Contacts of the strand formed by residues 976 - 986 (chain B) in PDB entry 3KHF
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 976 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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969B VAL 3.9 0.2 - - - +
970B TYR* 3.6 8.1 - - - -
971B MET* 2.9 31.9 + - + +
974B SER* 3.5 30.3 - - - +
975B ASP* 1.3 83.9 - - - +
977B TYR* 1.3 70.0 + - - +
978B THR* 4.7 8.5 - - + -
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Residues in contact with TYR 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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980A HIS* 5.1 0.9 - - - -
1002A LEU* 3.9 22.0 - - + +
1004A THR* 3.6 24.8 - - + +
1012A LEU* 3.8 21.7 - - + +
1035A THR* 5.3 2.0 - - + -
968B ARG* 3.7 39.8 + - + +
969B VAL 3.2 23.6 - - - -
970B TYR* 3.7 23.3 - + + -
976B VAL* 1.3 78.9 - - - +
978B THR* 1.3 59.6 - - - +
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Residues in contact with THR 978 (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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1037A LEU* 5.0 0.2 - - - +
968B ARG* 3.4 11.8 + - - +
969B VAL* 2.8 43.5 + - + -
971B MET* 3.9 17.9 - - + -
976B VAL* 4.7 8.5 - - + +
977B TYR* 1.3 74.7 - - - +
979B VAL* 1.3 68.5 + - - +
1012B LEU* 3.8 19.3 - - + -
1013B GLY* 3.6 17.7 + - - -
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Residues in contact with VAL 979 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1037A LEU* 3.6 26.5 - - + -
966B ALA* 3.8 12.1 - - + -
967B ILE 3.4 3.6 - - - -
969B VAL* 4.1 2.2 - - - -
978B THR* 1.3 84.4 + - - +
980B HIS* 1.3 73.9 + - - +
981B HIS* 4.4 0.4 - - + -
1012B LEU* 3.8 5.0 - - - +
1013B GLY* 2.8 45.9 + - - +
1014B LEU 3.3 29.6 - - - +
1015B VAL* 4.0 12.8 - - + +
1016B HIS 5.2 0.2 - - - +
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Residues in contact with HIS 980 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A VAL* 4.3 10.5 - - + -
970A TYR 4.4 6.5 + - - -
966B ALA* 3.3 5.7 - - - -
967B ILE* 2.9 33.1 + - + -
969B VAL* 3.8 20.4 - - + -
979B VAL* 1.3 75.8 - - - +
981B HIS* 1.3 83.0 + - - +
1002B LEU* 3.7 37.1 - - + +
1003B ILE 3.1 27.0 + - - -
1004B THR* 4.2 7.4 - - - +
1011B VAL* 3.9 4.7 - - + +
1012B LEU* 3.6 42.5 - - + +
1013B GLY 4.9 0.9 - - - +
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Residues in contact with HIS 981 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B LEU* 4.1 10.8 - - + -
965B ARG 3.4 16.6 - - - -
966B ALA* 3.6 17.4 - - + +
979B VAL* 4.4 0.4 - - + -
980B HIS* 1.3 87.6 + - - +
982B VAL* 1.3 64.0 + - - +
1002B LEU* 3.5 8.7 - - - +
1003B ILE* 3.0 37.0 + - + -
1011B VAL* 3.9 14.9 - - + +
1014B LEU 3.5 15.4 + - - -
1016B HIS* 2.9 38.6 + + - -
1019B VAL* 3.4 40.4 - - + +
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Residues in contact with VAL 982 (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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967A ILE* 4.1 24.9 - - + -
984A TRP* 3.8 21.3 - - + -
964B LEU* 3.2 5.2 - - - +
965B ARG* 3.0 36.8 + - + +
967B ILE* 3.9 29.6 - - + +
981B HIS* 1.3 78.5 - - - +
983B VAL* 1.3 66.6 + - - +
984B TRP* 3.9 17.3 - - + -
1000B GLY 4.3 3.8 - - - +
1001B ASP 3.2 11.7 - - - +
1002B LEU* 4.2 4.9 - - + -
1003B ILE* 3.8 5.4 - - - -
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Residues in contact with VAL 983 (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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984A TRP* 3.5 5.0 - - - -
962B PHE* 4.4 12.8 - - + -
963B SER 3.6 7.2 - - - +
982B VAL* 1.3 69.3 - - - +
984B TRP* 1.3 60.8 + - - +
985B SER 3.8 7.4 - - - +
986B VAL* 3.5 27.1 - - + -
997B LEU* 4.5 14.4 - - + -
998B ARG 3.5 22.9 - - - +
1000B GLY* 2.8 28.1 + - - -
1001B ASP* 2.8 26.2 + - + +
1003B ILE* 3.7 24.7 - - + +
1034B THR* 4.6 4.0 - - + -
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Residues in contact with TRP 984 (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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982A VAL* 4.1 6.5 - - + -
983A VAL 3.4 18.8 - - - -
984A TRP* 3.0 95.4 + + - +
999A ALA* 4.0 4.0 - - + +
1000A GLY* 3.5 22.0 - - - -
1041A GLU* 4.0 36.1 + - + -
963B SER* 2.8 25.2 + - - +
965B ARG* 3.5 43.4 - - + +
967B ILE* 4.9 1.3 - - + -
982B VAL* 3.3 8.0 + - + -
983B VAL* 1.3 72.0 - - - +
985B SER* 1.3 63.2 + - - +
999B ALA* 3.5 7.6 - - - +
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Residues in contact with SER 985 (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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1041A GLU* 5.1 2.4 + - - -
962B PHE* 3.3 7.0 - - - +
963B SER* 2.6 49.0 + - - +
983B VAL* 3.6 1.1 - - - +
984B TRP* 1.3 85.7 - - - +
986B VAL* 1.3 66.5 + - - +
987B GLU* 6.0 1.4 - - - +
999B ALA* 4.4 7.9 - - - -
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Residues in contact with VAL 986 (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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961B GLY 3.7 7.0 - - - +
962B PHE* 4.1 2.5 - - + -
983B VAL* 3.5 22.0 - - + -
985B SER* 1.3 82.8 - - - +
987B GLU* 1.3 64.8 + - - +
988B ASP* 3.6 5.4 + - - +
990B SER* 3.9 2.0 - - - +
992B ALA* 4.0 4.3 - - + -
993B GLN* 3.6 43.1 - - + +
997B LEU* 3.5 27.4 - - + +
998B ARG* 3.9 6.3 - - - +
999B ALA* 4.0 4.3 - - - +
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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