Contacts of the helix formed by residues 333 - 352 (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 LYS 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A VAL* 3.8 8.3 - - + -
330A ASP* 2.8 38.2 + - + +
332A GLU* 1.3 101.0 + - + +
334A ARG* 1.3 63.5 + - - +
335A ALA 3.2 2.6 + - - -
336A LYS* 3.6 11.6 - - + +
337A TYR* 3.2 36.0 + - + +
445A GLY 4.1 0.2 - - - +
450A TYR* 3.1 39.4 + - + -
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PHE* 3.4 29.7 + - + +
327A ARG* 2.8 58.3 + - - +
328A ASN* 4.9 0.2 - - - +
329A VAL* 3.1 32.2 + - + +
330A ASP 3.0 17.2 + - - +
331A LYS* 3.6 44.4 + - - +
332A GLU 3.6 1.0 - - - -
333A LYS* 1.3 76.7 - - - +
335A ALA* 1.3 59.0 + - - +
336A LYS 3.4 0.2 - - - -
337A TYR* 3.9 0.9 - - - +
338A LYS* 3.0 32.2 + - - +
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 5.0 1.2 + - - -
332A GLU 4.8 8.6 + - - +
333A LYS 3.2 0.6 - - - -
334A ARG* 1.3 80.0 - - - +
336A LYS* 1.3 60.2 + - - +
338A LYS* 4.1 4.7 - - - +
339A PRO* 3.7 13.9 - - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 3.6 13.4 - - + +
335A ALA* 1.3 78.8 - - - +
337A TYR* 1.3 97.5 + - + +
338A LYS 3.4 0.2 - - - -
339A PRO* 3.5 11.3 - - - +
340A MSE 4.9 3.1 + - - +
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Residues in contact with TYR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PHE* 4.5 0.9 - - - -
329A VAL* 4.2 13.0 - - + -
333A LYS* 3.2 35.3 + - + +
334A ARG* 3.9 1.8 - - - +
336A LYS* 1.3 106.3 + - + +
338A LYS* 1.3 64.4 + - - +
339A PRO 3.5 0.7 - - - -
340A MSE 3.4 28.1 + - - +
341A PHE* 3.1 31.9 + + + -
444A PRO* 4.0 19.5 - - + -
445A GLY* 3.7 25.4 - - - -
449A ASN 3.6 2.4 + - - -
450A TYR* 3.5 37.9 + + - +
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Residues in contact with LYS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A PHE* 3.6 28.3 - - + -
334A ARG 3.0 18.7 + - - +
335A ALA* 4.1 4.9 - - - +
337A TYR* 1.3 76.1 - - - +
339A PRO* 1.3 72.8 - - + +
340A MSE 3.1 0.3 + - - -
341A PHE* 3.2 3.1 + - - +
342A LEU* 2.9 45.8 + - + +
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Residues in contact with PRO 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ALA 3.7 9.9 - - - +
336A LYS* 3.5 17.0 - - - +
338A LYS* 1.3 99.8 - - + +
340A MSE 1.3 55.1 + - - +
342A LEU* 4.2 7.7 - - + +
343A SER* 3.0 31.7 + - - -
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Residues in contact with MSE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS 4.9 1.7 + - - +
337A TYR* 3.4 39.4 + - - +
338A LYS 3.1 0.6 - - - -
339A PRO* 1.3 79.8 - - - +
341A PHE* 1.3 61.0 + - + +
343A SER* 3.9 2.6 - - - -
344A ALA* 2.9 31.2 + - - +
360A MSE 3.7 32.3 - - + +
444A PRO* 4.7 13.5 - - + -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ALA* 3.4 26.9 - - + +
325A MSE 3.4 46.4 - - + -
326A PHE* 3.7 29.8 - + + -
329A VAL* 3.9 16.6 - - + -
337A TYR* 3.1 32.8 - + + -
338A LYS 3.2 6.1 + - - +
340A MSE 1.3 81.0 - - + +
342A LEU* 1.3 61.2 + - - +
344A ALA* 3.9 4.4 - - + +
345A ALA* 2.8 34.6 + - - +
360A MSE 4.1 12.6 - - - -
444A PRO* 3.9 22.0 - - + -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LYS* 2.9 42.6 + - + +
339A PRO* 4.2 5.6 - - + +
341A PHE* 1.3 76.9 - - - +
343A SER* 1.3 57.4 + - - +
345A ALA* 4.2 4.8 - - + +
346A LEU* 3.1 33.2 + - + +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A PRO 3.0 19.3 + - - -
340A MSE 4.0 2.7 - - - -
342A LEU* 1.3 76.1 - - - +
344A ALA* 1.3 59.7 + - - +
346A LEU* 3.5 6.9 + - - +
