Contacts of the helix formed by residues 327 - 342 (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 ASN 327 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D PRO* 5.8 0.4 - - - -
283D GLU* 5.3 4.7 - - - +
298D GLN* 4.2 16.3 + - - +
303D VAL* 5.5 1.1 - - - -
326D SER* 1.3 84.4 + - - +
328D ASP* 1.3 75.4 + - - +
329D GLU* 3.4 15.2 + - - +
330D GLU* 3.0 42.6 + - - +
331D ALA* 2.9 33.5 + - - +
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Residues in contact with ASP 328 (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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298D GLN* 5.2 5.6 - - - +
301D TYR* 3.9 10.4 - - + +
302D GLU* 2.9 52.3 + - - +
303D VAL* 3.2 17.9 + - - +
327D ASN* 1.3 82.4 + - - +
329D GLU* 1.3 62.1 + - - +
331D ALA* 3.3 4.3 + - - +
332D PHE* 3.2 28.3 + - - -
396D PHE* 3.3 19.2 - - + -
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Residues in contact with GLU 329 (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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327D ASN* 3.4 12.4 + - - +
328D ASP* 1.3 80.3 - - - +
330D GLU* 1.3 58.0 + - - +
332D PHE* 3.4 3.9 + - - +
333D THR* 3.0 37.0 + - + +
395D GLY 2.9 20.2 - - - +
396D PHE* 3.3 39.1 - - + +
397D LEU 4.7 4.9 - - - +
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Residues in contact with GLU 330 (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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325D LYS 4.0 4.3 - - - +
326D SER* 3.4 9.9 - - - -
327D ASN* 3.0 52.7 + - + +
329D GLU* 1.3 76.8 - - - +
331D ALA* 1.3 78.7 + - + +
332D PHE 2.9 1.8 - - - -
333D THR* 2.7 22.8 + - - +
334D PHE* 3.1 20.2 + - + -
352D SER* 5.8 0.8 - - - -
355D ALA* 4.1 21.8 - - + +
356D VAL* 5.6 2.8 - - - +
359D LYS* 4.2 17.0 + - - -
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Residues in contact with ALA 331 (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* 3.8 17.7 - - + -
327D ASN 2.9 21.1 + - - +
328D ASP 3.7 4.3 - - - +
330D GLU* 1.3 78.8 - - - +
332D PHE* 1.3 62.8 + - - +
335D ALA* 3.4 9.4 + - - +
348D GLY 4.0 3.5 - - - +
351D GLY* 3.0 24.6 - - - -
352D SER* 3.2 39.5 - - - +
355D ALA* 5.2 0.2 - - - -
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Residues in contact with PHE 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D GLU* 4.0 22.0 - - + -
303D VAL* 3.8 24.9 - - + -
328D ASP* 3.2 17.2 + - - +
329D GLU* 3.7 4.7 - - - +
330D GLU 2.9 0.6 - - - -
331D ALA* 1.3 80.5 - - - +
333D THR* 1.3 68.1 + - - +
334D PHE 3.0 1.6 - - - -
335D ALA* 3.0 14.3 + - - +
336D ARG* 3.3 16.3 + - - +
348D GLY* 4.1 9.6 - - - -
381D TYR* 5.4 4.9 - + - -
384D LYS 5.0 0.4 - - - -
385D PHE* 3.8 36.0 - + + -
390D TRP* 3.6 30.1 - + - -
391D MET* 4.2 18.4 - - + -
396D PHE* 3.8 25.1 - + - -
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Residues in contact with THR 333 (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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329D GLU* 3.0 24.6 + - + +
330D GLU* 2.7 25.6 + - - +
332D PHE* 1.3 75.3 - - - +
334D PHE* 1.3 64.1 + - - +
336D ARG* 3.7 9.1 + - - +
337D MET* 3.0 28.7 + - - +
391D MET* 5.5 3.8 - - + -
397D LEU* 4.8 19.3 - - - +
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Residues in contact with PHE 334 (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* 4.3 0.6 - - + +
99D PHE* 3.6 30.1 - + - -
330D GLU* 3.1 28.0 + - + +
331D ALA 3.9 5.4 - - - +
332D PHE 3.0 0.4 - - - -
333D THR* 1.3 83.8 + - - +
335D ALA* 1.3 55.9 + - - +
337D MET* 3.2 33.5 - - + +
338D LEU* 2.6 38.7 + - + +
351D GLY* 3.9 13.0 - - - +
354D VAL* 3.6 29.4 - - + -
355D ALA* 3.6 35.0 - - + -
358D VAL* 4.1 7.4 - - + -
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Residues in contact with ALA 335 (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 3.4 11.7 + - - +
