Contacts of the helix formed by residues 242 - 251 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A GLY 3.6 0.4 - - - -
241A HIS* 1.3 77.3 - - - +
243A ASP* 1.3 59.1 + - - +
244A TYR* 3.0 20.2 + - - +
245A SER* 3.0 14.1 + - - +
246A ASN* 2.9 27.6 + - - +
455A ARG* 2.9 33.1 + - - -
456A PRO* 3.5 18.8 - - + +
457A VAL 2.9 19.9 + - - -
474D ARG* 3.6 23.0 - - - +
525D GLU 4.9 0.2 + - - -
534D GLY 4.8 0.2 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ARG* 2.8 28.7 + - - +
241A HIS 3.5 2.4 + - - +
242A ASP* 1.3 69.0 - - - +
244A TYR* 1.3 67.4 + - - +
246A ASN* 2.8 23.3 + - - +
247A PHE* 3.0 34.0 + - + +
457A VAL* 2.8 22.4 + - + +
458A ASP* 5.2 0.2 - - - -
459A PHE* 3.0 38.1 + - + +
594A PRO* 3.8 17.5 - - + +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASP* 3.0 14.4 + - - +
243A ASP* 1.3 80.3 - - - +
245A SER* 1.3 58.0 + - - +
248A LEU* 3.1 45.5 + - + +
448A LYS* 3.8 3.3 - - - -
449A PRO* 2.6 51.4 + - + +
451A PRO* 4.0 23.9 - - + +
455A ARG* 3.3 54.7 - - + +
457A VAL* 4.1 6.8 - - + +
479A ARG* 5.1 0.3 + - - -
593A PHE* 3.3 22.6 - + - -
594A PRO* 3.8 11.2 - - + +
477D ASP 4.5 1.7 + - - -
478D GLY* 3.9 14.5 - - - -
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASP* 3.0 17.8 + - - +
244A TYR* 1.3 79.4 - - - +
246A ASN* 1.3 60.1 + - - +
248A LEU* 4.4 4.3 - - - -
249A GLN* 2.9 55.7 + - - +
455A ARG* 3.0 25.1 + - - -
474D ARG* 5.3 1.0 + - - -
525D GLU* 6.5 0.4 - - - -
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Residues in contact with ASN 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ARG* 3.7 18.1 - - - +
239A GLN* 3.9 11.4 + - + +
240A GLY* 3.0 46.2 + - - +
241A HIS 4.3 0.2 - - - -
242A ASP 2.9 19.7 + - - +
243A ASP* 2.8 29.4 + - - +
245A SER* 1.3 76.7 - - - +
247A PHE* 1.3 64.2 + - + +
249A GLN* 4.1 6.5 + - - +
250A ALA* 3.3 23.6 + - - +
256A PHE* 4.3 8.5 - - + -
525D GLU* 4.9 2.3 - - - +
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 3.6 35.2 - - + +
220A PHE* 3.6 21.3 - + + -
238A ARG* 4.2 8.5 - - - -
243A ASP* 3.0 40.0 + - + +
246A ASN* 1.3 76.4 - - - +
248A LEU* 1.3 66.0 + - - +
250A ALA* 3.3 4.7 + - - +
251A GLY 3.1 26.7 + - - +
252A SER 5.1 1.0 - - - +
253A ALA* 5.7 0.2 - - - -
256A PHE* 3.5 52.3 - + + -
459A PHE* 3.9 19.7 - + - -
593A PHE* 3.6 18.6 - - + -
594A PRO* 3.8 10.3 - - + -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 3.1 45.0 + - + +
245A SER* 4.0 4.3 - - - +
247A PHE* 1.3 77.6 - - - +
249A GLN* 1.3 63.2 + - + +
251A GLY* 3.4 12.3 + - - -
446A PRO 3.8 11.4 - - - +
447A ALA* 3.5 23.3 - - - +
448A LYS* 5.3 0.2 - - - -
449A PRO* 4.1 6.5 - - + -
593A PHE* 3.6 6.1 - - + -
598A ARG* 3.7 38.1 + - - +
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Residues in contact with GLN 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLN* 5.0 6.3 - - - +
245A SER* 2.9 38.5 + - - +
246A ASN* 4.1 8.4 + - - +
248A LEU* 1.3 79.1 - - + +
250A ALA* 1.3 61.8 + - - +
251A GLY* 3.5 0.5 + - - -
525D GLU* 3.6 22.8 + - - +
583D ARG* 5.2 9.9 + - - -
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ASN 3.3 16.9 + - - +
247A PHE 3.8 4.5 - - - +
248A LEU 3.3 0.2 - - - -
249A GLN* 1.3 79.9 - - - +
251A GLY* 1.3 58.2 + - - +
252A SER 4.8 0.4 - - - +
255A ASP* 3.1 24.1 - - - +
256A PHE* 3.9 36.1 - - + +
259A ALA* 6.0 2.5 - - + -
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Residues in contact with GLY 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLN* 5.7 0.2 - - - +
247A PHE* 3.1 14.1 + - - +
248A LEU 3.4 4.7 + - - -
249A GLN 3.3 3.8 - - - -
250A ALA* 1.3 76.1 - - - +
252A SER* 1.3 65.7 + - - -
255A ASP* 3.9 3.8 - - - -
593A PHE* 5.7 1.0 - - - -
598A ARG* 2.9 30.5 + - - -
615A TYR* 4.2 3.1 - - - -
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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