Contacts of the helix formed by residues 347 - 361 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B ALA* 4.0 7.2 - - - +
346B CYS* 1.3 78.3 - - - +
348B GLY* 1.3 70.4 + - - +
349B SER* 3.2 4.0 - - - -
350B ALA* 2.8 17.0 + - - +
351B GLY 3.4 5.7 + - - -
376B ASP 3.3 9.1 + - - -
377B SER 3.9 0.2 + - - -
381B TYR* 3.4 24.7 - - - -
385B PHE* 3.8 6.3 - - - -
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Residues in contact with GLY 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 4.3 13.9 - - - -
304B GLU 5.5 1.3 - - - -
331B ALA* 4.4 3.4 - - - +
332B PHE* 4.2 26.6 - - - -
335B ALA* 4.4 4.5 - - - -
347B GLY* 1.3 68.0 - - - -
349B SER* 1.3 69.0 + - - +
351B GLY* 2.8 12.3 + - - -
352B SER* 3.1 11.3 + - - -
381B TYR* 3.9 11.1 - - - -
385B PHE* 4.1 7.5 - - - -
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 3.3 7.5 + - - -
303B VAL* 4.3 7.0 - - - +
304B GLU 4.4 4.6 + - - -
306B ILE* 4.6 7.4 - - - -
347B GLY 2.9 5.3 + - - -
348B GLY* 1.3 73.8 - - - +
350B ALA* 1.3 69.0 + - - +
352B SER* 3.2 2.9 + - - -
353B THR* 3.0 22.0 + - - -
375B PRO* 3.4 20.1 - - - +
376B ASP* 3.5 17.0 + - - -
381B TYR* 4.9 1.0 + - - -
1210B PLP 2.9 40.1 - - - +
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Residues in contact with ALA 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 3.9 2.7 - - + -
346B CYS* 3.8 22.4 - - + -
347B GLY 2.8 10.8 + - - +
349B SER* 1.3 77.1 + - - +
351B GLY* 1.3 70.3 + - - +
353B THR* 2.6 10.8 + - - -
354B VAL* 2.6 26.8 + - - +
373B ILE 4.7 2.0 - - - -
374B LEU* 3.1 35.9 - - + +
375B PRO* 4.7 0.2 - - - +
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Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ALA 3.0 27.1 - - - -
334B PHE* 3.3 8.6 - - - +
335B ALA* 3.5 17.7 - - - +
338B LEU* 5.4 0.2 - - - -
347B GLY 3.4 4.4 + - - -
348B GLY 2.8 10.9 + - - -
350B ALA* 1.3 73.4 - - - +
352B SER* 1.3 50.2 + - - -
354B VAL* 5.3 0.7 - - - -
355B ALA* 2.6 38.9 + - - +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B SER* 4.2 3.8 - - - -
280B VAL* 4.1 6.9 - - - +
303B VAL* 4.2 3.8 - - - +
306B ILE* 4.0 23.4 - - - +
326B SER* 3.2 20.1 + - - -
331B ALA* 3.0 25.0 - - - +
348B GLY 3.1 6.2 + - - -
349B SER 3.4 8.1 - - - -
350B ALA 3.1 0.2 - - - -
351B GLY* 1.3 73.5 - - - +
353B THR* 1.3 64.0 + - - +
355B ALA* 3.3 11.4 + - - +
356B VAL* 3.0 25.5 - - - +
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Residues in contact with THR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 3.4 39.1 - - + +
253B ALA 4.3 2.0 - - - +
254B SER* 2.4 31.9 + - - +
280B VAL* 4.5 6.3 - - - -
349B SER 3.0 8.0 + - - -
350B ALA* 2.6 14.4 + - - -
352B SER* 1.3 75.3 - - - +
354B VAL* 1.3 62.0 + - - +
356B VAL* 3.4 6.4 + - - +
357B ALA 3.6 1.2 + - - -
372B VAL* 3.7 18.2 - - + -
373B ILE 3.5 31.4 + - - +
375B PRO* 4.5 0.2 - - - +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 5.5 9.2 - - + -
95B ILE* 4.4 11.7 - - + -
105B LEU* 4.7 12.3 - - + -
