Contacts of the helix formed by residues 324 - 341 (chain A) in PDB entry 4IYM
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 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 5.6 11.2 - - + -
175A ARG* 3.6 32.1 - - - +
322A VAL* 3.5 3.7 - - - +
323A VAL* 1.3 89.4 - - + +
325A LYS* 1.3 58.8 + - - +
326A GLU* 3.5 19.1 + - - +
327A ALA* 3.1 23.0 + - - +
328A GLU* 3.0 26.7 + - - +
361A HIS* 3.5 12.6 - - - -
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Residues in contact with LYS 325 (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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324A THR* 1.3 73.2 - - - +
326A GLU* 1.3 67.1 + - - +
328A GLU* 3.2 20.8 + - - +
329A GLN* 2.8 62.9 + - + +
361A HIS* 3.6 22.9 + - + +
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Residues in contact with GLU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR* 3.5 20.7 - - - +
325A LYS* 1.3 82.5 + - - +
327A ALA* 1.3 60.8 + - - +
329A GLN* 3.2 5.9 + - - +
330A ARG* 2.9 31.8 + - - +
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Residues in contact with ALA 327 (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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147A PHE* 6.1 0.9 - - + -
277A GLU* 5.0 2.0 - - - +
322A VAL* 4.5 8.3 - - + -
323A VAL* 4.2 12.1 - - + -
324A THR* 3.1 27.4 + - - +
326A GLU* 1.3 75.0 - - - +
328A GLU* 1.3 65.1 + - - +
330A ARG* 3.3 8.3 + - - +
331A ILE* 2.9 37.0 + - + +
383A PHE 6.0 0.7 - - - +
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.7 14.9 - - + +
324A THR 3.0 13.9 + - - +
325A LYS* 3.2 25.5 + - - +
327A ALA* 1.3 77.0 - - - +
329A GLN* 1.3 67.8 + - - +
331A ILE* 3.3 2.4 + - - +
332A ARG* 2.7 71.8 + - - +
360A GLY 4.1 3.6 - - - +
361A HIS* 3.2 30.2 - - - +
362A PHE 4.1 1.4 - - - +
363A ILE* 3.8 18.2 - - + -
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Residues in contact with GLN 329 (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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325A LYS* 2.8 60.1 + - + +
326A GLU* 3.9 5.2 - - - +
328A GLU* 1.3 80.1 - - - +
330A ARG* 1.3 60.6 + - - +
332A ARG* 3.7 17.6 - - - +
333A SER* 2.8 32.3 + - - -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU 2.9 18.1 + - - +
327A ALA* 3.7 8.5 - - - +
329A GLN* 1.3 76.3 - - - +
331A ILE* 1.3 60.6 + - + +
333A SER* 3.6 6.3 + - - -
334A LEU* 3.1 37.9 + - + +
380A THR* 3.5 18.6 - - - +
381A GLU* 3.1 29.1 + - - +
382A ILE 3.3 18.2 + - - -
383A PHE* 5.1 2.2 - - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.8 24.9 - - + -
327A ALA* 2.9 28.8 + - + +
328A GLU 3.6 4.0 - - - +
330A ARG* 1.3 74.1 - - + +
332A ARG* 1.3 61.0 + - - +
334A LEU* 3.1 5.1 + - - +
335A ILE* 2.9 33.0 + - + +
363A ILE* 3.6 18.2 - - + -
382A ILE* 3.6 27.3 - - + +
383A PHE 3.8 6.5 - - - +
384A GLY* 3.7 21.5 - - - -
385A PRO* 4.6 0.9 - - + -
386A VAL* 3.9 26.2 - - + -
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Residues in contact with ARG 332 (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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328A GLU* 2.7 51.3 + - + +
329A GLN* 3.7 22.7 - - - +
331A ILE* 1.3 72.9 - - - +
333A SER* 1.3 66.9 + - - +
335A ILE* 3.4 11.0 + - + +
336A ASP* 3.1 29.0 + - - +
349A GLY 5.5 0.2 + - - -
350A ARG* 2.9 45.2 + - + +
352A PHE 4.7 5.9 + - - -
353A LYS* 5.2 6.9 - - - +
362A PHE 3.1 22.8 + - - -
363A ILE* 4.3 17.9 - - + +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLN 2.8 18.4 + - - -
330A ARG* 3.9 7.0 + - - -
332A ARG* 1.3 77.4 - - - +
334A LEU* 1.3 64.0 + - - +
336A ASP* 3.3 9.8 + - - +
337A SER* 3.0 22.4 + - - -
