Contacts of the helix formed by residues 271 - 276 (chain J) in PDB entry 1MVW
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 GLU 271 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245J ARG* 2.6 52.2 + - + +
269J LEU 3.9 0.2 + - - -
270J LEU* 1.3 69.9 - - - +
272J MLY 1.3 63.7 + - - +
273J SER* 3.2 18.5 + - - +
274J ARG* 2.5 47.8 + - + +
285J TYR* 2.5 29.3 + - - +
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Residues in contact with MLY 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270J LEU* 2.8 23.8 + - + +
271J GLU* 1.3 71.8 - - - +
273J SER* 1.3 64.4 + - - +
274J ARG 3.2 0.9 + - - -
275J VAL* 3.3 27.3 + - - +
431J MLY 3.4 42.7 - - + +
432J ALA* 5.2 1.3 - - - +
435J GLU* 2.8 50.9 + - + +
436J MLY 4.2 5.8 - - - -
598J MLY 4.8 14.1 - - - -
601J ASP* 3.5 38.7 + - - -
649J VAL* 4.8 16.4 - - - -
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Residues in contact with SER 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J GLU* 4.1 15.6 + - - +
272J MLY 1.3 79.7 + - - +
274J ARG* 1.3 51.5 + - - +
276J THR* 2.9 4.3 + - - -
277J PHE* 2.7 47.9 + - - +
431J MLY 4.6 21.6 - - - -
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Residues in contact with ARG 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235J ALA* 3.7 19.2 - - - +
236J MLY 4.2 3.6 + - - -
237J THR* 4.5 5.6 + - - +
245J ARG* 3.4 19.6 - - - +
271J GLU* 2.5 56.2 + - - +
272J MLY 3.2 0.4 + - - -
273J SER* 1.3 75.7 - - - +
275J VAL* 1.3 59.8 + - - +
276J THR 2.8 4.9 + - - -
277J PHE* 2.5 26.2 + - - +
278J GLN* 3.3 7.3 + - - +
279J LEU 5.1 1.4 - - - +
282J GLU* 2.2 55.1 + - - +
283J ARG 3.0 23.0 + - - -
284J SER* 3.2 15.4 + - - +
285J TYR* 3.2 26.5 - - + -
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Residues in contact with VAL 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272J MLY 3.3 21.1 - - + +
274J ARG* 1.3 76.6 - - - +
276J THR* 1.3 58.6 + - - +
284J SER* 4.1 7.0 - - - -
285J TYR* 3.9 15.7 - - + -
288J PHE* 4.9 6.9 - - + -
314J TYR* 3.7 21.6 - - - +
315J VAL* 4.7 4.5 - - - +
358J VAL* 3.9 26.1 - - + +
430J ALA* 4.4 14.6 - - + +
431J MLY 4.4 9.4 - - + -
434J TYR* 3.9 35.4 - - + -
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Residues in contact with THR 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J SER* 2.9 7.0 + - - -
274J ARG 2.9 0.2 - - - -
275J VAL* 1.3 78.8 + - - +
277J PHE* 1.3 58.7 + - + +
313J HIS* 5.6 0.5 + - - -
314J TYR* 3.8 40.5 - - + +
317J GLU* 2.6 22.8 - - - +
427J GLY* 4.2 8.4 + - - -
430J ALA* 4.8 0.7 - - - +
431J MLY 3.6 39.6 - - + +
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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