER 4.9 2.1 + - - -
331A LYS* 5.9 0.4 - - - -
359A VAL 3.0 7.0 + - - +
360A ASP* 3.3 22.3 + - - +
362A VAL* 1.3 77.2 - - - +
364A THR* 1.3 57.4 + - - +
366A ALA* 3.4 4.9 + - - +
367A TYR* 3.1 26.7 + - - +
121B ILE* 3.2 46.7 + - - +
122B SER* 4.7 0.2 - - - +
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Residues in contact with THR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS* 4.0 26.7 + - - +
360A ASP* 2.9 28.4 + - - -
361A PHE* 3.5 7.4 - - - -
362A VAL 3.2 0.2 - - - -
363A ASN* 1.3 74.1 - - - +
365A LYS* 1.3 69.9 + - - +
367A TYR* 3.2 8.2 + - + +
368A GLU* 3.0 47.3 + - + +
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Residues in contact with LYS 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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361A PHE* 3.1 42.2 + - + +
362A VAL 3.2 0.4 + - - +
364A THR* 1.3 82.2 - - - +
366A ALA* 1.3 60.9 + - - +
368A GLU* 2.8 33.2 + - - +
369A GLY* 2.9 27.0 + - - -
429B MSE 4.2 6.1 - - - +
432B LEU* 3.8 40.9 - - + +
433B LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 4.3 11.0 - - + -
308A SER* 5.1 4.7 - - - -
311A LEU* 5.8 1.1 - - + -
362A VAL 3.0 13.3 + - - +
363A ASN* 3.4 10.1 - - - +
364A THR 3.2 0.2 - - - -
365A LYS* 1.3 78.2 - - - +
367A TYR* 1.3 55.4 + - - +
369A GLY 3.9 0.2 - - - -
370A THR* 2.7 39.8 + - - +
121B ILE* 4.0 15.9 - - + -
425B TYR* 6.0 0.9 - - + -
429B MSE 3.8 28.5 - - - +
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Residues in contact with TYR 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.5 38.6 + + + -
329A VAL* 3.7 24.0 - - + -
331A LYS* 3.4 41.8 - - + +
363A ASN 3.1 13.2 + - - +
364A THR* 3.5 11.2 - - + +
366A ALA* 1.3 75.9 - - - +
368A GLU* 1.3 78.7 + - + +
370A THR* 3.8 1.4 - - - -
371A LEU* 2.9 51.8 + - + +
383A ILE* 3.1 36.9 - - - +
385A ASN* 5.0 0.3 + - - -
449B LEU* 6.4 0.4 - - + -
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A THR* 3.0 25.7 + - - +
365A LYS* 2.8 40.6 + - - +
367A TYR* 1.3 94.3 - - + +
369A GLY* 1.3 62.7 + - - +
371A LEU* 3.4 4.6 + - - +
372A LEU* 3.2 28.9 + - - +
432B LEU* 3.8 9.8 - - + +
449B LEU* 3.7 41.1 - - + +
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Residues in contact with GLY 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS 2.9 17.6 + - - -
366A ALA 3.9 0.2 - - - -
368A GLU* 1.3 77.1 - - - +
370A THR* 1.3 57.4 + - - +
372A LEU* 3.6 1.5 + - - -
373A ALA* 3.0 24.8 + - - +
425B TYR 4.5 3.8 - - - -
428B ASN* 3.1 35.9 + - - +
429B MSE 4.3 1.8 - - - -
432B LEU* 3.5 9.4 - - - +
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Residues in contact with THR 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 3.4 19.5 - - - +
307A PHE* 4.4 1.8 - - + -
311A LEU* 3.6 18.4 - - + +
366A ALA 2.7 21.5 + - - -
369A GLY* 1.3 75.6 - - - +
371A LEU* 1.3 60.1 + - - +
373A ALA* 3.7 0.2 - - - +
374A HIS* 2.8 64.9 + - + +
425B TYR* 3.5 29.5 + - + +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.9 27.8 - - + -
329A VAL* 5.0 3.6 - - + -
367A TYR* 2.9 36.3 + - + +
368A GLU* 3.4 5.6 + - - +
370A THR* 1.3 75.8 - - - +
