Contacts of the strand formed by residues 844 - 850 (chain B) in PDB entry 3HS0
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 TYR 844 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826B VAL 3.7 0.9 - - - +
827B GLU* 3.2 6.5 - - - -
828B LEU* 3.2 26.1 + - + +
837B ALA* 3.3 34.3 - - + +
838B SER* 3.0 23.1 + - - +
842B GLN* 3.8 1.9 + - - -
843B ARG* 1.3 70.9 - - - +
845B ARG* 1.3 68.0 + - - +
846B GLN* 3.5 20.3 + - + -
860B PHE* 4.3 13.5 - + - -
1366C THR* 3.0 40.7 + - - +
1426C VAL* 5.7 1.8 - - + -
1428C PHE* 3.7 29.8 + - + -
1430C GLN* 2.9 33.0 + - + +
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Residues in contact with ARG 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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825B ARG* 3.2 58.2 - - + +
826B VAL 3.5 2.9 - - - -
827B GLU* 3.0 27.9 + - + +
843B ARG* 3.4 8.2 + - - +
844B TYR* 1.3 85.9 - - - +
846B GLN* 1.3 73.8 + - - +
847B GLN* 3.6 16.3 - - + +
1426C VAL* 4.6 9.5 - - - +
66D LYS* 5.6 6.3 - - - +
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Residues in contact with GLN 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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825B ARG* 3.1 5.0 - - - +
826B VAL* 2.8 39.3 + - + +
844B TYR* 3.5 21.0 + - + +
845B ARG* 1.3 78.7 - - - +
847B GLN* 1.3 66.6 + - - +
848B PHE* 3.7 27.3 - - + -
856B ARG* 4.9 3.3 + - - -
858B VAL* 4.1 21.7 - - - +
859B PRO* 4.2 6.4 + - - +
860B PHE* 4.1 4.9 - - + -
1366C THR* 4.0 18.0 + - + +
1367C GLY 5.4 0.2 + - - -
1424C PHE* 4.2 8.7 - - + -
1426C VAL* 4.9 5.2 - - + -
1430C GLN* 3.5 25.9 - - - +
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Residues in contact with GLN 847 (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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715B ASP* 5.4 0.9 - - - +
717B PHE* 3.1 23.1 - - - -
823B TYR* 3.5 28.4 + - + +
824B VAL 3.1 9.6 - - - +
825B ARG* 3.8 25.3 + - + +
845B ARG* 3.6 25.3 - - + +
846B GLN* 1.3 80.7 - - - +
848B PHE* 1.3 67.1 + - - +
879B GLN* 5.3 0.2 + - - -
1424C PHE* 3.5 23.3 - - - +
1426C VAL* 5.2 1.6 - - - +
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Residues in contact with PHE 848 (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 LEU* 4.1 2.2 - - + -
823B TYR* 3.4 10.5 - - - -
824B VAL* 3.0 41.0 + - + +
826B VAL* 3.7 30.7 - - + -
846B GLN* 3.7 21.8 - - + -
847B GLN* 1.3 79.6 - - - +
849B PRO* 1.3 83.9 - - + +
850B ILE* 3.8 9.9 - - + -
856B ARG* 3.3 43.7 - - + +
858B VAL* 3.9 13.2 - - + -
1423C HIS* 5.2 0.9 - - + -
1424C PHE* 3.8 28.0 - + + -
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Residues in contact with PRO 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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822B ILE 3.4 10.3 - - - +
823B TYR* 4.0 16.2 - - + -
848B PHE* 1.3 98.2 - - + +
850B ILE* 1.3 66.9 + - - +
851B LYS* 4.2 2.7 - - + +
856B ARG* 3.9 8.5 + - - -
1423C HIS* 4.1 25.0 - - + +
1424C PHE* 5.3 3.1 - - + -
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Residues in contact with ILE 850 (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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792B PHE* 4.8 3.1 - - + -
814B LEU* 3.7 39.3 - - + +
816B ASN* 3.5 23.6 + - + +
821B ASP* 4.9 0.9 - - - -
822B ILE* 3.0 36.1 + - + -
824B VAL* 3.8 19.5 - - + -
848B PHE* 3.8 15.0 - - + -
849B PRO* 1.3 80.3 - - - +
851B LYS* 1.3 74.1 + - - +
854B SER* 4.0 13.5 - - - +
855B SER 5.1 1.3 - - - -
856B ARG* 4.2 16.4 - - + +
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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