Contacts of the helix formed by residues 327 - 340 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282C PRO* 6.2 0.7 - - - -
283C GLU* 4.3 20.7 + - + +
298C GLN* 6.3 1.1 - - + -
303C VAL* 4.9 1.8 - - - -
326C SER* 1.3 80.4 + - - +
328C ASP* 1.3 65.6 + - - +
329C GLU* 2.6 38.6 + - - +
330C GLU* 2.9 43.7 + - - +
331C ALA* 3.2 9.4 + - - +
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Residues in contact with ASP 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C PRO* 5.5 1.9 - - - +
298C GLN* 5.8 0.3 - - - +
301C TYR* 3.2 20.8 - - - +
302C GLU* 2.7 38.3 + - + +
303C VAL* 3.2 26.4 - - + +
327C ASN* 1.3 71.8 + - - +
329C GLU* 1.3 58.5 + - - +
330C GLU 2.9 11.1 + - - -
331C ALA* 3.6 1.0 + - - +
332C PHE* 3.3 29.8 + - + +
396C PHE* 4.1 20.2 - - + -
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ASN* 2.6 16.4 + - - +
328C ASP* 1.3 73.1 - - - +
330C GLU* 1.3 54.5 + - - -
332C PHE* 4.4 2.5 - - - -
333C THR* 2.9 32.6 - - + +
395C GLY 2.8 24.5 - - - +
396C PHE* 3.6 39.6 - - + +
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Residues in contact with GLU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325C LYS 4.8 0.5 - - - +
326C SER* 3.5 24.7 - - - -
327C ASN* 2.9 39.8 + - - +
328C ASP 2.9 1.6 - - - -
329C GLU* 1.3 77.9 - - - +
331C ALA* 1.3 63.0 + - - +
332C PHE 3.1 1.1 - - - -
333C THR* 2.9 22.1 + - - -
334C PHE* 3.4 14.7 + - + -
355C ALA* 3.3 30.8 - - + +
356C VAL* 4.5 1.0 - - - +
359C LYS* 3.3 27.4 + - - -
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C VAL* 4.7 8.5 - - + -
327C ASN 3.2 8.4 + - - +
328C ASP 4.4 2.0 - - - +
330C GLU* 1.3 79.8 - - - +
332C PHE* 1.3 52.8 + - + +
335C ALA* 2.7 18.9 + - - +
348C GLY* 3.2 10.9 - - - +
351C GLY* 2.7 35.6 + - - -
352C SER* 2.8 41.1 - - - +
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Residues in contact with PHE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C GLU* 4.3 22.2 - - + -
303C VAL* 4.9 9.9 - - + -
328C ASP* 3.3 20.5 + - + +
329C GLU* 4.7 3.6 - - - -
330C GLU 3.1 0.8 - - - -
331C ALA* 1.3 80.5 - - + +
333C THR* 1.3 67.7 + - + +
335C ALA* 2.9 3.1 + - - +
336C ARG* 2.8 26.5 + - - +
348C GLY* 4.0 13.2 - - - -
381C TYR* 5.6 5.4 - + - -
384C LYS* 5.8 1.1 - - + -
385C PHE* 3.3 42.6 - + + -
390C TRP* 3.3 32.1 - + - -
391C MET* 3.9 16.6 - - + -
396C PHE* 3.6 26.5 - + + -
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Residues in contact with THR 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C GLU* 2.9 29.2 - - + +
330C GLU* 2.9 11.4 + - - -
332C PHE* 1.3 74.1 - - + +
334C PHE* 1.3 74.5 + - - +
336C ARG* 2.8 13.9 + - - +
337C MET* 2.7 37.5 + - - +
391C MET* 4.5 8.5 - - + +
396C PHE* 6.1 2.5 - - + +
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Residues in contact with PHE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 4.7 3.1 - - + -
99C PHE* 3.3 44.0 - + - -
