Contacts of the helix formed by residues 347 - 361 (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 GLY 347 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335F ALA* 3.8 8.2 - - - +
346F CYS* 1.3 75.6 - - - +
348F GLY* 1.3 67.3 + - - -
349F SER* 3.2 3.4 - - - -
350F ALA* 2.9 15.2 + - - +
351F GLY 3.1 8.1 + - - -
376F ASP* 2.8 26.2 + - - -
377F SER 3.6 7.5 + - - -
381F TYR* 4.1 7.4 - - - -
385F PHE* 4.1 6.7 - - - -
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Residues in contact with GLY 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F VAL* 3.9 11.2 - - - -
304F GLU 5.6 0.2 - - - -
331F ALA 3.9 0.6 - - - +
332F PHE* 3.8 26.7 - - - -
335F ALA* 3.9 8.3 - - - -
347F GLY* 1.3 69.0 - - - -
349F SER* 1.3 55.9 + - - +
351F GLY* 2.5 23.4 + - - -
352F SER* 2.6 14.0 + - - -
381F TYR* 4.3 11.3 - - - -
385F PHE* 3.9 8.3 - - - -
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Residues in contact with SER 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F SER* 4.3 2.3 + - - -
303F VAL* 4.1 3.2 - - - +
304F GLU 4.6 6.5 + - - -
306F ILE* 4.4 10.3 - - - -
347F GLY 4.1 0.2 - - - -
348F GLY* 1.3 70.0 - - - +
350F ALA* 1.3 65.9 + - - -
352F SER* 3.1 7.5 + - - -
353F THR* 2.8 28.6 + - - -
375F PRO* 3.5 14.5 - - - +
376F ASP* 3.1 25.3 + - - -
381F TYR* 4.2 0.5 + - - -
1610F PLP 3.2 36.1 - - - +
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Residues in contact with ALA 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F LEU* 4.0 0.4 - - - -
346F CYS* 2.9 44.0 - - + -
347F GLY 2.9 7.9 + - - +
349F SER* 1.3 80.8 + - - +
351F GLY* 1.3 66.2 + - - +
353F THR* 3.7 1.0 - - - -
354F VAL* 2.9 27.4 + - - +
373F ILE 4.5 5.6 - - - -
374F LEU* 3.5 24.2 - - + +
375F PRO* 4.8 0.4 - - - +
376F ASP 5.1 0.2 - - - +
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Residues in contact with GLY 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F ALA* 3.2 19.5 - - - -
334F PHE* 3.6 11.7 - - - +
335F ALA* 3.4 17.8 - - - +
338F LEU* 4.4 2.5 - - - -
347F GLY 3.1 4.2 + - - -
348F GLY 2.5 12.5 + - - -
350F ALA* 1.3 78.1 - - - +
352F SER* 1.3 62.3 + - - -
354F VAL* 3.1 2.8 + - - +
355F ALA* 3.0 18.0 + - - +
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Residues in contact with SER 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F VAL* 4.3 8.1 - - - -
303F VAL* 3.6 2.5 - - - +
306F ILE* 3.5 28.7 - - - +
326F SER* 4.0 16.9 + - - -
327F ASN 4.1 2.4 + - - -
331F ALA* 2.9 32.4 - - - +
348F GLY 2.6 11.1 + - - -
349F SER 3.5 7.0 - - - -
351F GLY* 1.3 69.6 - - - +
353F THR* 1.3 66.7 + - - +
355F ALA* 3.0 20.3 + - - +
356F VAL* 3.5 8.8 + - - +
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Residues in contact with THR 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F VAL* 2.9 39.9 - - + +
253F ALA* 4.3 0.8 - - - -
254F SER* 3.1 28.9 + - - -
280F VAL* 4.1 10.7 - - - +
349F SER 2.8 18.6 + - - -
350F ALA 3.7 3.4 - - - -
352F SER* 1.3 71.6 - - - +
354F VAL* 1.3 65.6 + - - +
356F VAL* 3.0 17.0 + - - +
357F ALA 3.2 8.5 + - - -
372F VAL* 3.7 13.5 - - + -
373F ILE 3.7 19.9 + - - +
375F PRO* 4.9 1.2 - - - +
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Residues in contact with VAL 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F ILE* 6.3 1.1 - - + -
95F ILE* 4.5 9.6 - - + -
105F LEU* 5.1 8.5 - - + -
334F PHE* 4.1 16.2 - - + -
338F LEU* 3.6 35.0 - - + -
350F ALA 2.9 17.6 + - - +
351F GLY 3.5 5.8 - - - +
353F THR* 1.3 72.3 - - - +
355F ALA* 1.3 65.8 + - - +
356F VAL 3.1 0.7 + - - -
