Contacts of the helix formed by residues 242 - 251 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A ARG* 3.5 22.2 - - - +
534A GLY 4.8 0.4 + - - -
535A GLY* 6.0 0.2 - - - -
240D GLY* 3.5 0.4 - - - -
241D HIS* 1.3 76.1 - - - +
243D ASP* 1.3 57.8 + - - +
244D TYR* 3.0 19.6 + - - +
245D SER* 3.0 15.1 + - - +
246D ASN* 2.9 27.2 + - - +
455D ARG* 2.9 33.8 + - - -
456D PRO* 3.5 19.1 - - + +
457D VAL 2.8 20.8 + - - -
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Residues in contact with ASP 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ARG* 2.8 36.9 + - - +
241D HIS 3.5 2.4 + - - +
242D ASP* 1.3 68.7 - - - +
244D TYR* 1.3 66.1 + - - +
246D ASN* 2.9 16.2 + - - +
247D PHE* 3.0 35.4 + - + +
457D VAL* 2.8 21.7 + - + +
458D ASP* 4.5 1.9 - - - +
459D PHE* 3.0 35.5 + - + +
594D PRO* 3.7 16.6 - - + +
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Residues in contact with TYR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477A ASP 4.8 1.6 - - - -
478A GLY* 3.9 14.5 - - - -
242D ASP* 3.0 14.4 + - - +
243D ASP* 1.3 78.7 - - - +
245D SER* 1.3 60.5 + - - +
248D LEU* 3.2 46.5 + - + +
448D LYS* 3.7 4.0 - - - -
449D PRO* 2.6 52.2 + - + +
451D PRO* 4.0 24.6 - - + +
455D ARG* 3.4 51.6 - - + +
457D VAL* 4.2 7.0 - - + +
479D ARG* 5.2 0.3 + - - -
593D PHE* 3.3 21.6 - + - -
594D PRO* 3.8 10.5 - - + +
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ARG* 5.3 0.3 - - - -
242D ASP* 3.0 17.9 + - - +
244D TYR* 1.3 78.4 - - - +
246D ASN* 1.3 66.5 + - - +
248D LEU* 4.5 4.5 - - - -
249D GLN* 3.0 47.9 + - - +
455D ARG* 3.0 25.3 + - - -
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Residues in contact with ASN 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A GLU* 4.9 1.4 - - - +
238D ARG* 3.7 17.1 - - - +
239D GLN* 3.9 11.8 + - + +
240D GLY* 2.9 47.5 + - - +
241D HIS 4.3 0.4 - - - -
242D ASP 2.9 22.5 + - - +
243D ASP* 2.9 29.7 + - - +
245D SER* 1.3 75.1 - - - +
247D PHE* 1.3 65.2 + - + +
249D GLN* 4.1 7.7 + - - +
250D ALA* 3.3 21.5 + - - +
256D PHE* 4.3 9.8 - - + -
3007D GOL 5.5 0.2 - - - -
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Residues in contact with PHE 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLN* 3.6 34.5 - - + +
220D PHE* 3.6 22.0 - + + -
238D ARG* 4.2 7.0 - - - -
243D ASP* 3.0 43.3 + - + +
246D ASN* 1.3 77.1 - - + +
248D LEU* 1.3 66.4 + - - +
250D ALA* 3.3 4.4 + - - +
251D GLY 3.1 27.3 + - - +
252D SER 5.1 1.0 - - - +
256D PHE* 3.5 52.0 - + + -
459D PHE* 3.7 20.4 - + - -
593D PHE* 3.6 19.5 - - + -
594D PRO* 3.9 8.7 - - + -
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D TYR* 3.2 45.7 + - + +
245D SER* 4.0 4.0 - - - +
247D PHE* 1.3 76.7 - - - +
249D GLN* 1.3 62.9 + - + +
251D GLY* 3.4 12.1 + - - -
446D PRO 3.7 12.1 - - - +
447D ALA* 3.4 23.3 - - - +
449D PRO* 4.1 6.1 - - + -
593D PHE* 3.6 5.3 - - + -
598D ARG* 3.6 39.5 + - - +
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Residues in contact with GLN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A GLU* 3.9 20.4 + - - +
583A ARG* 5.0 11.9 + - - +
239D GLN* 4.9 8.5 - - - +
245D SER* 3.0 36.6 + - - +
246D ASN* 4.1 7.4 + - - +
248D LEU* 1.3 77.5 - - + +
250D ALA* 1.3 62.9 + - - +
251D GLY* 3.6 0.5 + - - -
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D ASN 3.3 15.7 + - - +
247D PHE 3.3 5.5 + - - +
249D GLN* 1.3 80.1 - - - +
251D GLY* 1.3 59.3 + - - +
252D SER 4.8 0.2 - - - +
255D ASP* 3.1 24.0 - - - +
256D PHE* 3.9 36.8 - - + -
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Residues in contact with GLY 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D GLN* 5.7 0.2 - - - +
247D PHE* 3.1 14.1 + - - +
248D LEU 3.4 5.3 + - - -
249D GLN 3.3 3.2 - - - -
250D ALA* 1.3 75.6 - - - +
252D SER* 1.3 62.9 + - - -
255D ASP* 3.9 3.8 - - - -
593D PHE* 5.7 1.0 - - - -
598D ARG* 2.9 30.2 + - - -
615D TYR* 4.2 2.7 - - - -
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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