Contacts of the helix formed by residues 606 - 610 (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 ASN 606 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C THR 2.8 28.1 + - - -
275C ALA* 3.9 11.4 - - - +
548C ARG* 4.7 0.9 - - - +
604C VAL* 3.3 7.4 - - - +
605C PRO* 1.3 84.7 - - + +
607C ILE* 1.3 64.3 + - - +
608C PHE* 3.1 27.2 + - - +
609C PHE* 3.1 41.8 + - + +
610C ALA 3.6 6.2 + - - -
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Residues in contact with ILE 607 (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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252C SER* 4.2 5.7 - - - -
253C ALA 5.0 0.3 + - - -
275C ALA* 5.8 0.6 - - - +
512C ASP* 3.7 22.9 - - - +
546C ARG* 3.8 37.9 - - - +
548C ARG* 3.7 15.9 - - - +
597C ASP* 3.6 21.2 - - - +
598C ARG 3.8 20.0 - - - +
599C ASN* 4.2 6.3 - - - +
600C PRO* 3.8 18.4 - - + -
604C VAL* 3.8 15.4 - - + +
606C ASN* 1.3 70.3 + - - +
608C PHE* 1.3 65.4 + - - +
609C PHE 3.1 0.9 + - - -
610C ALA* 3.3 14.4 + - + +
615C TYR* 4.6 0.8 + - - +
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Residues in contact with PHE 608 (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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210C PHE* 3.7 21.8 - + - -
215C PHE* 3.5 44.2 - + + -
252C SER* 3.1 8.5 + - - -
253C ALA* 4.0 9.6 - - + -
254C GLY* 2.9 29.4 + - - +
268C TRP* 3.6 32.1 - + - -
271C LEU* 3.7 24.5 - - + -
272C THR* 3.8 23.8 - - + -
275C ALA* 4.0 10.8 - - + -
597C ASP* 4.7 4.7 + - - -
606C ASN* 3.1 23.5 + - - +
607C ILE* 1.3 78.2 - - + +
609C PHE* 1.3 64.2 + - + +
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Residues in contact with PHE 609 (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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252C SER* 4.4 1.6 - - - -
254C GLY* 4.4 14.8 - - - -
263C GLU* 4.8 12.8 - - - -
268C TRP* 5.2 3.8 - - - -
272C THR* 3.6 36.6 - - + -
606C ASN* 3.1 40.9 + - + +
608C PHE* 1.3 84.7 - - + +
610C ALA* 1.3 65.7 + - - +
611C LYS* 3.5 9.9 + - - +
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Residues in contact with ALA 610 (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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252C SER* 3.6 16.0 + - - -
255C ASP* 4.3 6.8 - - - +
600C PRO* 4.2 20.2 - - + -
604C VAL* 4.5 4.9 - - + -
606C ASN 3.6 3.4 + - - -
607C ILE* 3.3 19.8 + - - +
608C PHE 3.5 1.0 + - - -
609C PHE* 1.3 79.9 - - - +
611C LYS* 1.3 61.3 + - - +
614C ASP* 3.9 8.7 - - - +
615C TYR* 3.6 27.2 - - + +
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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