Contacts of the helix formed by residues 347 - 361 (chain D) in PDB entry 1M54
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 GLY 347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335D ALA* 4.5 4.2 - - - +
346D CYS* 1.3 78.1 - - - +
348D GLY* 1.3 69.0 + - - +
349D SER* 3.3 3.6 - - - -
350D ALA* 2.7 21.7 + - - +
351D GLY 3.2 2.6 + - - -
376D ASP* 3.3 19.0 + - - -
377D SER 4.3 0.9 - - - -
381D TYR* 4.2 6.7 - - - -
385D PHE* 3.7 15.9 - - - -
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Residues in contact with GLY 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D VAL* 4.2 13.0 - - - -
331D ALA* 4.0 5.3 - - - +
332D PHE* 4.1 27.6 - - - -
335D ALA* 5.1 0.4 - - - -
347D GLY* 1.3 68.3 - - - -
349D SER* 1.3 54.0 + - - +
351D GLY* 2.4 30.4 + - - -
352D SER* 3.2 4.9 + - - -
381D TYR* 4.1 12.6 - - - -
385D PHE* 3.4 11.7 - - - -
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Residues in contact with SER 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D SER* 4.1 1.5 + - - -
303D VAL* 4.0 7.6 - - - +
304D GLU 4.5 2.0 + - - -
306D ILE* 4.1 12.1 - - - -
347D GLY 4.0 0.3 + - - -
348D GLY* 1.3 71.6 - - - +
350D ALA* 1.3 71.3 + - - +
351D GLY 3.0 1.4 + - - -
352D SER* 3.2 5.0 + - - +
353D THR* 3.1 26.0 + - - -
375D PRO* 3.0 27.0 - - - +
376D ASP* 3.7 8.7 + - - -
381D TYR* 4.7 1.6 + - - -
1410D PLP 2.9 41.4 - - - +
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D ALA* 6.0 0.2 - - - -
338D LEU* 4.1 4.1 - - + +
346D CYS* 3.4 33.0 - - + -
347D GLY 2.7 17.8 + - - +
349D SER* 1.3 77.8 + - - +
351D GLY* 1.3 63.2 + - - +
353D THR* 3.6 3.9 + - - -
354D VAL* 3.2 26.5 + - - +
374D LEU* 3.8 30.3 - - + +
376D ASP 5.0 0.2 - - - +
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Residues in contact with GLY 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D ALA* 3.0 26.0 - - - -
334D PHE* 3.9 12.7 - - - +
335D ALA* 4.3 5.3 - - - +
338D LEU* 5.5 0.4 - - - -
347D GLY 3.2 5.2 + - - -
348D GLY 2.4 18.6 + - - -
350D ALA* 1.3 67.7 - - - +
352D SER* 1.3 65.0 + - - -
354D VAL* 3.0 5.7 + - - +
355D ALA* 3.0 21.8 + - - +
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D SER* 5.2 1.3 - - - -
280D VAL* 3.6 23.6 - - - -
303D VAL* 4.5 1.6 - - - +
306D ILE* 3.9 16.1 - - - +
326D SER* 3.4 19.9 + - - -
330D GLU* 5.8 1.3 - - - -
331D ALA* 3.2 25.9 - - - +
348D GLY 3.2 5.4 + - - -
349D SER 3.7 6.3 - - - -
351D GLY* 1.3 72.3 - - - +
353D THR* 1.3 63.8 + - - +
355D ALA* 3.3 4.6 + - - +
356D VAL* 3.0 28.8 + - - +
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Residues in contact with THR 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D VAL* 2.9 44.4 - - + +
253D ALA* 4.2 0.7 - - - -
254D SER* 3.7 21.3 + - - -
280D VAL* 4.1 9.3 - - - +
349D SER 3.1 17.2 + - - -
350D ALA 3.7 4.9 - - - -
352D SER* 1.3 77.3 - - - +
354D VAL* 1.3 57.8 + - - +
357D ALA* 3.1 21.0 + - - +
372D VAL* 3.6 12.6 - - + -
373D ILE 3.3 23.3 + - - +
375D PRO* 4.6 1.2 - - - +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 5.8 3.4 - - + -
95D ILE* 4.1 22.4 - - + -
105D LEU* 4.7 13.0 - - + -
334D PHE* 3.6 21.5 - - + -
338D LEU* 4.1 21.3 - - + -
350D ALA 3.2 15.9 + - - +
