Contacts of the strand formed by residues 808 - 816 (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 VAL 808 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802B VAL* 4.4 32.3 - - + -
803B VAL 5.3 2.0 - - - +
806B GLU* 3.5 18.2 - - + +
807B GLN* 1.3 80.6 - - - +
809B GLU* 1.3 66.7 + - - +
810B ILE* 4.9 5.8 - - + -
860B PHE 3.9 0.2 - - - +
861B VAL* 3.6 5.4 - - - +
862B ILE* 3.1 56.1 + - + +
864B PRO* 4.9 3.8 - - + -
891B LEU* 5.3 0.2 - - + -
1449C PHE* 4.1 8.3 - - - -
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Residues in contact with GLU 809 (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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808B VAL* 1.3 77.9 - - - +
810B ILE* 1.3 67.1 + - - +
811B ARG* 3.0 37.3 + - - +
859B PRO* 3.2 25.4 - - + +
860B PHE 3.4 11.2 - - - +
861B VAL* 4.6 7.0 - - + +
1363C SER* 2.9 29.9 + - - -
1433C SER* 3.5 17.6 + - - +
1435C LYS* 3.6 20.8 + - - +
1447C THR* 6.2 0.9 - - + +
1449C PHE* 4.2 11.6 - - + -
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Residues in contact with ILE 810 (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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796B LEU* 3.6 25.1 - - + -
797B GLN 5.3 2.9 - - - +
798B MET* 3.5 38.1 - - + -
799B PRO* 5.3 5.2 - - + -
808B VAL* 4.1 6.2 + - + -
809B GLU* 1.3 76.3 - - - +
811B ARG* 1.3 59.9 + - - +
812B ALA 3.7 2.4 + - - +
859B PRO* 3.5 1.0 - - - +
860B PHE* 2.7 57.2 + - + +
862B ILE* 3.5 30.5 - - + -
872B VAL* 4.3 8.1 - - + -
874B ILE* 5.2 0.4 - - + -
891B LEU* 4.2 12.8 - - + -
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Residues in contact with ARG 811 (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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302A SER 2.8 29.3 + - - -
303A GLY 4.9 2.9 + - - -
304A SER* 4.4 19.4 - - - +
795B ASP 4.3 2.1 - - - +
796B LEU* 4.3 7.5 - - - +
797B GLN* 4.5 14.1 + - - +
809B GLU* 3.0 36.1 + - - +
810B ILE* 1.3 71.9 - - - +
812B ALA* 1.3 64.8 + - - +
813B ILE* 4.2 8.9 - - + +
857B ALA* 4.2 25.1 - - + -
858B VAL 4.2 0.7 - - - -
859B PRO* 4.5 13.2 - - + -
1361C ASP* 2.8 43.1 + - - -
1363C SER* 4.1 9.8 - - - -
1400C ALA* 3.3 16.5 - - - +
1433C SER* 4.7 2.0 + - - -
1435C LYS* 3.6 11.4 - - - +
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Residues in contact with ALA 812 (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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794B ILE* 4.0 11.2 - - + -
795B ASP 3.4 9.6 - - - +
796B LEU* 4.1 7.7 - - + +
810B ILE 3.7 2.0 + - - -
811B ARG* 1.3 75.0 - - - +
813B ILE* 1.3 66.4 + - - +
814B LEU* 4.2 1.6 - - + -
857B ALA* 3.5 0.5 - - - +
858B VAL* 2.8 44.2 + - + +
860B PHE* 4.2 3.8 - - + -
874B ILE* 3.8 30.1 - - + -
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Residues in contact with ILE 813 (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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229A TYR* 6.0 0.2 - - - +
302A SER* 3.6 24.2 - - - +
304A SER* 3.9 23.1 - - - +
793B PHE 3.6 0.2 - - - +
794B ILE* 3.5 3.7 - - - -
795B ASP* 2.7 59.0 + - + +
811B ARG* 4.2 4.0 - - + +
812B ALA* 1.3 85.2 - - - +
814B LEU* 1.3 65.3 + - - +
815B HIS* 3.6 26.4 + - + +
855B SER* 4.0 18.2 - - - -
856B ARG 3.7 4.7 - - - +
857B ALA* 4.0 17.9 - - + -
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Residues in contact with LEU 814 (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* 4.3 19.7 - - + -
793B PHE 3.7 3.4 - - - +
794B ILE* 3.8 30.3 - - + -
812B ALA* 4.2 1.5 - - + -
813B ILE* 1.3 73.2 - - - +
815B HIS* 1.3 62.0 + - - +
816B ASN 3.9 0.9 + - - -
824B VAL* 3.7 29.6 - - + -
826B VAL* 3.8 27.1 - - + -
848B PHE* 4.1 7.2 - - + -
850B ILE* 3.7 20.7 - - + +
854B SER 4.0 0.3 - - - +
855B SER* 3.3 6.1 - - - -
856B ARG* 3.0 35.3 + - + +
858B VAL* 4.2 12.8 - - + -
876B ALA* 4.5 1.8 - - + -
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Residues in contact with HIS 815 (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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229A TYR* 4.2 20.0 - + - -
231A TYR* 3.4 20.4 + - - -
791B VAL 4.5 0.2 - - - -
792B PHE* 3.3 11.4 - - - -
793B PHE* 3.0 60.0 + + + +
795B ASP* 3.3 34.4 + - + +
813B ILE* 3.6 22.2 - - + +
814B LEU* 1.3 72.5 - - - +
816B ASN* 1.3 59.8 + - - +
817B TYR* 3.7 25.0 + - + -
854B SER 4.1 2.9 + - - +
855B SER* 3.6 16.5 + - - -
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Residues in contact with ASN 816 (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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791B VAL 4.1 1.7 - - - +
792B PHE* 4.5 3.5 - - + -
814B LEU 3.9 0.8 + - - -
815B HIS* 1.3 71.2 - - - +
817B TYR* 1.3 61.4 + - - +
818B VAL* 3.0 29.5 + - - +
820B GLU 3.6 7.1 + - - -
822B ILE* 3.4 27.1 - - + +
850B ILE* 3.5 25.0 + - + -
851B LYS 3.2 23.8 + - - -
852B ALA* 3.5 14.3 - - - +
853B LEU* 3.2 4.9 - - - +
854B SER 3.1 29.6 + - - +
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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