Contacts of the strand formed by residues 887 - 890 (chain A) in PDB entry 5AMN
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 LYS 887 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785A PRO 5.6 0.2 - - - +
786A HIS* 5.0 10.3 - - + +
857A GLN* 3.4 12.1 - - - +
881A LEU 3.5 2.3 - - - +
882A VAL* 3.6 0.5 - - - -
883A ALA* 3.0 30.0 + - + -
884A GLU 3.4 18.4 - - - +
885A GLY 3.9 10.8 - - - +
886A ARG* 1.3 79.2 - - - +
888A MET* 1.3 65.8 + - - +
889A LYS* 3.7 18.5 + - - +
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Residues in contact with MET 888 (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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786A HIS* 3.2 24.8 + - + -
812A LEU* 3.9 22.9 - - - -
854A PHE* 3.2 67.8 - - + +
857A GLN* 2.7 27.8 + - + +
858A ILE* 3.8 18.2 - - + +
880A ILE* 4.2 6.3 - - + -
881A LEU 3.5 1.1 - - - -
882A VAL* 3.8 28.0 - - + -
886A ARG 3.7 13.2 - - - +
887A LYS* 1.3 73.3 - - - +
889A LYS* 1.3 69.3 + - - +
890A ILE* 4.2 0.9 - - + -
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Residues in contact with LYS 889 (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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784A HIS 4.9 0.2 + - - -
785A PRO* 2.6 29.5 + - - +
786A HIS* 3.6 4.9 - - - -
787A VAL 4.4 6.1 + - - +
788A ILE* 4.3 14.6 - - + +
805A GLU* 3.5 31.2 + - - +
807A ALA* 5.4 2.2 - - + -
880A ILE* 4.1 3.1 - - - +
881A LEU* 2.8 52.4 + - + +
883A ALA* 4.3 22.2 - - + -
887A LYS* 3.9 17.4 - - - +
888A MET* 1.3 82.6 - - - +
890A ILE* 1.3 65.5 + - - +
891A SER* 3.3 1.9 + - - -
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Residues in contact with ILE 890 (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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786A HIS 2.9 20.6 + - - +
787A VAL* 4.7 2.2 - - + -
788A ILE 3.2 22.0 + - - -
858A ILE* 3.9 18.4 - - + +
861A GLY* 3.9 22.7 - - - +
862A MET* 3.7 31.0 - - + -
865A LEU* 4.4 4.5 - - + -
872A HIS* 3.7 32.8 - - + +
875A LEU* 4.9 2.2 - - + -
880A ILE* 3.8 24.9 - - + -
888A MET 6.0 0.4 - - - -
889A LYS* 1.3 70.5 - - - +
891A SER* 1.3 61.1 + - - +
893A PHE* 3.2 18.7 - - + -
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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