Contacts of the helix formed by residues 327 - 341 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282F PRO* 5.9 0.9 - - - -
283F GLU* 3.6 29.6 + - - +
298F GLN* 4.8 4.3 - - - +
303F VAL* 4.1 2.4 - - - +
326F SER* 1.3 76.8 - - - +
328F ASP* 1.3 64.6 + - - +
329F GLU* 2.4 39.2 + - - +
330F GLU* 2.5 36.7 + - - +
331F ALA* 3.4 17.7 + - - +
352F SER* 4.1 2.1 + - - -
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Residues in contact with ASP 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F GLN* 5.6 1.6 - - - +
301F TYR* 5.3 7.3 - - + +
302F GLU* 3.1 36.4 - - - +
303F VAL* 2.4 42.6 + - + +
327F ASN* 1.3 72.9 + - - +
329F GLU* 1.3 70.2 + - - +
330F GLU 2.8 2.1 + - - -
331F ALA* 2.9 13.9 + - - +
332F PHE* 3.4 23.7 + - - +
390F TRP* 5.5 0.5 - - - -
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Residues in contact with GLU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F ASN* 2.4 19.6 + - - +
328F ASP* 1.3 76.9 - - - +
330F GLU* 1.3 63.1 + - - +
332F PHE* 3.8 3.6 + - - +
333F THR* 3.1 30.6 + - + +
391F MET* 5.2 1.0 - - - +
392F LEU* 4.2 33.6 - - + +
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Residues in contact with GLU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325F LYS 4.9 0.3 - - - +
326F SER* 4.0 23.4 + - - -
327F ASN* 2.5 37.9 + - - +
328F ASP 2.8 1.2 + - - -
329F GLU* 1.3 65.8 - - - +
331F ALA* 1.3 65.8 + - - +
332F PHE 2.9 1.9 + - - -
333F THR* 2.9 26.4 + - - -
334F PHE* 3.1 15.1 + - + -
355F ALA* 3.8 23.7 - - + +
359F LYS* 3.3 25.4 + - - -
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Residues in contact with ALA 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F VAL* 3.2 36.1 - - + -
327F ASN 3.4 2.5 + - - +
328F ASP 2.9 5.6 + - - +
330F GLU* 1.3 75.0 - - - +
332F PHE* 1.3 54.0 + - + +
335F ALA* 2.6 34.8 + - - +
348F GLY 3.9 1.5 - - - +
351F GLY* 3.2 7.5 - - - -
352F SER* 2.9 42.3 + - - +
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Residues in contact with PHE 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F GLU* 4.1 20.2 - - + -
303F VAL* 4.5 9.6 - - + -
304F GLU 5.5 0.2 - - - -
328F ASP* 3.4 26.7 + - - +
329F GLU* 4.5 1.8 - - - +
330F GLU 2.9 2.4 + - - -
331F ALA* 1.3 82.6 - - + +
333F THR* 1.3 65.7 + - - +
335F ALA* 3.5 2.4 - - - +
336F ARG* 2.9 28.2 + - - +
348F GLY* 3.8 23.8 - - - -
381F TYR* 5.2 9.6 - + - -
384F LYS* 5.9 2.9 - - + -
385F PHE* 3.8 25.8 - + + -
390F TRP* 3.3 31.2 - + - -
391F MET* 3.2 37.9 - - + -
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Residues in contact with THR 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F GLU* 3.1 26.2 - - + +
330F GLU* 2.9 9.6 + - - -
332F PHE* 1.3 75.9 - - - +
334F PHE* 1.3 78.9 + - - +
336F ARG* 2.8 13.3 + - - +
337F MET* 2.6 34.2 + - - +
391F MET* 4.3 10.1 - - + +
392F LEU* 5.7 2.2 - - + -
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Residues in contact with PHE 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ILE* 5.2 0.2 - - + -
99F PHE* 3.5 27.8 - + - -
330F GLU* 3.1 17.8 + - + +
333F THR* 1.3 101.6 + - - +
335F ALA* 1.3 66.9 + - - +
337F MET* 2.8 42.4 + - + +
338F LEU* 2.9 18.9 + - + +
351F GLY* 3.6 20.6 - - - +
354F VAL* 4.1 11.4 - - + -