332D PHE* 3.0 8.5 + - - +
334D PHE* 1.3 76.0 - - - +
336D ARG* 1.3 53.1 + - - +
338D LEU* 2.6 32.0 + - - +
339D ILE* 2.6 22.7 + - + +
346D CYS* 5.4 2.2 - - - +
347D GLY* 4.5 12.8 - - - +
348D GLY 4.8 0.2 - - - +
351D GLY* 4.3 5.4 - - - +
385D PHE* 3.3 37.2 - - + -
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Residues in contact with ARG 336 (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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183C ALA* 5.3 15.9 - - + +
332D PHE 3.7 11.4 - - - +
333D THR* 3.8 8.7 - - - +
335D ALA* 1.3 75.8 - - - +
337D MET* 1.3 56.8 + - - +
339D ILE* 2.8 12.9 + - + +
340D ALA* 2.6 41.0 + - + +
385D PHE* 3.0 37.1 + - + +
386D LEU* 3.4 20.8 + - + +
387D SER 3.6 9.1 + - - -
388D ASP* 2.7 30.8 + - - -
391D MET* 4.2 14.4 - - - +
397D LEU* 4.0 17.9 - - - +
398D LYS* 5.6 1.4 - - - +
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Residues in contact with MET 337 (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* 3.2 39.7 - - + -
99D PHE* 3.5 20.0 - - + -
333D THR* 3.0 16.3 + - - +
334D PHE* 3.2 48.9 - - + +
336D ARG* 1.3 73.9 - - - +
338D LEU* 1.3 57.8 + - - +
340D ALA* 5.0 2.2 - - - -
341D GLN* 2.8 63.9 + - - +
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Residues in contact with LEU 338 (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* 4.0 8.7 - - + -
95D ILE* 3.7 12.6 - - + -
334D PHE 2.6 18.6 + - - +
335D ALA* 2.6 15.8 + - - +
337D MET* 1.3 73.4 - - - +
339D ILE* 1.3 53.7 + - - -
342D GLU* 3.3 21.9 + - + +
343D GLY 3.1 9.7 + - - -
344D LEU* 3.1 48.6 + - + -
346D CYS* 3.1 29.2 - - - -
350D ALA* 4.1 12.1 - - + +
354D VAL* 4.1 23.6 - - + -
374D LEU* 3.9 12.6 - - + -
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Residues in contact with ILE 339 (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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159C ALA* 4.7 0.2 - - - +
183C ALA* 4.0 23.1 - - + +
184C LEU* 3.8 14.1 - - + +
335D ALA* 2.6 20.8 + - - +
336D ARG* 2.8 9.5 + - + +
338D LEU* 1.3 74.3 - - + +
340D ALA* 1.3 58.9 + - - +
343D GLY* 3.1 19.4 - - - -
344D LEU 3.4 13.9 - - - +
345D LEU* 2.2 53.8 - - + +
346D CYS* 4.9 1.1 - - - +
378D VAL* 3.7 10.8 - - + -
385D PHE* 4.2 16.8 - - + -
386D LEU* 3.6 27.6 - - + -
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Residues in contact with ALA 340 (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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159C ALA* 4.1 14.8 - - - +
183C ALA 3.1 21.3 - - - +
184C LEU 4.2 14.3 - - - +
185C GLY* 4.3 5.9 - - - +
336D ARG* 2.6 20.3 + - + +
337D MET* 3.5 2.5 - - - +
339D ILE* 1.3 73.5 - - - +
341D GLN* 1.3 67.5 + - - +
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Residues in contact with GLN 341 (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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159C ALA 4.2 8.1 - - - +
160C VAL* 4.9 1.4 - - - +
94D LYS* 3.1 60.6 + - + +
95D ILE* 4.0 12.5 + - + +
98D LYS* 5.7 8.8 + - - +
337D MET* 2.8 44.6 + - - +
340D ALA* 1.3 83.4 + - - +
342D GLU* 1.3 61.5 + - - +
343D GLY 3.7 0.2 - - - -
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Residues in contact with GLU 342 (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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79C ASP* 5.8 0.5 - - - +
80C ILE* 3.4 21.8 + - - +
160C VAL* 3.8 12.4 - - - +
91D ARG 3.7 4.0 - - - +
92D ILE* 2.8 26.0 - - + +
93D ASN* 2.7 20.6 + - - +
94D LYS* 2.5 35.2 + - - +
95D ILE* 3.0 17.7 + - + -
338D LEU* 3.3 25.8 + - + +
341D GLN* 1.3 79.6 - - - +
343D GLY* 1.3 61.5 + - - +
344D LEU* 3.3 20.8 + - + +
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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