330C GLU* 3.4 13.2 + - + +
332C PHE 3.2 0.4 - - - -
333C THR* 1.3 98.8 + - - +
335C ALA* 1.3 58.8 + - - +
336C ARG 2.9 1.8 - - - -
337C MET* 3.3 19.5 - - + +
338C LEU* 2.7 38.1 + - + +
351C GLY* 3.3 20.9 - - - +
354C VAL* 3.7 27.6 - - + -
355C ALA* 3.5 30.3 - - + -
358C VAL* 3.9 15.3 - - + -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C ALA 2.7 23.2 + - - +
332C PHE* 2.9 1.5 + - - +
334C PHE* 1.3 76.3 - - - +
336C ARG* 1.3 56.2 + - - +
338C LEU* 3.9 6.1 + - - +
339C ILE* 3.0 31.0 + - - +
346C CYS* 4.6 3.2 - - - +
347C GLY 4.2 2.9 - - - +
348C GLY* 4.0 7.0 - - - -
351C GLY* 3.7 11.7 - - - +
385C PHE* 2.8 39.9 - - + -
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Residues in contact with ARG 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332C PHE 2.8 12.9 + - - +
333C THR* 3.1 11.4 - - - +
335C ALA* 1.3 78.0 - - - +
337C MET* 1.3 57.8 + - - +
338C LEU 3.1 1.8 - - - -
339C ILE* 3.2 10.7 + - + +
340C ALA* 2.8 32.7 + - - +
385C PHE* 2.1 42.9 + - + -
386C LEU* 3.3 19.0 + - + +
387C SER 3.5 1.2 - - - -
388C ASP* 3.4 15.1 + - - -
391C MET* 2.9 36.6 - - - +
397C LEU* 3.1 36.7 - - - +
183D ALA* 4.5 3.8 - - + +
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Residues in contact with MET 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ILE* 3.2 37.5 - - + -
98C LYS* 4.7 11.2 - - + -
99C PHE* 3.9 28.9 - - + -
333C THR* 2.7 21.5 + - - +
334C PHE* 3.3 31.2 - - + +
336C ARG* 1.3 75.3 - - - +
338C LEU* 1.3 57.3 + - - +
340C ALA* 3.2 1.0 + - - -
341C GLN* 2.7 57.0 + - + +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 4.2 14.8 - - + -
95C ILE* 3.6 19.7 - - + -
334C PHE* 2.7 18.2 + - + +
335C ALA 4.1 0.4 - - - +
337C MET* 1.3 74.8 - - - +
339C ILE* 1.3 63.1 + - - +
341C GLN 3.0 9.4 - - - +
342C GLU* 3.4 1.9 - - + +
344C LEU* 2.8 42.7 + - + +
346C CYS* 3.7 30.5 - - - -
350C ALA* 3.5 29.2 - - + +
351C GLY* 4.5 0.7 - - - +
354C VAL* 3.7 25.1 - - + -
374C LEU* 4.4 5.6 - - + -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ALA 3.0 26.2 + - - +
336C ARG* 3.2 10.4 + - + +
338C LEU* 1.3 76.5 - - - +
340C ALA* 1.3 58.2 + - - +
341C GLN 3.9 0.2 - - - -
343C GLY* 3.9 7.8 - - - -
344C LEU 2.9 18.2 - - - +
345C LEU* 3.1 28.9 - - + -
346C CYS 4.0 6.1 - - - +
378C VAL* 3.8 21.8 - - + -
385C PHE* 4.6 7.6 - - + -
386C LEU* 4.0 20.0 - - + -
159D ALA* 5.4 0.2 - - - +
183D ALA* 3.3 28.0 - - + +
184D LEU* 3.1 21.1 - - + +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ARG 2.8 14.3 + - - +
337C MET* 3.3 0.4 - - - -
338C LEU 3.1 0.4 - - - -
339C ILE* 1.3 78.4 - - - +
341C GLN* 1.3 73.6 + - - +
343C GLY 5.2 0.2 - - - +
159D ALA* 4.7 11.5 - - + +
182D ARG 5.7 0.2 - - - +
183D ALA 2.6 25.6 - - - +
184D LEU* 4.1 11.0 - - - +
185D GLY* 4.3 4.3 - - - +
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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