Contacts of the helix formed by residues 830 - 836 (chain A) in PDB entry 2MYS
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 PRO 830 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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828A HIS 3.6 8.9 - - - +
829A TRP* 1.3 91.9 - - + -
831A TRP* 1.3 64.2 + - + +
833A MLY 2.9 16.4 + - + +
834A LEU* 2.7 36.3 + - - +
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Residues in contact with TRP 831 (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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829A TRP* 3.0 49.9 + + + -
830A PRO* 1.3 88.4 - - + +
832A MET* 1.3 62.1 + - - +
834A LEU* 3.6 22.9 - - + +
835A PHE* 3.1 22.0 + - - +
67B MET* 3.6 30.8 - - - +
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Residues in contact with MET 832 (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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826A VAL* 3.1 39.7 - - + +
827A MLY 5.6 0.4 - - - -
829A TRP* 2.5 30.3 + - + +
831A TRP* 1.3 73.5 - - - +
833A MLY 1.3 63.1 + - - +
835A PHE* 3.3 33.5 + - + +
836A PHE* 3.0 47.8 + - + -
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Residues in contact with MLY 833 (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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826A VAL 5.5 0.2 + - - -
827A MLY 3.8 16.3 + - - +
828A HIS* 3.7 49.1 - - - -
829A TRP 2.9 13.2 + - - +
830A PRO* 3.5 13.0 - - + +
832A MET* 1.3 74.5 + - - +
834A LEU* 1.3 64.8 + - - +
836A PHE* 3.0 13.4 + - - +
837A MLY 2.9 46.7 + - + +
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Residues in contact with LEU 834 (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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830A PRO 2.7 15.9 + - - +
831A TRP* 3.6 27.1 - - + +
832A MET 3.1 0.2 - - - -
833A MLY 1.3 77.8 + - - +
835A PHE* 1.3 65.8 + - - +
836A PHE 2.9 0.5 + - - -
837A MLY 3.0 9.1 + - - +
838A ILE* 2.8 47.0 + - + +
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Residues in contact with PHE 835 (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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831A TRP 3.1 11.3 + - - +
832A MET* 3.3 41.7 - - + +
834A LEU* 1.3 81.5 - - - +
836A PHE* 1.3 62.6 + + - +
838A ILE* 4.4 11.2 - - + -
839A MLY 2.5 74.8 + - + +
842A LEU* 5.1 13.5 - - + -
27B PHE* 4.5 19.7 - - - -
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Residues in contact with PHE 836 (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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823A PHE* 5.2 12.1 - + - -
826A VAL* 5.4 1.8 - - + -
827A MLY 5.0 15.5 - - + -
832A MET* 3.0 50.8 + - + -
833A MLY 3.0 16.1 + - - +
834A LEU 2.9 1.4 - - - -
835A PHE* 1.3 88.6 - + - +
837A MLY 1.3 65.8 + - + +
838A ILE 3.0 0.9 - - - -
839A MLY 3.3 13.5 + - + +
840A PRO* 3.0 18.9 - - - +
159B HIS* 4.4 9.9 - - - -
160B GLY* 3.7 31.6 - - - -
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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