347A ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A MSE 2.9 19.6 + - - +
341A PHE* 3.9 3.1 - - - +
343A SER* 1.3 77.4 - - - +
345A ALA* 1.3 62.7 + - - +
347A ALA* 3.3 3.6 + - - +
348A VAL* 3.1 29.1 + - - +
356A PRO* 3.9 19.5 - - + +
357A ILE* 4.0 8.5 - - + -
360A MSE 3.7 25.1 - - + -
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A MSE 3.5 22.6 - - - +
322A ALA* 4.2 10.5 - - + -
341A PHE 2.8 21.7 + - - +
342A LEU* 4.2 5.8 - - + +
344A ALA* 1.3 72.5 - - - +
346A LEU* 1.3 53.2 + - - +
348A VAL 3.2 0.9 + - - -
349A PHE* 2.7 37.0 + - - +
357A ILE* 3.6 18.3 - - + +
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Residues in contact with LEU 346 (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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342A LEU* 3.1 25.7 + - + +
343A SER* 3.9 6.7 - - - +
344A ALA 3.3 0.4 - - - -
345A ALA* 1.3 75.4 - - - +
347A ALA* 1.3 55.4 + - - +
349A PHE* 4.2 10.1 - - + -
350A LEU* 3.0 65.4 + - + +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 4.3 22.2 - - + -
343A SER* 3.0 18.7 + - - +
344A ALA* 3.7 6.5 - - - +
346A LEU* 1.3 75.2 - - - +
348A VAL* 1.3 61.5 + - - +
350A LEU* 5.2 0.4 - - - -
351A THR* 2.6 39.8 + - - -
353A VAL 4.4 0.7 - - - -
356A PRO* 4.7 7.2 - - + -
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.5 18.3 - - - -
318A LEU* 3.6 22.2 - - + -
319A MSE 3.8 16.8 - - + -
344A ALA 3.1 17.3 + - - +
347A ALA* 1.3 75.9 - - - +
349A PHE* 1.3 59.8 + - - +
352A GLY* 2.9 26.0 + - - -
353A VAL 3.1 24.0 - - - +
354A THR* 3.8 11.0 - - - -
356A PRO* 4.2 11.2 - - + -
357A ILE* 3.6 20.0 - - + +
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Residues in contact with PHE 349 (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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314A SER* 3.4 9.9 + - - +
315A THR* 3.3 45.8 + - + -
319A MSE 4.0 12.6 - - + -
345A ALA 2.7 21.9 + - - +
346A LEU* 3.8 13.2 - - + +
348A VAL* 1.3 76.0 - - - +
350A LEU* 1.3 74.0 + - + +
352A GLY* 4.9 0.2 - - - -
394A GLY* 4.0 1.2 - - - -
395A PHE* 3.0 71.0 + + - +
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Residues in contact with LEU 350 (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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31A SER* 5.3 0.7 + - - -
346A LEU* 3.0 46.9 + - + +
347A ALA* 5.2 0.4 - - - -
349A PHE* 1.3 96.1 - - + +
351A THR* 1.3 64.6 + - + +
393A PHE 4.7 0.2 - - - +
394A GLY* 3.3 2.4 - - - -
395A PHE* 3.0 27.8 + - + +
396A ILE* 3.2 42.5 + - + +
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Residues in contact with THR 351 (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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24A PRO* 3.4 33.8 - - + +
27A GLY* 4.7 0.9 - - - -
28A LEU* 4.2 27.8 - - + +
31A SER* 4.8 5.3 + - - -
347A ALA* 2.6 25.5 + - - +
350A LEU* 1.3 81.4 - - + +
352A GLY* 1.3 60.2 + - - +
353A VAL* 3.2 20.4 + - - +
393A PHE* 3.4 29.6 - - - +
394A GLY* 3.4 5.2 - - - -
396A ILE* 5.4 0.4 - - - -
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Residues in contact with GLY 352 (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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310A GLN* 3.1 25.1 + - - -
314A SER* 3.7 16.2 - - - -
348A VAL 2.9 18.4 + - - -
351A THR* 1.3 76.6 - - - +
353A VAL* 1.3 61.6 + - - +
354A THR* 3.4 4.3 + - - +
393A PHE* 3.2 11.8 - - - -
394A GLY* 3.4 14.0 - - - -
2B GLC 4.0 0.7 + - - -
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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