Contacts of the helix formed by residues 343 - 353 (chain B) in PDB entry 3MTG
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 ASP 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A GLU* 4.2 4.8 - - - +
504A LEU* 4.0 2.0 - - - -
523A PHE* 3.5 17.5 - - + +
524A LYS* 2.9 40.5 + - - +
530A TYR* 4.1 2.4 + - - -
1B NAD 3.5 9.9 - - - +
341B GLU* 2.9 13.9 + - - +
342B ILE* 1.3 77.4 - - - +
344B PRO* 1.4 65.3 - - - +
345B ILE* 2.9 37.3 + - - +
346B CYS* 3.7 10.9 - - + +
347B ALA* 2.9 28.1 + - - +
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Residues in contact with PRO 344 (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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490A GLU* 3.3 39.7 - - + +
493A ALA* 3.4 4.1 - - - +
494A SER* 3.7 22.4 - - - +
497A LEU* 4.0 5.1 - - + +
504A LEU* 4.0 23.3 - - + -
523A PHE* 3.9 16.2 - - + -
342B ILE 3.5 9.6 - - - +
343B ASP* 1.4 87.6 - - - +
345B ILE* 1.4 55.5 + - - +
347B ALA* 3.8 2.4 - - + +
348B LEU* 2.9 29.8 + - - +
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Residues in contact with ILE 345 (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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282A VAL* 4.1 17.5 - - + -
283A THR* 3.7 18.8 - - + +
286A LYS* 5.6 1.8 - - + -
486A LYS* 4.8 1.1 - - + +
489A ASP* 3.8 38.8 - - + +
490A GLU* 3.9 13.0 - - + +
493A ALA* 3.7 7.6 - - + -
530A TYR* 3.5 47.1 - - + +
343B ASP* 2.9 9.8 + - - +
344B PRO* 1.4 75.1 - - - +
346B CYS* 1.4 57.6 + - - +
348B LEU* 3.3 5.1 + - - +
349B GLN* 2.9 35.9 + - + +
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Residues in contact with CYS 346 (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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524A LYS* 3.5 27.8 - - - -
528A TYR* 4.6 4.9 - - - -
530A TYR* 4.2 12.8 - - - -
1B NAD 3.5 7.0 - - - -
319B TYR* 3.4 25.7 - - - +
324B LYS* 4.0 9.6 - - - -
341B GLU* 3.5 25.1 - - + +
343B ASP* 3.3 6.6 + - + +
345B ILE* 1.4 73.6 - - - +
347B ALA* 1.3 60.3 + - - +
349B GLN* 3.2 14.7 + - - +
350B ALA* 3.0 22.3 + - - +
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Residues in contact with ALA 347 (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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497A LEU* 3.9 12.6 - - + -
504A LEU* 3.7 22.4 - - + -
341B GLU* 4.1 8.4 - - + +
343B ASP 2.9 16.7 + - - +
344B PRO 3.8 4.3 - - - +
346B CYS* 1.3 72.4 - - - +
348B LEU* 1.4 64.8 + - - +
350B ALA* 3.1 6.5 + - - +
351B CYS* 3.0 25.6 + - - -
357B VAL* 3.4 23.5 - - + +
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Residues in contact with LEU 348 (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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283A THR* 4.0 9.9 - - + -
287A PHE* 3.7 29.4 - - + -
453A PHE* 4.5 0.7 - - + -
457A ILE* 3.8 16.8 - - + -
493A ALA* 3.9 20.9 - - + +
496A HIS* 4.0 13.7 - - + -
497A LEU* 3.6 12.9 - - + +
500A PHE* 3.4 35.7 - - + -
344B PRO 2.9 19.5 + - - +
345B ILE 3.6 4.7 - - - +
347B ALA* 1.4 74.1 - - - +
349B GLN* 1.3 63.0 + - + +
351B CYS* 3.3 3.8 + - - +
352B MET* 3.1 28.7 + - - +
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Residues in contact with GLN 349 (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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286A LYS* 4.4 22.2 - - + +
290A LEU* 5.6 2.0 - - + +
530A TYR* 3.3 39.6 + - - +
319B TYR* 3.9 10.5 - - + -
324B LYS* 3.2 26.2 + - - +
345B ILE* 2.9 20.6 + - + +
346B CYS* 3.3 19.0 - - - +
348B LEU* 1.3 76.4 - - - +
350B ALA* 1.4 56.0 + - - +
352B MET* 3.5 5.9 + - - +
353B ASP* 3.1 34.0 + - - +
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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
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319B TYR* 3.5 25.7 - - + -
339B ILE* 3.9 16.2 - - + -
346B CYS 3.0 12.6 + - - +
347B ALA 3.1 8.7 + - - +
349B GLN* 1.4 72.7 - - - +
351B CYS* 1.4 60.7 + - - +
353B ASP* 3.1 9.6 + - - +
354B GLY 3.3 0.3 + - - -
355B PHE* 2.9 35.2 + - + +
357B VAL* 3.8 15.5 - - + -
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Residues in contact with CYS 351 (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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497A LEU* 4.2 3.4 - - - -
500A PHE* 3.7 50.1 - - + -
502A ALA* 4.0 13.2 - - - -
347B ALA 3.0 22.1 + - - -
348B LEU 3.5 8.1 - - - +
350B ALA* 1.4 72.6 - - - +
352B MET* 1.3 61.7 + - - +
354B GLY* 3.2 18.5 + - - -
355B PHE 3.4 12.5 + - - +
357B VAL* 3.6 17.3 - - - -
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Residues in contact with MET 352 (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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287A PHE* 3.3 40.4 - - + -
290A LEU* 3.5 24.0 - - + -
294A ARG* 2.9 24.7 + - - -
453A PHE* 5.1 2.7 - - + -
500A PHE* 3.1 41.3 - - + -
348B LEU* 3.1 16.2 + - + +
349B GLN* 3.8 5.6 - - - +
351B CYS* 1.3 80.0 - - - +
353B ASP* 1.3 57.4 + - - +
354B GLY 3.2 3.1 + - - -
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Residues in contact with ASP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.7 4.9 - - - +
294A ARG* 3.0 26.1 + - - +
319B TYR* 2.6 33.5 + - - +
324B LYS* 5.3 2.3 - - - +
331B LYS* 3.2 28.5 + - - +
349B GLN* 3.1 18.9 + - - +
350B ALA 3.1 6.3 + - - +
352B MET* 1.3 75.0 - - - +
354B GLY* 1.3 59.1 + - - +
355B PHE* 3.5 12.0 - - + -
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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
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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