372A LEU* 1.3 70.8 + - + +
374A HIS* 4.0 1.0 - - - +
375A SER* 2.6 43.6 + - - +
381A ASN* 3.8 32.2 + - + +
383A ILE* 3.8 35.0 - - + -
449B LEU* 5.1 5.2 - - + -
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Residues in contact with LEU 372 (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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11A LYS* 5.6 2.9 - - + -
368A GLU 3.2 15.7 + - - +
369A GLY* 4.1 0.4 - - - +
371A LEU* 1.3 90.0 - - + +
373A ALA* 1.3 64.9 + - - +
375A SER* 3.5 4.4 - - - +
376A ASP* 3.0 29.7 + - - +
428B ASN* 4.0 11.2 - - - +
432B LEU* 5.0 2.0 - - + -
445B LEU* 3.7 41.3 - - + +
448B ARG* 4.0 39.5 - - + +
449B LEU* 3.7 28.7 - - + -
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Residues in contact with ALA 373 (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 GLN* 3.0 32.5 + - - +
369A GLY 3.0 19.8 + - - +
370A THR 3.3 3.8 + - - +
372A LEU* 1.3 75.7 - - - +
374A HIS* 1.3 63.0 + - + +
376A ASP* 3.2 8.5 + - - +
377A GLY 3.0 9.7 + - - -
424B ALA* 3.8 6.7 - - + -
425B TYR* 3.7 24.5 - - + +
428B ASN* 3.4 13.6 - - - +
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Residues in contact with HIS 374 (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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307A PHE* 3.9 3.8 - + - -
311A LEU* 3.7 18.3 - - + +
315A GLY* 4.6 4.9 + - - -
318A VAL* 3.5 29.8 - - + +
319A GLN* 3.3 22.9 - - - +
327A GLU* 2.8 34.6 + - - +
370A THR* 2.8 47.6 + - + +
371A LEU* 4.1 0.4 - - - +
373A ALA* 1.3 72.2 - - + +
375A SER* 1.3 66.2 + - - +
377A GLY* 3.1 8.8 + - - -
378A GLY 3.2 0.9 + - - -
379A VAL* 2.9 29.2 + - + +
381A ASN* 3.8 9.5 + - - +
425B TYR* 5.2 3.8 - - + +
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Residues in contact with SER 375 (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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11A LYS 4.2 12.9 + - - -
15A PHE* 3.2 25.5 - - - -
371A LEU* 2.6 34.0 + - - +
372A LEU* 3.5 8.5 - - - -
373A ALA 3.3 0.2 - - - -
374A HIS* 1.3 74.7 - - - +
376A ASP* 1.3 66.3 + - - +
378A GLY 3.1 11.1 + - - -
379A VAL 3.4 16.3 + - - -
381A ASN* 4.1 6.6 + - - +
448B ARG* 4.6 5.8 - - - -
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Residues in contact with ASP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 4.8 0.9 - - - +
372A LEU 3.0 19.6 + - - +
373A ALA* 3.6 7.5 - - - +
375A SER* 1.3 76.4 - - - +
377A GLY* 1.3 57.5 + - - +
378A GLY 3.3 1.6 + - - -
428B ASN* 5.2 3.1 + - - -
448B ARG* 2.7 43.6 + - - -
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Residues in contact with GLY 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A GLN* 3.7 26.9 - - - +
323A ARG* 2.9 30.3 + - - -
373A ALA 3.0 9.1 + - - -
374A HIS 3.1 6.6 + - - -
376A ASP* 1.3 76.4 - - - +
378A GLY* 1.3 56.7 + - - +
379A VAL 3.7 0.4 - - - -
297B GLN* 5.8 1.2 + - - -
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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
------------------------------------------------------------
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