334B PHE* 4.0 16.7 - - + -
338B LEU* 4.1 24.0 - - + -
350B ALA 2.6 17.9 + - - +
351B GLY 4.2 0.9 - - - +
353B THR* 1.3 68.5 - - - +
355B ALA* 1.3 56.6 + - - +
356B VAL 2.7 12.3 + - - -
357B ALA* 3.1 20.1 + - + +
358B VAL* 3.6 11.7 + - + +
372B VAL* 3.7 28.5 - - + -
374B LEU* 4.0 13.7 - - + -
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B SER* 5.5 0.2 - - - +
330B GLU* 3.3 28.3 - - + +
334B PHE* 3.3 30.9 - - + -
351B GLY 2.6 24.8 + - - +
352B SER* 3.5 10.3 - - - +
353B THR 3.3 0.4 - - - -
354B VAL* 1.3 72.3 - - - +
356B VAL* 1.3 52.9 + - + +
358B VAL* 3.8 1.6 - - - -
359B LYS* 2.7 36.6 - - - -
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Residues in contact with VAL 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 4.1 6.1 - - + -
278B ILE* 4.6 0.7 - - + -
280B VAL* 3.3 26.9 - - + -
324B PHE* 3.3 47.6 - - + -
325B LYS 4.8 7.9 - - - +
326B SER* 5.2 1.6 - - - -
330B GLU* 5.0 3.4 - - - +
352B SER 3.0 20.4 - - - +
353B THR 3.6 5.2 - - - +
354B VAL 2.7 2.2 + - - -
355B ALA* 1.3 82.4 - - + +
357B ALA* 1.3 54.2 + - - +
358B VAL 3.1 2.7 - - - -
359B LYS* 3.0 8.1 + - + +
360B ALA* 2.7 37.2 + - + +
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 0.4 - - - -
105B LEU* 4.1 28.7 - - + -
252B VAL* 3.8 26.8 - - + +
353B THR 3.6 2.6 + - - -
354B VAL* 3.1 11.7 + - - +
356B VAL* 1.3 77.4 - - - +
358B VAL* 1.3 54.9 + - - +
360B ALA* 4.5 0.9 - - - -
361B ALA* 2.3 47.9 + - + +
372B VAL* 4.1 8.5 - - + -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.3 12.8 - - + +
96B GLY* 5.1 2.7 - - - -
99B PHE* 3.4 43.7 - - + -
101B LEU* 3.1 14.1 - - + +
105B LEU* 5.2 2.5 - - + -
334B PHE* 3.6 28.5 - - + -
354B VAL* 3.6 7.2 + - + +
355B ALA 3.5 13.9 - - - +
357B ALA* 1.3 72.9 - - - +
359B LYS* 1.3 81.3 + - + +
362B GLN* 2.5 34.2 + - - +
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.5 10.5 - - + -
324B PHE* 4.9 14.5 - - + -
330B GLU* 3.6 16.8 + - - +
334B PHE* 3.8 19.2 - - - -
355B ALA 2.7 25.9 + - - +
356B VAL* 3.0 12.8 + - + +
358B VAL* 1.3 83.1 - - + +
360B ALA* 1.3 59.6 + - - +
362B GLN* 2.8 25.3 - - - +
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B MET* 3.5 24.8 - - - +
252B VAL* 5.7 0.9 - - + -
278B ILE* 4.7 9.9 - - + -
324B PHE* 3.6 32.7 - - + -
356B VAL* 2.7 25.4 + - + +
357B ALA* 4.3 2.0 - - - +
359B LYS* 1.3 70.8 - - - +
361B ALA* 1.3 57.4 + - - +
362B GLN 2.8 11.8 + - - -
363B GLU* 3.7 13.7 + - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 2.8 40.2 - - + +
102B LYS 4.5 1.0 + - - -
103B CYS* 3.8 9.6 - - - +
250B MET* 4.0 10.8 - - - -
357B ALA* 2.3 49.9 + - + +
360B ALA* 1.3 68.1 - - - +
362B GLN* 1.3 61.1 + - - +
363B GLU 3.7 0.4 - - - -
364B LEU* 3.7 16.0 - - - +
370B CYS* 4.5 10.5 - - - -
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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
------------------------------------------------------------
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