Contacts of the helix formed by residues 252 - 260 (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 SER 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLN* 4.7 1.8 - - - -
247A PHE* 5.1 0.9 - - - +
251A GLY* 1.3 75.8 + - - +
253A ALA* 1.3 63.8 + - - +
255A ASP* 3.1 28.2 + - - -
256A PHE* 3.2 22.0 + - - +
597A ASP* 6.0 0.7 - - - -
607A ILE 4.2 3.1 - - - -
608A PHE 2.9 21.5 + - - -
609A PHE* 4.3 1.6 - - - -
610A ALA 3.5 19.8 + - - -
615A TYR* 3.2 23.5 + - - -
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Residues in contact with ALA 253 (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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215A PHE* 4.1 9.4 - - + -
217A GLN* 3.4 25.6 + - - +
220A PHE* 3.6 12.7 - - + -
252A SER* 1.3 74.2 - - - +
254A GLY* 1.3 56.9 + - - +
256A PHE* 3.5 2.8 + - - +
257A ALA* 3.0 29.1 + - - +
268A TRP* 4.4 1.3 - - - -
597A ASP* 3.9 25.6 + - + +
607A ILE 5.0 0.4 + - - -
608A PHE* 4.0 18.3 + - + +
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Residues in contact with GLY 254 (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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252A SER* 3.7 0.4 - - - -
253A ALA* 1.3 77.0 - - - +
255A ASP* 1.3 60.0 + - - +
257A ALA* 3.9 0.5 - - - +
258A LYS* 2.9 32.6 + - - +
268A TRP* 4.1 16.3 + - - -
608A PHE* 2.9 24.0 + - - +
609A PHE* 4.4 14.8 - - - -
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Residues in contact with ASP 255 (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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250A ALA* 3.1 25.8 - - - +
251A GLY* 3.9 2.4 - - - -
252A SER* 3.1 35.6 + - - +
254A GLY* 1.3 74.5 - - - +
256A PHE* 1.3 65.1 + - - +
258A LYS* 3.4 24.6 + - - +
259A ALA* 3.0 25.5 + - - +
609A PHE* 6.0 0.7 - - - -
610A ALA 4.3 7.7 - - - +
611A LYS* 5.8 3.8 - - - -
612A PRO* 5.4 6.9 - - - +
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Residues in contact with PHE 256 (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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220A PHE* 3.8 25.6 - + + -
236A ILE* 4.2 23.1 - - + -
237A ALA 5.7 0.9 - - - -
238A ARG* 4.1 28.5 - - - -
246A ASN* 4.3 9.9 - - + -
247A PHE* 3.5 54.3 - + + +
250A ALA* 3.9 24.3 - - + +
252A SER 3.2 9.5 + - - +
253A ALA* 3.7 7.2 - - - +
255A ASP* 1.3 78.8 - - - +
257A ALA* 1.3 62.1 + - - +
259A ALA* 3.3 5.5 + - + +
260A ALA* 3.0 26.6 + - + +
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Residues in contact with ALA 257 (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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220A PHE* 3.7 11.7 - - + -
253A ALA 3.0 17.8 + - - +
254A GLY 3.9 1.3 - - - +
256A PHE* 1.3 75.9 - - - +
258A LYS* 1.3 65.9 + - - +
260A ALA* 3.2 5.8 + - - -
262A LEU* 3.0 41.4 + - + +
263A GLU 5.2 0.2 - - - -
268A TRP* 3.4 37.5 - - + +
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A GLY 2.9 21.0 + - - +
255A ASP* 3.4 30.6 + - - +
257A ALA* 1.3 75.5 - - - +
259A ALA* 1.3 63.6 + - - +
261A GLY* 3.2 13.3 + - - -
262A LEU 4.9 0.2 - - - +
263A GLU* 4.1 39.6 - - - +
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Residues in contact with ALA 259 (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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250A ALA* 6.0 2.0 - - + -
255A ASP 3.0 17.8 + - - +
256A PHE* 3.7 6.7 - - + +
258A LYS* 1.3 79.0 - - - +
260A ALA* 1.3 57.0 + - - +
261A GLY 3.2 1.1 + - - -
39C ALA* 2.9 24.4 - - - +
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Residues in contact with ALA 260 (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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236A ILE* 3.6 36.0 - - + +
256A PHE* 3.0 20.0 + - + +
257A ALA* 3.2 6.4 + - - +
259A ALA* 1.3 75.0 - - - +
261A GLY* 1.3 60.2 + - - +
262A LEU* 3.4 13.7 + - + +
36C PHE* 3.8 14.9 - - - -
39C ALA* 4.0 16.9 + - - +
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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