Contacts of the strand formed by residues 885 - 891 (chain B) in PDB entry 1CJT
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 885 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B TYR* 3.5 33.9 - - + -
884B CYS* 1.3 74.4 - - - +
886B CYS* 1.3 64.6 + - - +
887B VAL* 3.9 8.0 + - + +
947B ALA* 4.0 21.3 - - + -
948B THR 3.5 11.4 - - - +
949B GLY 3.7 18.6 - - - +
950B LEU* 3.9 12.8 - - + -
968B HIS* 4.9 0.2 - - - -
1002B HIS* 3.3 4.3 - - - -
1003B GLY 3.0 29.4 + - - +
1005B VAL* 3.6 23.1 - - + -
1019B ILE* 5.0 1.3 - - + -
1023B THR* 4.3 3.6 - - - +
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Residues in contact with CYS 886 (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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884B CYS 4.2 1.0 + - - -
885B VAL* 1.3 71.9 - - - +
887B VAL* 1.3 59.7 + - - +
947B ALA* 3.1 6.4 - - - +
948B THR* 2.9 49.3 + - - +
968B HIS* 4.2 1.1 - - + -
969B ILE* 4.0 34.3 - - + -
972B MET* 3.6 22.0 - - - +
1000B ILE* 3.4 31.9 - - - -
1001B ASN 3.5 7.2 - - - -
1002B HIS* 4.0 3.1 - - + -
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Residues in contact with VAL 887 (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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885B VAL* 4.4 12.3 - - + +
886B CYS* 1.3 76.2 - - - +
888B MET* 1.3 64.7 + - - +
889B PHE* 3.8 27.6 - - + -
945B MET* 4.5 4.3 - - + -
946B ALA 3.7 7.9 - - - +
947B ALA* 4.4 0.2 - - + -
1000B ILE* 3.4 8.8 - - - +
1001B ASN 2.9 31.5 + - - +
1005B VAL* 4.4 6.1 - - + -
1019B ILE* 3.7 28.7 - - + -
1023B THR* 4.7 5.8 - - + +
1024B VAL* 4.0 20.2 - - + -
1027B ALA* 3.9 13.8 - - + +
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Residues in contact with MET 888 (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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887B VAL* 1.3 76.3 - - - +
889B PHE* 1.3 67.3 + - - +
890B ALA* 3.7 24.7 - - + -
944B TYR* 3.5 22.7 - - + +
945B MET* 3.4 6.4 - - - +
946B ALA* 2.8 37.0 + - + +
972B MET* 3.3 42.6 - - + +
975B PHE* 4.4 3.6 - - + -
976B ALA* 4.0 25.1 - - - -
979B LEU* 3.9 13.2 - - + -
998B VAL* 3.6 20.9 - - + -
999B GLY 3.5 6.1 - - - +
1000B ILE* 3.9 4.5 - - + -
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Residues in contact with PHE 889 (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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102A DAD 4.4 12.8 - + - -
887B VAL* 3.8 16.6 - - + -
888B MET* 1.3 77.7 - - - +
890B ALA* 1.3 60.8 + - - +
940B ILE* 3.8 23.8 - - + -
943B THR* 4.2 15.7 - - + -
944B TYR 3.5 2.5 - - - -
945B MET* 3.7 27.4 - - + -
998B VAL* 3.5 2.9 - - - +
999B GLY 3.0 29.9 + - - +
1024B VAL* 3.5 27.1 - - + -
1027B ALA* 3.9 5.2 - - + -
1028B SER* 3.5 34.5 - - - -
1031B ASP* 3.4 28.1 - - + +
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Residues in contact with ALA 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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888B MET* 3.7 21.5 - - + +
889B PHE* 1.3 71.3 - - - +
891B SER* 1.3 61.1 + - - +
892B ILE* 5.1 0.2 - - - +
922B PHE* 5.8 0.2 - - - -
942B SER 4.1 1.7 - - - +
943B THR* 3.3 4.4 - - - +
944B TYR* 2.7 40.6 + - + +
979B LEU* 3.8 8.5 - - + -
996B LEU* 3.8 32.0 - - + +
997B ARG 3.8 4.5 - - - -
998B VAL* 4.3 5.6 - - + +
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Residues in contact with SER 891 (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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890B ALA* 1.3 73.9 - - - +
892B ILE* 1.3 64.1 + - - +
893B PRO* 3.5 7.3 - - - +
943B THR* 2.7 25.0 + - - +
996B LEU* 3.3 11.3 - - - +
997B ARG* 3.0 46.6 + - - -
1031B ASP* 2.8 32.1 + - - -
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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