Contacts of the helix formed by residues 351 - 367 (chain A) in PDB entry 2MX7
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ILE* 5.3 0.9 - - - -
349A LYS 3.5 5.9 + - - -
350A LEU* 1.3 76.4 - - - +
352A LYS* 1.3 66.1 + - + +
353A GLU* 3.1 27.8 - - - +
354A GLU* 2.6 33.6 + - - -
355A LEU* 2.8 32.6 + - - +
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Residues in contact with LYS 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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296A GLU* 2.7 47.8 + - + +
299A VAL* 5.1 12.1 - - + -
303A TYR* 4.5 27.6 + - + +
316A ILE* 5.6 0.2 - - - +
351A THR* 1.3 82.0 - - + +
353A GLU* 1.3 95.1 + - - +
355A LEU* 3.0 25.0 + - - +
356A TYR* 3.0 11.4 + - - +
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Residues in contact with GLU 353 (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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293A ILE* 3.1 41.1 - - + +
294A TYR* 4.5 23.8 - - + -
296A GLU* 3.7 15.4 - - + +
351A THR* 3.1 22.1 - - - +
352A LYS* 1.3 108.8 + - + +
354A GLU* 1.3 64.9 + - + +
356A TYR* 2.9 24.7 + - - +
357A THR 3.2 4.0 + - - -
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Residues in contact with GLU 354 (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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293A ILE* 5.3 0.4 - - - -
342A ALA* 3.7 24.3 - - + +
343A ASN* 5.9 2.7 - - + -
345A THR* 2.7 35.3 + - - +
348A GLY 5.5 0.3 - - - +
349A LYS 3.2 9.6 - - - +
350A LEU* 4.0 7.5 - - + +
351A THR* 2.6 47.6 + - - +
353A GLU* 1.3 82.4 - - + +
355A LEU* 1.3 56.9 + - - +
357A THR* 3.1 25.5 + - - -
358A VAL* 3.1 18.6 + - - +
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Residues in contact with LEU 355 (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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303A TYR* 3.4 30.1 - - + -
306A ILE* 4.3 14.1 - - + -
316A ILE* 3.6 35.2 - - + -
339A TRP* 3.9 19.5 - - + -
350A LEU* 4.5 3.6 - - + +
351A THR 2.8 11.1 + - - +
352A LYS* 3.0 12.1 + - - +
354A GLU* 1.3 73.5 - - - +
356A TYR* 1.3 58.7 + - - +
358A VAL* 2.8 35.3 - - + +
359A LEU* 3.1 31.3 + - + +
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Residues in contact with TYR 356 (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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292A TRP* 3.4 34.7 - + + +
293A ILE* 3.7 21.3 - - + +
298A LEU* 6.4 1.6 - - + -
300A PRO* 3.4 44.1 - - + +
302A ALA* 6.0 0.4 - - + -
352A LYS 3.0 6.7 + - - +
353A GLU* 2.9 16.4 + - - +
355A LEU* 1.3 78.0 - - - +
357A THR* 1.3 57.5 + - - +
359A LEU* 3.7 8.2 - - + +
360A ALA* 3.0 34.4 + - + +
383A ALA* 3.3 40.0 + - + +
384A PRO 5.7 1.6 - - - -
385A ILE* 4.5 10.3 - - + +
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Residues in contact with THR 357 (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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289A MET* 6.0 2.7 - - + +
293A ILE* 3.5 25.5 - - + +
341A LEU 3.7 23.8 - - - +
342A ALA* 4.5 6.1 - - - -
343A ASN* 4.5 6.3 + - - +
353A GLU 3.4 10.4 + - - -
354A GLU* 3.1 16.8 + - - -
356A TYR* 1.3 78.9 - - - +
358A VAL* 1.3 59.0 + - - +
360A ALA* 4.2 1.8 - - - +
361A MET* 3.1 45.0 + - + +
377A LEU* 5.8 4.7 - - + +
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Residues in contact with VAL 358 (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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338A ILE* 3.3 22.9 - - - +
339A TRP* 3.0 51.6 - - + +
342A ALA* 5.7 1.3 - - + +
350A LEU* 4.7 4.7 - - + -
354A GLU 3.1 11.8 + - - +
355A LEU* 2.8 55.0 - - + +
357A THR* 1.3 75.5 - - - +
359A LEU* 1.3 63.5 + - - +
361A MET 3.3 0.9 + - - -
362A ILE* 2.9 35.7 + - - +
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Residues in contact with LEU 359 (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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300A PRO* 4.3 10.1 - - + -
302A ALA* 3.6 22.7 - - + +
303A TYR* 3.7 15.7 - - + +
306A ILE* 3.3 34.5 - - + -
339A TRP* 5.9 2.0 - - + -
355A LEU* 3.1 37.7 + - + +
356A TYR* 3.7 10.3 - - + +
