Contacts of the strand formed by residues 899 - 904 (chain E) in PDB entry 6BAA
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 TRP 899 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707E GLN* 3.2 33.2 - - + +
708E LEU 3.1 6.0 + - - +
709E THR* 3.4 5.8 - - + -
710E MET* 2.4 38.1 + - - +
894E LEU 6.1 1.6 - - - -
897E ALA* 3.7 1.6 - - - +
898E ASP* 1.3 98.5 + - + +
900E ILE* 1.3 57.8 + - - +
911E GLU* 6.1 1.1 - - + -
912E GLY* 3.4 27.8 - - - -
913E THR* 3.2 34.3 - - - -
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Residues in contact with ILE 900 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709E THR* 5.6 0.4 - - - -
710E MET* 3.4 15.5 - - + -
712E VAL* 5.4 7.4 - - + -
894E LEU* 5.4 12.6 - - + +
899E TRP* 1.3 77.1 - - - +
901E ILE* 1.3 61.9 + - - +
902E ALA* 4.1 2.0 + - + +
910E ARG 4.2 0.2 - - - +
911E GLU* 3.5 22.9 - - - +
912E GLY 3.6 17.0 + - - +
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Residues in contact with ILE 901 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709E THR* 5.3 5.8 - - + -
710E MET 2.7 17.7 + - - +
711E ILE* 4.1 8.6 - - + +
712E VAL* 2.4 37.7 + - - +
900E ILE* 1.3 73.2 - - - +
902E ALA* 1.3 56.7 + - - +
903E MET* 3.9 0.9 + - - +
908E ILE* 6.0 5.6 - - + -
910E ARG 4.0 4.3 - - - -
911E GLU* 4.6 8.7 - - + -
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Residues in contact with ALA 902 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712E VAL* 3.3 9.2 - - + +
713E GLY* 5.8 1.1 - - - -
900E ILE* 4.1 2.6 - - + -
901E ILE* 1.3 71.9 - - - +
903E MET* 1.3 61.4 + - - +
908E ILE* 3.6 5.2 - - - +
909E GLN* 2.8 30.8 + - + -
910E ARG* 3.0 24.4 + - + +
922E CYS* 6.5 1.1 - - + -
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Residues in contact with MET 903 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712E VAL 2.6 17.7 + - - +
713E GLY* 3.3 19.3 - - - -
714E GLN* 4.1 1.7 + - - +
717E CYS* 3.7 21.6 - - + +
718E GLY 5.5 1.1 - - - -
719E LYS* 5.2 10.8 - - + +
722E LEU* 6.4 1.6 - - + -
901E ILE 5.2 0.9 - - - +
902E ALA* 1.3 75.1 - - - +
904E LYS* 1.3 63.1 + - - +
906E GLY 5.9 0.2 - - - -
907E THR 3.3 12.3 - - - +
908E ILE* 4.4 1.6 - - + +
909E GLN* 4.9 1.3 - - - -
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Residues in contact with LYS 904 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E GLN* 6.3 1.6 - - + -
717E CYS* 3.8 6.3 - - - -
903E MET* 1.3 76.8 - - - +
905E ASP* 1.3 66.0 + - + +
906E GLY 3.2 2.5 - - - -
907E THR* 2.9 28.8 + - - +
909E GLN* 4.7 13.1 - - + +
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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