Contacts of the helix formed by residues 242 - 251 (chain B) in PDB entry 1MPX
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 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B GLY 3.6 0.2 - - - -
241B HIS* 1.3 75.9 - - - +
243B ASP* 1.3 57.8 + - - +
244B TYR* 3.0 20.3 + - - +
245B SER* 3.1 14.4 + - - +
246B ASN* 2.9 27.7 + - - +
455B ARG* 2.8 33.3 + - - -
456B PRO* 3.5 19.5 - - + +
457B VAL 2.8 20.1 + - - -
474C ARG* 3.5 22.8 - - - +
525C GLU 4.9 0.4 + - - -
534C GLY 4.8 0.4 + - - -
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Residues in contact with ASP 243 (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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238B ARG* 2.8 35.9 + - - +
241B HIS 3.5 2.9 + - - +
242B ASP* 1.3 69.4 - - - +
244B TYR* 1.3 67.3 + - - +
245B SER 3.2 0.2 - - - -
246B ASN* 2.9 15.4 + - - +
247B PHE* 3.0 33.9 + - + +
457B VAL* 2.7 21.1 + - + +
458B ASP* 4.9 1.5 - - - +
459B PHE* 3.0 38.4 + - + +
594B PRO* 3.8 16.7 - - + +
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Residues in contact with TYR 244 (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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242B ASP* 3.0 15.0 + - - +
243B ASP* 1.3 78.7 - - - +
245B SER* 1.3 58.2 + - - +
248B LEU* 3.1 47.0 + - + +
448B LYS* 3.8 3.3 - - - -
449B PRO* 2.6 51.6 + - + +
451B PRO* 4.0 26.3 - - + +
455B ARG* 3.3 49.8 - - + +
457B VAL* 4.1 6.4 - - + +
479B ARG* 5.1 0.2 + - - -
593B PHE* 3.3 22.8 - + - -
594B PRO* 3.8 10.9 - - + +
477C ASP 4.7 1.8 - - - -
478C GLY* 3.9 15.2 - - - -
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ASP* 3.1 17.9 + - - +
244B TYR* 1.3 79.1 - - - +
246B ASN* 1.3 67.6 + - - +
248B LEU* 4.5 4.0 - - - -
249B GLN* 2.9 48.8 + - - +
455B ARG* 3.0 25.1 + - - -
474C ARG* 5.2 0.9 + - - -
525C GLU* 6.5 0.9 - - - -
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Residues in contact with ASN 246 (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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238B ARG* 3.7 17.3 - - - +
239B GLN* 3.9 12.1 + - + +
240B GLY* 2.8 48.6 + - - +
242B ASP 2.9 18.6 + - - +
243B ASP* 2.9 29.7 + - - +
245B SER* 1.3 77.6 - - - +
247B PHE* 1.3 65.5 + - + +
249B GLN* 4.0 7.2 + - - +
250B ALA* 3.2 23.4 + - - +
256B PHE* 4.4 8.1 - - + -
525C GLU* 5.0 1.6 - - - +
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Residues in contact with PHE 247 (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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217B GLN* 3.6 33.7 - - + +
220B PHE* 3.6 20.6 - + + -
238B ARG* 4.2 5.4 - - - -
243B ASP* 3.0 42.2 + - + +
246B ASN* 1.3 76.9 - - + +
248B LEU* 1.3 65.9 + - - +
250B ALA* 3.4 4.4 + - - +
251B GLY 3.1 26.7 + - - +
252B SER 5.1 1.3 - - - +
256B PHE* 3.4 52.5 - + + -
459B PHE* 3.7 20.2 - + - -
593B PHE* 3.6 18.4 - - + -
594B PRO* 3.9 9.0 - - + -
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Residues in contact with LEU 248 (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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244B TYR* 3.1 44.4 + - + +
245B SER* 4.0 4.0 - - - +
247B PHE* 1.3 77.2 - - - +
249B GLN* 1.3 63.7 + - + +
251B GLY* 3.4 11.6 + - - -
446B PRO 3.7 12.3 - - - +
447B ALA* 3.5 23.1 - - - +
449B PRO* 4.1 7.2 - - + -
593B PHE* 3.6 5.9 - - + -
598B ARG* 3.6 38.3 + - - +
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Residues in contact with GLN 249 (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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239B GLN* 5.0 7.7 - - - +
245B SER* 2.9 36.4 + - - +
246B ASN* 4.0 7.2 + - - +
248B LEU* 1.3 79.4 - - + +
250B ALA* 1.3 60.5 + - - +
251B GLY* 3.5 0.7 + - - -
525C GLU* 3.7 23.2 + - - +
583C ARG* 5.1 11.1 + - - +
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Residues in contact with ALA 250 (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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246B ASN 3.2 17.5 + - - +
247B PHE 3.8 4.9 - - - +
248B LEU 3.3 0.2 - - - -
249B GLN* 1.3 81.0 - - - +
251B GLY* 1.3 57.3 + - - +
252B SER 4.9 0.2 - - - +
255B ASP* 3.1 23.3 - - - +
256B PHE* 4.0 35.0 - - + +
259B ALA* 6.1 2.2 - - + -
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Residues in contact with GLY 251 (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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247B PHE* 3.1 14.3 + - - +
248B LEU 3.4 4.9 + - - -
249B GLN 3.3 3.2 - - - -
250B ALA* 1.3 77.4 - - - +
252B SER* 1.3 63.9 + - - -
255B ASP* 3.8 4.0 - - - -
593B PHE* 5.7 1.0 - - - -
598B ARG* 2.8 32.3 + - - -
615B TYR* 4.2 3.6 - - - -
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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