351D GLY 3.0 3.7 + - - +
353D THR* 1.3 72.8 - - - +
355D ALA* 1.3 66.5 + - - +
356D VAL 3.2 1.6 - - - -
357D ALA* 3.9 4.5 - - - -
358D VAL* 3.0 26.1 + - + +
372D VAL* 3.5 25.8 - - + -
374D LEU* 4.3 1.8 - - + -
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D GLU* 4.1 27.8 - - + +
334D PHE* 3.6 34.0 - - + -
351D GLY 3.0 16.6 + - - +
352D SER* 3.7 6.5 - - - +
354D VAL* 1.3 76.2 - - - +
356D VAL* 1.3 60.6 + - + +
358D VAL* 3.2 19.2 - - - +
359D LYS* 3.7 15.4 + - - +
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Residues in contact with VAL 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D VAL* 4.1 3.8 - - + -
278D ILE* 4.0 11.4 - - + -
280D VAL* 3.4 33.4 - - + -
324D PHE* 3.3 46.0 - - + +
325D LYS 5.0 6.5 - - - +
326D SER* 5.1 3.4 - - - -
330D GLU* 5.6 2.0 - - - +
352D SER 3.0 20.5 + - - +
353D THR 3.8 1.8 - - - +
355D ALA* 1.3 81.2 - - + +
357D ALA* 1.3 51.2 + - - +
358D VAL 3.6 0.2 - - - -
359D LYS* 3.3 9.9 + - - +
360D ALA* 2.5 34.0 + - - +
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Residues in contact with ALA 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.3 2.8 - - - +
105D LEU* 4.5 12.1 - - + -
252D VAL* 4.3 14.4 - - + -
353D THR 3.1 18.8 + - - +
354D VAL* 3.2 8.3 + - - +
356D VAL* 1.3 74.4 - - - +
358D VAL* 1.3 62.2 + - - +
359D LYS 2.9 4.9 - - - -
360D ALA* 4.3 0.9 - - - +
361D ALA* 3.1 30.8 + - - +
370D CYS* 5.0 2.5 - - - -
372D VAL* 3.7 24.9 - - + -
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Residues in contact with VAL 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ILE* 4.2 11.7 - - + +
96D GLY* 5.6 0.2 - - - -
99D PHE* 3.7 54.4 - - + +
101D LEU* 3.3 21.0 - - + +
105D LEU* 5.7 2.0 - - + -
334D PHE* 4.1 13.7 - - + -
354D VAL* 3.0 18.4 + - + +
355D ALA 3.2 17.7 - - - +
357D ALA* 1.3 75.1 - - + +
359D LYS* 1.3 62.6 + - + +
362D GLN* 2.9 27.7 + - - +
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Residues in contact with LYS 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D PHE* 4.5 27.1 - - + -
325D LYS 5.5 4.2 + - - -
330D GLU* 4.2 19.6 + - - -
355D ALA 3.7 14.9 + - - +
356D VAL* 3.4 11.6 - - - +
357D ALA 2.9 0.8 - - - -
358D VAL* 1.3 83.5 - - + +
360D ALA* 1.3 69.9 + - - +
362D GLN* 3.1 19.9 + - - +
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Residues in contact with ALA 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D MET* 4.5 3.0 - - - +
252D VAL* 4.4 5.4 - - + -
278D ILE* 4.0 28.3 - - + -
322D LYS* 5.8 2.5 + - + +
324D PHE* 3.3 31.3 - - + -
356D VAL* 2.5 23.6 + - + +
359D LYS* 1.3 76.2 - - - +
361D ALA* 1.3 58.2 + - - +
362D GLN 3.0 4.3 + - - -
363D GLU* 3.8 16.1 + - - +
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Residues in contact with ALA 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.4 8.5 - - + +
103D CYS* 4.2 17.3 - - - -
105D LEU* 6.0 0.4 - - + -
250D MET* 3.9 1.3 - - - -
357D ALA* 3.1 17.9 + - + +
360D ALA* 1.3 73.8 - - - +
362D GLN* 1.3 52.5 + - - +
363D GLU 2.7 18.4 + - - -
364D LEU* 2.9 32.8 + - + +
370D CYS* 3.9 28.0 - - - -
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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