Contacts of the helix formed by residues 606 - 610 (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 ASN 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A THR 2.8 27.7 + - - -
275A ALA* 3.9 13.2 - - - +
548A ARG* 4.7 0.9 - - - +
604A VAL* 3.3 6.7 - - - +
605A PRO* 1.3 84.2 - - + +
607A ILE* 1.3 64.1 + - - +
608A PHE* 3.2 26.3 + - - -
609A PHE* 3.0 42.2 + - + +
610A ALA 3.5 6.9 + - - -
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Residues in contact with ILE 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 4.2 5.5 - - - -
253A ALA 5.0 0.2 + - - -
275A ALA* 5.8 1.0 - - - +
512A ASP* 3.7 11.0 - - - +
546A ARG* 3.7 37.2 - - - +
548A ARG* 3.7 27.9 - - - +
597A ASP* 3.6 20.7 - - - +
598A ARG 3.7 20.2 - - - +
599A ASN* 4.1 4.3 - - - +
600A PRO* 3.8 21.3 - - + -
604A VAL* 3.8 15.7 + - + -
606A ASN* 1.3 71.2 + - - +
608A PHE* 1.3 65.3 + - - +
609A PHE 3.1 1.0 + - - -
610A ALA* 3.3 15.6 + - + +
615A TYR* 4.5 1.0 + - - +
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Residues in contact with PHE 608 (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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210A PHE* 3.7 21.3 - + - -
215A PHE* 3.4 44.0 - + + -
252A SER* 2.9 9.5 + - - -
253A ALA* 4.1 10.5 - - + -
254A GLY* 2.9 28.8 + - - +
268A TRP* 3.6 30.7 - + - -
271A LEU* 3.5 24.9 - - + -
272A THR* 3.7 24.9 - - + -
275A ALA* 4.0 9.6 - - + -
597A ASP* 4.7 5.3 + - - -
606A ASN* 3.1 23.5 + - - +
607A ILE* 1.3 76.9 - - - +
609A PHE* 1.3 64.7 + - + +
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Residues in contact with PHE 609 (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* 4.3 1.8 - - - -
254A GLY* 4.4 14.4 - - - -
255A ASP* 6.0 0.7 - - - -
263A GLU* 5.3 9.2 - - - -
268A TRP* 5.3 4.3 - - - -
272A THR* 3.5 37.7 - - + -
606A ASN* 3.0 42.8 + - + +
608A PHE* 1.3 83.3 - - + +
610A ALA* 1.3 63.9 + - - +
611A LYS* 3.0 29.1 + - - +
614A ASP* 4.8 0.3 - - - +
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Residues in contact with ALA 610 (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* 3.5 16.7 + - - -
255A ASP* 4.3 7.6 - - - +
600A PRO* 4.2 19.3 - - + -
604A VAL* 4.5 4.0 - - + -
606A ASN 3.5 3.7 + - - -
607A ILE* 3.3 15.8 + - - +
608A PHE 3.5 1.2 + - - -
609A PHE* 1.3 78.7 - - - +
611A LYS* 1.3 63.7 + - - +
614A ASP* 3.7 10.8 - - + +
615A TYR* 3.5 30.7 - - + +
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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