Contacts of the strand formed by residues 971 - 977 (chain B) in PDB entry 4RIB
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 PHE 971 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827B PHE* 5.0 1.8 - - - -
931B LEU* 5.5 1.6 - - + -
934B CYS* 3.1 40.2 - - + -
935B LEU* 3.6 36.1 - - + -
939B VAL* 4.7 7.4 - - + -
962B VAL* 5.0 6.5 - - + -
963B VAL 3.3 11.0 - - - +
964B TRP* 3.8 11.7 - - + -
969B ARG 4.6 1.3 - - - -
970B HIS* 1.3 76.3 - - - +
972B LYS* 1.3 70.6 + - - +
973B LEU* 4.3 12.1 - - + -
998B GLY 5.0 1.6 - - - -
999B ALA* 3.7 34.1 - - + -
1000B GLU* 3.2 27.6 - - + +
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Residues in contact with LYS 972 (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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822B TYR* 4.1 13.9 - - + -
827B PHE* 3.8 28.1 - - + -
961B LEU 4.0 0.3 - - - +
962B VAL* 3.5 3.6 - - - +
963B VAL* 2.7 51.5 + - + +
971B PHE* 1.3 75.7 - - - +
973B LEU* 1.3 64.2 + - - +
974B VAL* 4.1 2.6 + - + -
1000B GLU* 3.3 38.9 + - + +
1002B GLU* 3.2 40.3 + - + +
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Residues in contact with LEU 973 (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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838B PHE* 3.6 29.2 - - + -
935B LEU* 5.1 4.5 - - + -
939B VAL* 6.2 0.9 - - + -
959B PRO* 4.1 12.1 - - + -
961B LEU 3.4 2.7 - - - +
962B VAL* 3.6 31.4 - - + -
971B PHE* 4.3 21.5 - - + -
972B LYS* 1.3 72.7 - - - +
974B VAL* 1.3 61.9 + - - +
991B LEU* 5.3 1.6 - - - +
994B LEU* 3.7 36.1 - - + -
999B ALA* 4.4 4.3 - - + -
1000B GLU 2.8 12.9 + - - +
1001B VAL* 3.4 15.4 - - + +
1002B GLU* 2.9 27.5 + - - +
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Residues in contact with VAL 974 (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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822B TYR* 3.6 33.7 - - + +
959B PRO* 3.6 4.8 - - - +
960B ASP 3.2 2.3 + - - -
961B LEU* 2.9 50.7 + - + +
963B VAL* 4.5 7.6 - - + -
972B LYS* 4.4 9.9 - - + +
973B LEU* 1.3 80.4 - - - +
975B GLU* 1.3 61.1 + - - +
976B VAL* 3.7 18.5 + - + -
1002B GLU* 3.1 11.2 - - + +
1004B CYS* 3.8 29.2 - - + -
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Residues in contact with GLU 975 (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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958B LEU 3.9 3.6 - - - +
959B PRO* 3.4 16.3 - - + +
960B ASP* 2.1 42.5 + - - +
973B LEU 4.3 0.2 + - - -
974B VAL* 1.3 71.5 - - - +
976B VAL* 1.3 63.7 + - - +
977B LYS* 3.4 23.4 + - + -
983B LEU* 4.1 13.2 - - + -
987B GLN* 3.1 28.5 + - + +
991B LEU* 5.0 9.8 - - + +
1002B GLU 3.0 9.7 + - - +
1003B VAL* 3.5 11.2 - - + +
1004B CYS 2.9 24.1 + - - -
1101B CA 2.3 15.8 - - - -
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Residues in contact with VAL 976 (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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814B VAL* 3.8 42.2 - - + +
815B GLU* 4.3 16.2 - - + +
818B ALA* 3.6 16.8 - - + -
960B ASP* 3.6 8.6 + - + +
961B LEU* 3.5 32.1 - - + -
974B VAL* 3.7 8.9 + - + -
975B GLU* 1.3 75.4 + - - +
977B LYS* 1.3 61.0 + - - +
978B GLY 4.2 0.9 + - - -
1004B CYS 3.4 10.1 - - - +
1006B VAL* 4.9 2.5 - - + -
1101B CA 2.3 32.1 - - - -
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Residues in contact with LYS 977 (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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975B GLU* 3.4 12.1 + - - +
976B VAL* 1.3 83.1 - - - +
978B GLY* 1.3 67.8 + - - +
981B ASP* 3.0 28.2 + - - +
982B ARG 3.0 32.4 + - - +
983B LEU* 3.6 18.8 - - + +
987B GLN* 3.1 25.1 + - - +
1003B VAL* 4.3 18.8 - - + -
1004B CYS 2.9 10.1 + - - +
1005B HIS* 3.3 20.8 - - + +
1006B VAL* 2.9 27.5 + - - +
1101B CA 4.2 2.8 - - - -
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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