Contacts of the strand formed by residues 784 - 787 (chain A) in PDB entry 1MUK
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 LEU 784 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563A VAL* 4.2 26.5 - - + -
566A LYS* 3.7 43.1 - - + +
568A ILE* 3.9 23.1 - - + -
779A ALA 3.9 0.5 - - - +
780A GLU* 3.4 7.8 - - - +
781A TYR 3.2 25.0 + - - +
782A LEU 4.0 7.4 - - - +
783A LYS* 1.3 85.9 - - - +
785A TYR* 1.3 62.4 + - - +
786A PHE* 3.5 25.4 - - + -
791A ARG* 4.3 10.3 - - - +
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Residues in contact with TYR 785 (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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278A PRO* 5.9 3.4 - - + -
282A LEU* 3.8 24.0 - - + -
283A HIS* 5.5 2.9 - + - -
369A MET* 3.7 17.7 - - + -
778A THR* 5.6 0.4 - - + -
779A ALA 3.7 4.3 - - - +
780A GLU* 3.5 36.9 + - + -
783A LYS* 3.4 20.8 - - - +
784A LEU* 1.3 74.3 - - - +
786A PHE* 1.3 67.7 + - - +
791A ARG* 3.4 5.1 - - - +
792A ILE* 2.8 43.2 + - + +
794A ASN* 3.4 37.9 + - + -
797A ARG* 2.8 34.5 + - - -
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Residues in contact with PHE 786 (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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282A LEU* 4.9 1.3 - - - -
566A LYS 5.7 0.9 - - - -
567A VAL 5.2 0.7 - - - -
568A ILE* 3.6 32.3 - - + -
571A GLY* 3.6 26.2 - - - +
572A VAL* 3.9 6.5 - - + -
575A SER* 3.5 20.9 - - - +
778A THR* 3.5 7.4 - - - +
779A ALA* 2.9 43.5 + - + +
781A TYR* 4.9 8.5 - - + -
784A LEU* 3.5 46.7 - - + -
785A TYR* 1.3 77.1 - - - +
787A ILE* 1.3 61.1 + - - +
790A CYS 3.3 6.1 - - - +
791A ARG* 3.6 34.5 - - + -
792A ILE 4.7 0.2 - - - +
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Residues in contact with ILE 787 (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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282A LEU* 3.7 23.8 - - + +
285A MET* 3.6 35.0 - - + +
286A TYR* 3.8 13.2 - - + -
357A HIS* 3.7 2.3 - - + +
362A VAL* 4.2 8.7 - - + -
365A ILE* 4.0 12.6 - - + -
575A SER* 4.3 1.1 - - - -
777A GLY 4.4 8.1 - - - +
778A THR* 4.2 6.7 - - - +
786A PHE* 1.3 74.6 - - - +
788A PHE* 1.3 85.4 + - + +
789A GLY 3.1 1.8 - - - -
790A CYS* 2.8 25.0 + - - +
792A ILE* 3.9 26.9 - - + -
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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