Contacts of the helix formed by residues 365 - 382 (chain A) in PDB entry 5IWS
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 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A PHE* 3.0 17.0 + - + +
362A MSE 3.5 4.8 - - - +
364A ILE* 1.3 81.0 - - + +
366A PRO* 1.3 68.2 - - - +
367A VAL* 3.3 4.5 - - + +
368A LEU* 3.6 25.6 - - + +
369A TYR 3.3 13.5 + - - -
441A LEU* 4.0 24.2 - - + -
442A PRO* 5.7 1.6 - - + -
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MSE 4.2 4.0 - - - +
363A PHE 5.3 2.0 - - - +
364A ILE 4.0 5.6 - - - +
365A ALA* 1.3 85.3 - - - +
367A VAL* 1.3 71.9 + - + +
369A TYR* 3.3 31.3 - - + -
370A VAL* 3.3 9.9 + - - +
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Residues in contact with VAL 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ALA* 4.8 8.3 - - + -
366A PRO* 1.3 86.6 - - + +
368A LEU* 1.3 66.0 + - + +
370A VAL* 3.3 14.2 - - + +
371A VAL* 3.2 26.3 - - + +
435A LEU* 5.6 0.8 - - - +
439A PHE* 6.1 4.9 - - + -
441A LEU* 5.5 9.4 - - + -
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MSE 5.8 0.7 - - - -
361A PHE* 3.7 34.5 - - + -
365A ALA* 3.3 20.0 + - + +
367A VAL* 1.3 82.9 - - + +
369A TYR* 1.3 54.9 + - - +
370A VAL 3.5 0.2 - - - -
371A VAL* 4.1 2.6 - - + +
372A TYR* 3.2 25.6 + - - +
432A PHE* 3.5 36.1 - - + -
435A LEU* 3.7 28.9 - - + -
436A ILE* 4.7 8.5 - - + -
441A LEU* 3.6 30.3 - - + -
443A THR* 5.0 3.1 - - + -
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Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 3.8 16.8 - - + -
233A LEU* 3.3 44.2 + - + +
236A PRO* 4.2 13.0 - - + -
237A PHE* 4.6 7.5 - + - -
361A PHE* 4.5 3.1 - - - -
362A MSE 3.6 51.4 - - + +
365A ALA 3.3 7.2 + - - +
366A PRO* 3.3 29.4 + - + -
367A VAL 3.3 0.2 - - - -
368A LEU* 1.3 78.4 - - - +
370A VAL* 1.3 64.2 + - + +
372A TYR* 3.9 10.4 - + - +
373A ALA* 3.2 20.3 + - - +
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 6.5 0.2 - - + -
233A LEU* 4.8 11.9 - - + -
366A PRO 3.3 15.1 + - - +
367A VAL* 3.3 20.6 - - + +
369A TYR* 1.3 83.7 - - + +
371A VAL* 1.3 72.4 + - + +
372A TYR 3.3 0.2 - - - -
373A ALA* 3.2 13.5 + - + +
374A ILE* 3.3 22.8 + - + +
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Residues in contact with VAL 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 3.2 19.2 + - + +
368A LEU 4.3 3.4 - - - +
370A VAL* 1.3 80.3 - - + +
372A TYR* 1.3 63.2 + - - +
374A ILE* 3.2 18.2 - - + +
375A THR* 3.1 24.5 + - + +
431A LEU* 3.9 28.9 - - + -
432A PHE* 5.3 3.6 - - + -
435A LEU* 4.4 20.0 - - + -
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Residues in contact with TYR 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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232A ARG* 3.4 26.9 + - + -
313A GLY* 5.7 4.1 - - - -
317A ALA* 5.9 0.4 - - + -
318A LEU* 3.6 30.7 - - + +
321A ILE* 3.5 22.4 - - + -
354A THR* 4.6 1.4 - - - +
358A GLU* 2.3 41.9 + - + +
361A PHE* 4.1 13.7 - + + -
362A MSE 5.0 7.9 - - + -
368A LEU 3.2 18.4 + - - +
369A TYR* 3.9 9.2 - + - +
370A VAL 3.3 0.2 - - - -
371A VAL* 1.3 78.7 - - - +
373A ALA* 1.3 60.2 + - - +
375A THR* 3.0 17.8 + - - -
376A THR* 2.8 38.1 + - + +
428A ASN* 5.1 2.0 - - - -
432A PHE* 3.6 13.2 - + + -
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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
----------------------------------------------------------
229A THR* 3.3 25.0 + - + -
232A ARG* 3.9 17.0 - - + -
233A LEU* 3.7 25.4 - - + -
369A TYR 3.2 15.2 + - - +
370A VAL* 3.2 11.1 + - + +
371A VAL 3.1 1.0 - - - -
372A TYR* 1.3 79.2 - - - +
374A ILE* 1.3 58.2 + - - +
376A THR* 2.8 16.6 + - - -
377A GLY 3.1 8.8 + - - -
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Residues in contact with ILE 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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225A PHE* 3.7 16.8 - - + -
229A THR* 4.0 20.0 - - + -
370A VAL* 3.3 15.2 + - + +