357F ALA* 3.1 19.6 + - + -
358F VAL* 3.2 22.5 + - + +
372F VAL* 4.1 21.5 - - + -
374F LEU* 4.2 1.6 - - + -
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Residues in contact with ALA 355 (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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326F SER* 5.0 0.2 - - - +
330F GLU* 3.8 32.8 - - + +
334F PHE* 3.9 29.2 - - + -
351F GLY 3.0 10.6 + - - +
352F SER* 3.0 14.2 + - - +
354F VAL* 1.3 77.1 - - - +
356F VAL* 1.3 58.7 + - + +
358F VAL* 3.2 12.8 - - - +
359F LYS* 3.1 22.4 + - - -
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Residues in contact with VAL 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F VAL* 4.0 6.5 - - + -
278F ILE* 4.3 1.6 - - + -
280F VAL* 3.3 30.5 - - + -
324F PHE* 3.2 45.1 - - + -
325F LYS 4.8 0.2 - - - +
326F SER* 3.1 27.8 - - - +
352F SER 3.6 7.0 - - - +
353F THR 3.0 5.6 + - - +
355F ALA* 1.3 77.9 - - - +
357F ALA* 1.3 56.1 + - - +
359F LYS* 2.9 13.3 + - - +
360F ALA* 2.6 38.2 + - + +
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Residues in contact with ALA 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F LEU* 4.9 1.1 - - - -
105F LEU* 4.6 13.7 - - + -
252F VAL* 3.9 18.1 - - + +
353F THR 3.2 4.0 + - - +
354F VAL* 3.1 12.5 + - + +
356F VAL* 1.3 75.2 - - - +
358F VAL* 1.3 69.2 + - + +
359F LYS 2.7 2.1 + - - -
360F ALA* 2.9 1.1 + - - -
361F ALA* 2.8 27.6 + - - +
370F CYS* 4.9 2.7 - - - -
372F VAL* 3.6 31.2 - - + -
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Residues in contact with VAL 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ILE* 4.9 6.5 - - + +
96F GLY* 5.7 0.2 - - - -
99F PHE* 4.1 36.1 - - + -
101F LEU* 3.7 24.8 - - + +
105F LEU* 5.4 2.2 - - + -
334F PHE* 4.0 20.0 - - + -
354F VAL* 3.3 20.6 - - + +
355F ALA* 3.2 22.9 - - - +
357F ALA* 1.3 76.4 - - + +
359F LYS* 1.3 77.7 + - + +
362F GLN* 2.9 29.0 + - - +
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Residues in contact with LYS 359 (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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324F PHE* 4.5 20.1 - - + -
325F LYS 5.5 4.6 + - - -
326F SER* 5.7 1.0 + - - -
330F GLU* 3.3 27.7 + - - -
355F ALA 3.1 23.5 + - - -
356F VAL* 2.9 8.7 + - - +
357F ALA 2.7 3.6 + - - -
358F VAL* 1.3 84.0 - - + +
360F ALA* 1.3 67.4 + - - +
361F ALA 3.1 1.6 - - - -
362F GLN* 3.0 28.7 + - + +
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Residues in contact with ALA 360 (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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250F MET* 3.5 28.4 - - - +
252F VAL* 4.0 7.4 - - + -
278F ILE* 4.4 8.3 - - + +
324F PHE* 4.1 24.6 - - + -
356F VAL* 2.6 27.4 + - + +
357F ALA* 3.7 5.4 - - - +
359F LYS* 1.3 73.6 - - - +
361F ALA* 1.3 59.6 + - - +
362F GLN 3.5 0.5 + - - -
363F GLU* 3.6 14.7 - - - +
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Residues in contact with ALA 361 (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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101F LEU* 4.5 12.2 - - + +
103F CYS* 3.8 24.0 - - - -
250F MET* 3.9 1.3 - - - -
357F ALA 2.8 18.5 + - - +
358F VAL 4.5 1.8 - - - -
360F ALA* 1.3 72.4 - - - +
362F GLN* 1.3 63.2 + - - -
363F GLU 3.1 4.0 + - - -
364F LEU* 3.2 36.0 + - + +
370F CYS* 3.9 20.0 - - - -
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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
------------------------------------------------------------
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