Contacts of the strand formed by residues 889 - 895 (chain B) in PDB entry 4BQ7
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 VAL 889 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887B PRO 3.8 6.3 + - - +
888B PRO* 1.3 78.7 - - - +
890B GLY* 1.3 62.5 + - - +
891B VAL* 3.3 5.2 + - - -
905B TRP* 3.4 4.0 - - - +
906B ALA* 2.6 58.6 + - + +
908B ASN* 3.3 41.7 - - - +
973B SER* 5.3 0.2 - - - -
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Residues in contact with GLY 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889B VAL* 1.3 78.4 - - - +
891B VAL* 1.3 64.9 + - - +
892B GLN* 3.4 16.3 + - - +
904B THR* 3.3 10.2 + - - +
905B TRP* 3.5 5.5 - - - -
906B ALA* 4.2 5.4 + - - +
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Residues in contact with VAL 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888B PRO 4.8 0.4 - - - +
889B VAL* 4.3 5.6 - - - +
890B GLY* 1.3 73.6 - - - +
892B GLN* 1.3 66.1 + - - +
903B ILE* 3.9 25.1 - - + -
904B THR 3.2 4.9 - - - +
905B TRP* 4.0 9.0 - - + -
959B PHE* 4.0 12.6 - - + +
961B VAL* 3.8 20.2 - - + -
973B SER* 3.4 31.9 - - - +
974B MET 4.1 7.4 - - - +
976B ALA* 3.4 31.9 - - + +
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Residues in contact with GLN 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B GLY* 4.0 12.5 + - - +
891B VAL* 1.3 81.1 - - - +
893B ALA* 1.3 61.4 + - - +
894B SER* 4.0 0.8 + - - -
902B ARG 3.5 2.3 - - - +
903B ILE* 3.4 8.3 - - - -
904B THR* 2.8 47.9 + - - +
976B ALA* 4.7 0.9 - - - -
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Residues in contact with ALA 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892B GLN* 1.3 71.9 - - - +
894B SER* 1.3 60.3 + - - +
895B ILE* 3.8 7.9 + - + +
901B ILE* 3.8 16.8 - - + -
902B ARG 3.7 4.5 - - - -
903B ILE* 3.8 10.8 - - + -
959B PHE* 4.1 6.7 - - + -
976B ALA* 4.9 4.4 - - + +
977B HIS 3.6 24.8 + - - +
978B GLY* 4.1 9.4 - - - -
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Residues in contact with SER 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892B GLN 4.0 1.7 + - - -
893B ALA* 1.3 71.0 - - - +
895B ILE* 1.3 64.0 + - - +
896B LEU* 3.5 15.4 + - - +
901B ILE* 3.3 2.7 - - - +
902B ARG* 2.8 53.8 + - - -
904B THR* 6.2 0.9 - - - -
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Residues in contact with ILE 895 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893B ALA 3.8 9.4 + - - +
894B SER* 1.3 73.0 + - - +
896B LEU* 1.3 68.0 + - - +
897B SER 3.6 19.3 - - - +
900B THR 4.2 4.3 - - - +
901B ILE* 3.6 23.8 - - + -
978B GLY* 3.8 18.8 - - - -
979B ALA 3.4 28.7 - - - +
980B THR* 3.9 4.7 - - - -
981B PHE* 3.6 37.4 - - + -
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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