Contacts of the helix formed by residues 242 - 251 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B ARG* 3.5 22.2 - - - +
525B GLU 4.9 0.2 + - - -
534B GLY 4.8 0.2 + - - -
241C HIS* 1.3 76.9 - - - +
243C ASP* 1.3 58.5 + - - +
244C TYR* 3.0 18.9 + - - +
245C SER* 3.1 15.0 + - - +
246C ASN* 2.8 27.6 + - - -
455C ARG* 2.9 35.0 + - - -
456C PRO* 3.4 18.7 - - + +
457C VAL* 2.8 21.2 + - - +
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C ARG* 2.8 45.0 + - - +
241C HIS 3.5 2.6 + - - +
242C ASP* 1.3 69.8 - - - +
244C TYR* 1.3 65.9 + - - +
246C ASN* 2.9 15.9 + - - +
247C PHE* 3.1 36.3 + - + +
457C VAL* 2.8 21.5 + - + +
458C ASP* 4.5 1.5 - - - +
459C PHE* 3.1 27.3 + - + -
594C PRO* 3.7 17.4 - - + +
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Residues in contact with TYR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ASP 4.8 1.3 - - - -
478B GLY* 4.0 14.0 - - - -
242C ASP* 3.0 14.8 + - - +
243C ASP* 1.3 78.9 - - - +
245C SER* 1.3 59.5 + - - +
248C LEU* 3.2 46.6 + - + +
448C LYS* 3.8 3.5 - - - -
449C PRO* 2.6 53.1 + - + +
451C PRO* 3.9 25.9 - - + +
455C ARG* 3.4 50.9 - - + +
457C VAL* 4.2 6.6 - - + +
479C ARG* 5.2 0.5 + - - -
593C PHE* 3.3 22.3 - + - -
594C PRO* 3.8 10.7 - - + +
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Residues in contact with SER 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B ARG* 5.3 0.5 + - - -
242C ASP* 3.1 17.1 + - - +
244C TYR* 1.3 80.1 - - - +
246C ASN* 1.3 67.9 + - - +
248C LEU* 4.5 4.3 - - - -
249C GLN* 3.0 46.2 + - - +
455C ARG* 3.0 25.1 + - - -
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Residues in contact with ASN 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLU* 4.8 1.6 - - - +
238C ARG* 3.6 19.4 - - - +
239C GLN* 3.9 10.3 + - + +
240C GLY* 2.8 47.6 + - - -
241C HIS 4.2 0.2 - - - -
242C ASP 2.8 22.3 + - - +
243C ASP* 2.9 28.9 + - - +
245C SER* 1.3 74.5 - - - +
247C PHE* 1.3 64.4 + - + +
249C GLN* 4.1 7.2 + - - +
250C ALA* 3.3 22.9 + - - +
256C PHE* 4.3 8.1 - - + -
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Residues in contact with PHE 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLN* 3.6 33.2 - - + +
220C PHE* 3.6 22.4 - + + -
238C ARG* 4.3 6.5 - - - -
243C ASP* 3.1 43.3 + - + +
246C ASN* 1.3 76.2 - - - +
248C LEU* 1.3 65.2 + - - +
250C ALA* 3.3 4.0 + - - +
251C GLY 3.1 27.4 + - - +
252C SER 5.1 0.7 - - - +
253C ALA* 5.8 0.2 - - - -
256C PHE* 3.4 52.0 - + + +
459C PHE* 3.6 22.2 - + - -
593C PHE* 3.6 19.5 - - + -
594C PRO* 3.9 8.5 - - + -
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Residues in contact with LEU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TYR* 3.2 43.5 + - + +
245C SER* 4.0 4.7 - - - +
247C PHE* 1.3 77.2 - - - +
249C GLN* 1.3 63.3 + - + +
251C GLY* 3.3 12.3 + - - -
446C PRO 3.7 11.7 - - - +
447C ALA* 3.4 23.1 - - - +
449C PRO* 4.1 5.6 - - + -
593C PHE* 3.6 5.7 - - + -
598C ARG* 3.7 39.4 + - - +
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525B GLU* 3.9 20.7 + - - +
583B ARG* 4.8 13.9 + - - +
239C GLN* 5.0 8.1 - - - +
245C SER* 3.0 36.9 + - - +
246C ASN* 4.1 8.0 + - - +
248C LEU* 1.3 78.3 - - + +
250C ALA* 1.3 62.6 + - - +
251C GLY* 3.5 0.5 + - - -
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C ASN 3.3 16.6 + - - +
247C PHE 3.3 6.5 + - - +
249C GLN* 1.3 78.8 - - - +
251C GLY* 1.3 58.7 + - - +
252C SER 4.9 0.4 - - - +
255C ASP* 3.0 25.3 - - - +
256C PHE* 4.0 34.8 - - + +
259C ALA* 6.0 2.7 - - + -
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Residues in contact with GLY 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C GLN* 5.7 0.2 - - - +
247C PHE* 3.1 14.1 + - - +
248C LEU 3.3 8.4 + - - -
249C GLN 3.3 4.0 - - - -
250C ALA* 1.3 75.2 - - - +
252C SER* 1.3 64.5 + - - -
255C ASP* 3.9 3.8 - - - -
593C PHE* 5.7 1.0 - - - -
598C ARG* 2.9 26.4 + - - -
615C TYR* 4.3 2.5 - - - -
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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
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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