Contacts of the strand formed by residues 848 - 856 (chain B) in PDB entry 3HKV
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 ILE 848 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837B PHE* 4.1 9.2 - - + -
838B TYR* 3.7 15.8 + - - -
841B LEU* 4.0 20.0 - - + -
844B ALA* 3.5 29.1 + - + +
845B ARG 3.9 6.1 + - - +
846B SER 3.6 1.9 - - - -
847B SER* 1.3 86.1 - - - +
849B ARG* 1.3 63.4 + - - +
850B VAL 4.9 0.2 - - - +
928B VAL* 4.5 12.1 - - + -
941B LYS* 4.4 15.5 - - + -
1004B CYS* 4.0 24.9 - - + -
1005B GLU 3.4 15.0 - - - +
1006B HIS* 4.1 20.4 - - + +
1007B VAL* 4.4 3.3 - - - +
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Residues in contact with ARG 849 (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 TYR* 3.8 5.8 - - - +
848B ILE* 1.3 75.3 - - - +
850B VAL* 1.3 73.9 + - - +
851B VAL* 3.6 0.8 + - - +
1004B CYS* 3.1 5.4 - - - -
1005B GLU* 2.7 64.8 + - + +
1007B VAL* 3.5 48.2 - - + +
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Residues in contact with VAL 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B GLU* 5.7 1.2 - - - +
830B PHE* 4.5 7.6 - - + -
834B VAL* 4.2 14.6 - - + -
837B PHE* 3.8 27.8 - - + -
838B TYR* 3.2 32.3 + - + +
849B ARG* 1.3 83.6 - - - +
851B VAL* 1.3 63.2 + - - +
852B ARG* 3.9 9.2 - - - +
853B VAL* 3.9 25.4 - - + -
1002B ILE* 4.2 7.6 - - + -
1003B THR 3.7 11.0 - - - +
1004B CYS* 4.0 1.6 - - - +
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Residues in contact with VAL 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B ARG* 4.0 12.7 + - - +
825B GLU* 5.0 7.4 - - - +
830B PHE* 5.9 1.0 - - - -
849B ARG* 5.9 0.4 - - - +
850B VAL* 1.3 74.3 - - - +
852B ARG* 1.3 75.7 + - + +
940B HIS* 3.6 39.7 - - + +
1003B THR* 2.7 18.8 + - + +
1004B CYS 4.0 5.6 - - - -
1005B GLU* 3.8 35.7 - - + +
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Residues in contact with ARG 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B ARG* 3.8 42.7 - - + +
830B PHE* 4.9 5.2 - - - -
850B VAL* 3.7 3.0 - - - +
851B VAL* 1.3 97.4 - - + +
853B VAL* 1.3 66.1 + - - +
854B GLU* 3.3 33.8 + - - +
940B HIS* 4.2 12.7 + - - -
1001B LEU* 3.8 1.4 - - - +
1002B ILE* 3.6 0.2 - - - -
1003B THR* 2.8 57.7 + - - +
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Residues in contact with VAL 853 (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 ARG* 3.8 3.0 - - - +
823B LEU* 3.0 48.2 + - + +
830B PHE* 3.5 32.2 - - + +
833B VAL* 4.1 21.1 - - + -
834B VAL* 3.9 11.7 - - + -
850B VAL* 3.9 13.5 - - + -
852B ARG* 1.3 80.1 - - - +
854B GLU* 1.3 64.3 + - - +
1000B HIS* 4.2 11.7 - - + -
1001B LEU 3.3 7.6 - - - +
1002B ILE* 4.3 12.3 - - + -
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Residues in contact with GLU 854 (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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820B LEU* 3.9 36.2 - - + +
821B GLU 3.3 8.5 - - - +
822B ARG* 3.8 24.4 + - + +
852B ARG* 3.3 36.9 + - - +
853B VAL* 1.3 73.9 - - - +
855B ARG* 1.3 60.4 + - - +
856B VAL* 4.2 0.2 - - - +
1000B HIS* 3.2 7.9 - - - +
1001B LEU* 2.8 58.7 + - + +
1003B THR* 4.1 3.3 + - - -
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Residues in contact with ARG 855 (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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819B ASN 3.6 1.0 - - - +
820B LEU* 3.4 6.4 - - - +
821B GLU* 2.6 74.1 + - + +
823B LEU* 3.2 21.5 - - + +
829B GLU* 2.6 43.0 + - - +
854B GLU* 1.3 71.8 - - - +
856B VAL* 1.3 69.6 + - - +
857B SER* 5.9 3.8 - - - -
999B THR 3.6 10.8 - - - +
1000B HIS* 3.8 4.7 - - + +
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Residues in contact with VAL 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819B ASN 3.5 6.1 - - - +
820B LEU* 3.6 19.1 - - + -
855B ARG* 1.3 82.2 - - - +
857B SER* 1.3 70.0 + - - +
858B HIS* 4.5 3.5 + - + -
862B GLN* 5.7 1.0 - - - +
898B CYS* 4.4 26.5 - - + +
944B PHE* 4.2 14.6 - - + -
998B PRO* 3.8 29.5 - - + +
999B THR* 2.8 19.7 + - - +
1000B HIS* 3.9 25.6 - - - +
1001B LEU 4.0 1.1 - - - +
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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