371A VAL* 3.2 31.6 - - + +
373A ALA* 1.3 76.6 - - - +
375A THR* 1.3 65.3 + - + +
377A GLY* 3.1 1.7 + - - -
378A LEU* 2.9 34.6 + - + +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 3.1 18.3 + - + +
372A TYR* 3.0 26.5 + - - -
374A ILE* 1.3 79.1 - - + +
376A THR* 1.3 59.8 + - - +
378A LEU* 3.2 22.0 + - + +
379A ALA 3.2 8.7 + - - -
424A PHE* 3.5 17.8 - - - -
428A ASN* 3.9 21.4 + - - +
431A LEU* 3.9 27.6 - - + -
432A PHE* 5.1 1.0 - - + -
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Residues in contact with THR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLY 4.2 2.1 + - - -
232A ARG* 3.2 22.1 - - - +
309A GLY 5.6 2.5 - - - +
313A GLY* 5.3 12.1 - - - -
317A ALA* 5.4 6.7 - - + -
372A TYR* 2.8 50.6 + - + +
373A ALA 2.8 14.2 + - - -
375A THR* 1.3 80.1 + - - +
377A GLY* 1.3 60.1 + - - +
379A ALA* 3.3 9.3 + - + +
380A PHE* 3.1 37.1 + - - -
424A PHE* 5.6 0.2 - - - -
428A ASN* 5.6 1.1 - - - +
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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
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225A PHE* 3.4 26.2 - - - -
228A GLY 4.3 1.3 - - - -
229A THR* 3.4 27.3 - - - +
373A ALA 3.1 8.7 + - - -
374A ILE 3.1 6.2 + - - -
376A THR* 1.3 78.1 - - - +
378A LEU* 1.3 55.6 + - - +
380A PHE* 3.4 1.8 + - - -
381A ALA* 2.9 23.2 + - - +
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Residues in contact with LEU 378 (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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225A PHE* 4.1 17.5 - - + -
374A ILE* 2.9 20.3 + - + +
375A THR* 3.2 17.7 + - + +
377A GLY* 1.3 73.2 - - - +
379A ALA* 1.3 60.0 + - - +
381A ALA* 3.7 6.8 - - + +
382A LEU* 2.9 30.8 + - - +
424A PHE* 4.1 12.1 - - + -
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Residues in contact with ALA 379 (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 ALA* 5.7 0.2 - - - +
309A GLY* 3.6 27.5 + - - +
312A ILE* 3.9 21.3 - - + +
313A GLY 5.6 0.4 - - - +
317A ALA* 5.9 1.8 - - + -
375A THR 3.2 6.7 + - - +
376A THR* 3.3 11.9 + - + +
378A LEU* 1.3 78.8 - - - +
380A PHE* 1.3 60.5 + - - +
382A LEU* 3.5 13.2 + - - +
383A ALA* 4.1 2.6 + - - +
388A LEU* 4.9 1.0 - - - +
424A PHE* 3.6 30.9 - - + -
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Residues in contact with PHE 380 (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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224A PRO* 3.2 35.3 - - + +
227A TYR* 3.8 11.2 - + - -
228A GLY* 3.5 18.8 - - - -
231A GLU* 3.6 21.8 - - - -
232A ARG* 5.6 2.7 - - - -
305A ARG 3.7 3.5 - - - +
306A PHE* 3.3 44.4 - - - -
307A LYS 3.8 2.7 - - - -
309A GLY* 3.4 12.6 - - - +
310A GLN* 3.3 35.4 - - + -
376A THR* 3.1 30.3 + - - +
377A GLY 3.7 4.7 - - - +
379A ALA* 1.3 76.7 - - - +
381A ALA* 1.3 60.2 + - - +
382A LEU 3.1 2.3 + - - -
383A ALA* 3.2 19.4 + - - +
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Residues in contact with ALA 381 (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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221A ILE* 3.4 43.3 - - + +
224A PRO* 3.8 10.7 - - - +
225A PHE* 3.7 11.4 - - + -
377A GLY 2.9 17.9 + - - +
378A LEU* 3.4 10.5 + - + +
380A PHE* 1.3 75.5 - - - +
382A LEU* 1.3 59.1 + - - +
383A ALA 3.2 1.5 + - - -
384A ASP* 3.6 12.7 + - - +
385A LEU* 4.3 6.3 + - - +
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Residues in contact with LEU 382 (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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378A LEU 2.9 16.0 + - - +
379A ALA 3.6 9.0 - - - +
380A PHE 3.1 1.0 - - - -
381A ALA* 1.3 73.3 - - - +
383A ALA* 1.3 58.7 + - - +
384A ASP 3.1 3.1 - - - -
385A LEU* 3.3 26.4 + - + +
386A ILE* 3.1 38.1 + - + +
388A LEU* 3.8 9.2 - - + +
420A VAL* 3.6 40.4 - - + -
424A PHE* 3.8 15.5 - - + -
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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