Contacts of the helix formed by residues 273 - 278 (chain B) in PDB entry 1MGV
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 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLY* 5.1 2.2 - - - -
246B GLU 4.8 0.6 + - - -
247B ILE* 3.8 18.2 - - - +
251B PHE* 4.2 4.9 - - - -
272B LEU* 1.3 77.8 - - - +
274B LYS* 1.3 70.5 + - - +
275B ALA 2.7 5.5 + - - -
276B LEU* 2.8 18.7 + - - +
283B LEU 3.7 16.8 - - - -
284B SER* 4.2 2.9 - - - -
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Residues in contact with LYS 274 (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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309A THR* 3.2 24.9 - - + +
310A PHE* 3.8 20.9 - - + -
52B TRP 3.4 8.5 - - - +
53B TRP* 3.3 40.0 - - + +
54B ALA* 3.6 23.3 - - + +
112B GLY* 5.8 0.6 - - - +
144B TYR* 5.0 0.2 - - - -
247B ILE* 3.2 24.0 - - + +
248B ALA* 4.5 0.4 - - - -
273B GLY* 1.3 65.6 - - - -
275B ALA* 1.3 60.7 + - + +
276B LEU* 2.9 6.1 + - - +
277B THR* 3.7 8.7 + - - +
279B GLY 4.2 0.5 + - - -
283B LEU 4.4 3.3 + - - +
630B IPA 4.0 6.3 - - - +
700B PLP 1.3 90.4 + - - +
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Residues in contact with ALA 275 (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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53B TRP* 4.1 5.8 - - + +
54B ALA* 3.4 20.6 - - - +
56B ILE* 3.7 30.3 - - + +
247B ILE 4.5 1.6 + - - +
248B ALA 6.0 0.9 - - - +
250B GLY 4.5 5.8 - - - +
251B PHE* 4.0 18.9 - - + -
273B GLY 2.7 5.1 + - - -
274B LYS* 1.3 75.2 - - - +
276B LEU* 1.3 63.3 + - - +
277B THR 3.2 0.9 - - - -
278B GLY* 2.9 14.2 + - - -
323B SER* 3.7 6.1 + - - -
324B LEU* 6.1 0.2 - - - +
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Residues in contact with LEU 276 (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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91B LEU* 4.3 7.6 - - + -
95B LEU* 4.1 16.8 - - + -
251B PHE* 3.6 32.3 - - + -
272B LEU* 4.7 2.0 - - + +
273B GLY* 2.8 20.4 + - - +
274B LYS 2.9 0.8 + - - +
275B ALA* 1.3 77.7 - - - +
277B THR* 1.3 58.8 + - + +
278B GLY 3.6 0.3 + - - -
283B LEU* 3.8 37.5 - - + +
284B SER* 3.8 20.2 - - - +
285B ALA* 4.1 9.9 - - + +
320B ALA* 3.4 33.8 - - + +
323B SER* 3.8 6.2 + - - -
324B LEU* 4.7 6.2 - - + +
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Residues in contact with THR 277 (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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310A PHE* 4.0 0.7 - - - -
64B LEU* 4.6 1.4 - - - +
274B LYS 3.7 6.0 + - - +
275B ALA 3.2 0.4 - - - -
276B LEU* 1.3 77.3 - - + +
278B GLY* 1.3 57.3 + - - +
279B GLY 3.6 2.9 + - - -
280B THR* 3.0 32.4 + - - +
281B MET* 2.5 39.3 + - + +
283B LEU* 3.4 33.4 - - + +
316B ALA 3.8 15.9 - - - +
319B ALA* 4.1 8.0 - - - +
320B ALA* 3.9 8.3 - - + +
323B SER* 3.9 5.9 - - - -
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Residues in contact with GLY 278 (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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54B ALA 3.3 10.1 - - - -
55B ALA* 3.6 11.1 - - - +
56B ILE* 4.4 1.5 + - - -
57B HIS* 3.9 14.8 - - - -
58B GLY 4.3 5.4 - - - +
64B LEU* 4.1 8.2 - - - +
275B ALA 2.9 16.6 + - - -
276B LEU 3.3 0.4 - - - -
277B THR* 1.3 76.0 - - - +
279B GLY* 1.3 64.5 + - - +
280B THR* 3.4 6.2 + - - +
323B SER* 3.6 13.8 + - - -
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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