358A VAL* 1.3 83.8 - - + +
360A ALA* 1.3 56.8 + - - +
362A ILE* 3.4 4.3 + - + +
363A ALA 3.0 22.3 + - - -
384A PRO 4.6 1.3 - - - +
386A PRO* 3.4 35.0 - - + +
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Residues in contact with ALA 360 (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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292A TRP* 4.1 14.4 - - + -
356A TYR* 3.0 18.2 + - + +
357A THR* 4.2 3.4 - - - +
359A LEU* 1.3 77.1 - - - +
361A MET* 1.3 59.0 + - - +
363A ALA* 3.2 2.3 + - - +
364A VAL* 2.9 34.8 + - + +
377A LEU* 4.6 8.1 - - + -
383A ALA* 3.9 27.4 - - + -
384A PRO* 4.0 12.6 - - + -
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Residues in contact with MET 361 (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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338A ILE* 3.2 54.5 - - + +
341A LEU* 3.8 28.7 - - + +
357A THR* 3.1 34.1 + - + +
358A VAL 3.3 0.6 + - - +
360A ALA* 1.3 74.4 - - - +
362A ILE* 1.3 58.5 + - - +
364A VAL* 3.1 11.7 - - + +
365A THR* 2.6 34.9 + - - -
371A ALA* 4.1 18.3 - - + +
377A LEU* 4.7 23.1 - - + -
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Residues in contact with ILE 362 (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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321A LEU* 4.9 4.7 - - + -
325A LEU* 3.5 32.3 - - + -
330A LEU* 4.0 6.2 - - + +
334A THR* 6.0 0.2 - - + -
335A LEU* 3.6 33.4 - - + -
338A ILE* 3.8 22.9 - - + -
339A TRP* 4.5 7.9 - - + -
358A VAL 2.9 23.2 + - - +
359A LEU* 3.6 6.3 - - + +
361A MET* 1.3 75.8 - - - +
363A ALA* 1.3 65.1 + - - +
365A THR* 3.1 5.9 + - - +
366A GLN* 3.0 25.8 + - - +
386A PRO* 3.6 20.0 - - + -
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Residues in contact with ALA 363 (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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359A LEU 3.0 11.0 + - - +
360A ALA 3.4 8.3 - - - +
362A ILE* 1.3 79.0 - - - +
364A VAL* 1.3 61.8 + - - +
366A GLN* 3.3 7.0 + - - +
367A ARG* 2.9 30.2 + - - +
384A PRO* 3.4 42.0 - - + +
385A ILE 3.7 2.0 - - - +
386A PRO* 3.6 17.7 - - - -
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Residues in contact with VAL 364 (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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360A ALA 2.9 20.0 + - - +
361A MET* 3.1 24.9 - - + +
363A ALA* 1.3 75.3 - - - +
365A THR* 1.3 54.7 + - - +
367A ARG* 3.1 14.3 + - + +
368A GLY 3.2 0.2 + - - -
369A VAL* 2.8 54.0 + - + +
370A PRO 5.1 4.9 - - - +
371A ALA* 5.2 4.0 - - + +
377A LEU* 5.2 4.7 - - + -
380A PHE* 3.5 35.0 - - + -
384A PRO* 3.7 17.5 - - + -
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Residues in contact with THR 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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330A LEU* 3.6 29.6 - - + +
331A PRO* 4.6 6.3 - - + -
334A THR* 4.2 24.9 - - + +
338A ILE* 4.8 3.6 - - - +
361A MET 2.6 23.5 + - - -
362A ILE* 3.1 6.6 + - - +
364A VAL* 1.3 77.7 - - - +
366A GLN* 1.3 58.1 + - - +
368A GLY* 2.8 21.5 + - - -
369A VAL 3.4 11.5 + - - -
370A PRO* 5.0 3.6 - - + +
371A ALA* 5.0 5.4 + - - +
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Residues in contact with GLN 366 (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 LEU* 3.8 7.3 - - - +
328A SER* 2.9 28.0 + - - +
330A LEU* 3.8 21.3 - - + -
362A ILE* 3.0 20.4 + - - +
363A ALA* 3.5 6.9 - - - +
365A THR* 1.3 77.4 - - - +
367A ARG* 1.3 73.0 + - - +
368A GLY* 3.2 4.0 + - - -
386A PRO* 3.5 5.7 - - - +
387A THR* 2.8 43.1 + - - -
388A LEU* 3.6 11.9 - - - +
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Residues in contact with ARG 367 (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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363A ALA 2.9 21.6 + - - +
364A VAL* 3.1 11.8 + - - +
366A GLN* 1.3 87.7 + - - +
368A GLY* 1.3 60.1 + - - +
369A VAL* 3.3 12.0 + - + +
384A PRO* 4.9 12.3 - - + +
385A ILE 3.2 19.8 + - - -
387A THR* 2.7 35.8 + - - +
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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