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Residues in contact with LEU 334 (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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330A ARG* 3.1 51.6 + - + +
331A ILE* 3.1 8.3 + - - +
333A SER* 1.3 78.4 - - - +
335A ILE* 1.3 60.3 + - - +
337A SER* 2.7 30.4 + - - +
338A GLY 3.1 5.9 + - - -
376A ASP* 4.4 14.1 - - + +
377A ILE* 3.1 9.8 - - - +
380A THR* 4.1 27.6 - - + +
382A ILE* 4.1 30.7 - - + -
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Residues in contact with ILE 335 (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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331A ILE* 2.9 28.5 + - + +
332A ARG* 3.7 11.0 - - + +
333A SER 3.3 0.2 - - - -
334A LEU* 1.3 73.9 - - + +
336A ASP* 1.3 63.3 + - - +
338A GLY 3.2 3.5 + - - -
339A ILE* 3.3 6.6 + - + +
345A LEU* 4.1 10.8 - - + -
350A ARG* 3.8 30.7 - - + -
363A ILE* 4.3 11.7 - - + -
366A CYS* 3.6 25.1 - - - -
368A PHE* 3.2 35.3 - - + -
377A ILE* 4.7 0.4 - - - -
382A ILE* 5.7 0.2 - - + -
386A VAL* 3.8 31.6 - - + -
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Residues in contact with ASP 336 (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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332A ARG* 3.1 17.1 + - - +
333A SER* 3.3 11.7 + - - +
335A ILE* 1.3 75.7 - - - +
337A SER* 1.3 63.6 + - - +
339A ILE* 3.2 9.2 + - - +
340A GLU* 3.0 23.7 + - - +
350A ARG* 3.2 34.5 + - - -
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Residues in contact with SER 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 3.0 12.7 + - - -
334A LEU* 2.7 24.0 + - - +
336A ASP* 1.3 75.6 - - - +
338A GLY* 1.3 55.8 + - - +
340A GLU* 3.4 11.3 + - - +
341A GLN* 2.9 49.9 + - - +
376A ASP* 3.9 22.2 - - - +
377A ILE* 4.1 1.9 - - - +
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Residues in contact with GLY 338 (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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334A LEU 3.1 6.1 + - - -
335A ILE 3.2 5.5 + - - -
337A SER* 1.3 81.7 + - - +
339A ILE* 1.3 61.3 + - - +
341A GLN* 3.4 5.6 + - - +
342A GLY 3.3 4.2 + - - -
343A ALA* 3.1 24.1 + - - +
368A PHE* 3.8 12.6 - - - -
375A MSE 4.8 0.2 - - - +
377A ILE* 3.9 28.0 - - - -
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Residues in contact with ILE 339 (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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335A ILE 3.3 12.6 + - - +
336A ASP* 3.2 11.0 + - - +
338A GLY* 1.3 73.7 - - - +
340A GLU* 1.3 66.4 + - - +
342A GLY* 3.0 16.6 + - - -
343A ALA 4.2 10.7 + - - +
345A LEU* 3.9 19.1 - - + -
350A ARG* 3.3 42.8 - - - +
368A PHE* 3.8 11.2 - - + -
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Residues in contact with GLU 340 (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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336A ASP 3.0 16.7 + - - +
337A SER* 3.6 9.2 - - - +
339A ILE* 1.3 77.5 - - - +
341A GLN* 1.3 87.5 + - - +
342A GLY 3.6 0.5 + - - -
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Residues in contact with GLN 341 (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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337A SER* 2.9 25.0 + - - +
338A GLY* 3.4 3.0 + - - +
339A ILE 3.1 0.6 - - - -
340A GLU* 1.3 96.3 + - - +
342A GLY* 1.3 56.9 + - - +
343A ALA 3.7 2.2 - - - -
374A ASP 5.4 1.3 - - - -
375A MSE 3.3 36.4 - - + +
376A ASP* 3.0 52.3 + - - +
377A ILE 4.9 0.3 + - - -
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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