355F ALA* 3.9 32.1 - - + -
358F VAL* 4.0 25.1 - - + -
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Residues in contact with ALA 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331F ALA 2.6 24.1 + - - +
332F PHE* 3.5 4.7 - - - +
333F THR 3.2 0.2 - - - -
334F PHE* 1.3 74.2 - - - +
336F ARG* 1.3 58.0 + - - +
338F LEU* 3.3 6.8 + - - +
339F ILE* 3.0 24.3 + - - +
346F CYS* 4.8 3.0 - - - +
347F GLY 3.8 15.7 - - - +
348F GLY* 3.9 3.8 - - - -
351F GLY* 3.4 9.8 - - - +
385F PHE* 3.0 36.1 - - + -
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Residues in contact with ARG 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ALA* 4.6 8.2 - - + +
332F PHE 2.9 11.6 + - - +
333F THR* 2.8 13.0 + - - +
335F ALA* 1.3 77.3 - - - +
337F MET* 1.3 60.6 + - - +
339F ILE* 3.3 19.1 + - + +
340F ALA* 3.4 15.9 + - - +
385F PHE* 3.2 19.1 - - + -
386F LEU* 3.7 14.7 - - - +
387F SER 3.2 10.3 - - - +
388F ASP* 2.5 66.2 + - - +
391F MET* 3.5 26.5 - - - +
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Residues in contact with MET 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F ILE* 2.8 51.2 - - + +
98F LYS* 6.2 1.3 - - + -
99F PHE* 3.4 20.2 - - + -
333F THR* 2.6 16.6 + - - +
334F PHE* 2.8 50.8 + - + +
336F ARG* 1.3 73.4 - - - +
338F LEU* 1.3 56.2 + - - +
339F ILE 3.2 1.1 - - - -
340F ALA* 4.2 1.1 - - - -
341F GLN* 3.4 32.5 + - + +
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Residues in contact with LEU 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ILE* 4.8 8.3 - - + -
95F ILE* 3.4 23.3 - - + -
334F PHE* 2.9 15.2 + - + +
335F ALA 3.7 4.7 - - - +
337F MET* 1.3 75.9 - - - +
339F ILE* 1.3 58.7 + - - +
340F ALA 3.6 0.2 - - - -
342F GLU* 4.1 4.4 - - + +
343F GLY 3.4 6.0 + - - -
344F LEU* 2.7 49.7 + - + +
346F CYS* 3.4 32.3 - - - -
350F ALA* 3.8 13.2 - - + -
351F GLY* 4.2 2.5 - - - +
354F VAL* 3.6 39.3 - - + -
374F LEU* 4.2 4.5 - - + -
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E VAL 5.1 0.4 - - - +
183E ALA* 3.3 30.5 - - + +
184E LEU* 3.4 27.5 - - + +
335F ALA 3.0 17.3 - - - +
336F ARG* 3.6 11.4 - - + +
337F MET 3.2 0.6 - - - -
338F LEU* 1.3 80.2 - - - +
340F ALA* 1.3 57.9 + - - +
343F GLY* 3.8 7.9 - - - -
344F LEU 3.3 15.3 - - - +
345F LEU* 4.8 10.1 - - + -
346F CYS 4.5 4.3 - - - +
378F VAL* 4.3 12.3 - - + -
385F PHE* 3.7 22.7 - - + -
386F LEU* 3.6 26.2 - - + -
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Residues in contact with ALA 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E ALA* 3.2 28.5 - - - +
183E ALA 3.0 18.8 - - - +
184E LEU* 4.2 11.1 - - - +
185E GLY* 4.4 4.3 - - - +
94F LYS* 4.7 0.9 + - - -
336F ARG 3.4 11.2 + - - +
337F MET* 5.4 0.4 - - - -
339F ILE* 1.3 79.2 - - - +
341F GLN* 1.3 65.0 + - + +
343F GLY 4.4 0.7 - - - -
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Residues in contact with GLN 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E VAL* 4.0 9.4 - - - +
94F LYS* 2.9 51.7 + - - +
95F ILE* 3.5 34.0 + - + +
98F LYS* 4.9 19.5 - - - +
337F MET* 3.4 26.5 + - + +
340F ALA* 1.3 82.2 - - + +
342F GLU* 1.3 63.5 + - - +
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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