Contacts of the strand formed by residues 840 - 846 (chain B) in PDB entry 3HW2
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 HIS 840 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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838B ARG 3.6 0.6 + - - -
839B PRO* 1.3 101.1 + - + +
841B ALA* 1.3 57.3 + - - +
842B PHE* 3.8 2.3 - - - -
855B SER* 3.5 7.3 + - - -
856B ALA 3.2 25.4 + - - +
857B GLU 3.2 34.4 + - - -
858B SER* 3.5 11.6 - - - +
859B GLU* 3.1 45.7 + - + +
862B MET* 3.3 28.5 - - + +
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Residues in contact with ALA 841 (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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793B TRP* 4.4 12.3 - - + -
832B ARG* 3.9 1.4 - - - +
833B ALA* 3.0 34.9 + - + +
835B THR* 4.5 9.5 - - + +
836B THR 5.7 0.7 - - - +
838B ARG 3.7 16.4 - - - +
839B PRO 3.6 2.8 + - - -
840B HIS* 1.3 74.4 - - - +
842B PHE* 1.3 65.2 + - - +
853B GLU* 4.7 2.0 - - - +
854B LEU 3.0 11.7 - - - +
855B SER* 4.0 7.6 - - - +
862B MET* 3.4 9.0 - - - +
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Residues in contact with PHE 842 (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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779B LEU* 4.3 14.6 - - + -
831B ARG 3.4 10.1 - - - +
832B ARG* 3.9 1.8 - - - -
833B ALA* 3.4 11.4 - - - +
840B HIS 3.8 4.9 - - - -
841B ALA* 1.3 75.7 - - - +
843B GLN* 1.3 70.5 + - - +
844B VAL* 5.0 0.9 - - + -
853B GLU* 3.9 1.4 - - - +
854B LEU* 2.6 67.1 + - + +
856B ALA* 4.4 3.6 - - + -
862B MET* 3.4 31.0 - - + -
865B TRP* 3.7 27.6 - + + -
866B MET* 3.5 29.2 - - + -
869B LEU* 3.6 26.0 - - + -
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Residues in contact with GLN 843 (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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57A GLU 4.0 9.1 + - - -
58A ARG* 5.4 0.2 - - - +
830B CYS* 3.3 9.4 - - - +
831B ARG* 3.0 76.4 + - + +
833B ALA* 3.2 11.6 - - + +
834B ASN* 3.9 4.3 + - - -
842B PHE* 1.3 77.9 - - - +
844B VAL* 1.3 63.7 + - - +
845B ILE* 3.9 5.5 - - + +
851B CYS* 4.1 22.4 - - + +
852B LEU 3.1 16.4 - - - +
853B GLU* 2.6 33.9 - - + +
854B LEU* 5.3 0.2 - - - -
866B MET* 4.6 0.2 - - - +
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Residues in contact with VAL 844 (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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805B LEU* 4.3 13.5 - - + -
820B VAL* 4.7 0.4 - - + -
822B MET* 3.7 27.6 - - + -
827B CYS* 4.4 1.6 - - - -
829B GLY 3.8 2.9 - - - +
830B CYS* 4.4 5.6 - - - -
842B PHE* 5.0 0.9 - - + -
843B GLN* 1.3 74.4 - - - +
845B ILE* 1.3 63.1 + - - +
846B LEU* 3.4 25.7 + - + +
851B CYS* 3.7 2.7 - - - -
852B LEU* 2.8 53.5 + - + -
854B LEU* 4.1 13.2 - - + -
869B LEU* 4.4 17.3 - - + -
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Residues in contact with ILE 845 (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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131A MET* 4.1 20.4 - - + -
827B CYS* 3.1 11.4 - - - +
828B GLY* 2.6 51.0 + - - +
829B GLY 2.6 35.3 + - - +
830B CYS* 3.8 6.7 - - - -
831B ARG* 3.7 35.0 - - + +
843B GLN* 3.9 6.7 - - + +
844B VAL* 1.3 69.4 - - - +
846B LEU* 1.3 62.2 + - - +
847B SER* 4.9 2.2 - - - +
851B CYS* 4.7 9.6 - - + -
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Residues in contact with LEU 846 (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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818B LEU* 3.9 15.5 - - + -
820B VAL* 3.4 39.7 - - + -
826B GLN 3.5 14.8 - - - +
827B CYS* 3.9 7.6 - - + -
844B VAL* 3.4 21.7 + - + +
845B ILE* 1.3 85.8 - - - +
847B SER* 1.3 56.0 + - - +
848B ASP 3.4 1.8 - - - +
849B ARG* 2.8 17.2 + - - +
850B PRO* 2.8 59.2 + - + +
851B CYS* 4.9 0.2 - - - +
852B LEU* 4.4 7.4 - - + -
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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