Contacts of the strand formed by residues 868 - 878 (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 GLY 868 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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867B GLN* 1.3 75.5 - - - +
869B LEU* 1.3 68.7 + - - -
870B HIS* 3.4 8.1 - - - -
891B LEU 3.4 3.3 - - - +
892B LYS* 5.2 1.3 - - - -
893B VAL 2.7 37.0 + - - -
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Residues in contact with LEU 869 (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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868B GLY* 1.3 69.4 - - - -
870B HIS* 1.3 76.2 + - - +
890B LYS* 4.1 37.7 - - + +
891B LEU 3.7 1.8 - - - -
892B LYS* 3.7 43.1 - - + +
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Residues in contact with HIS 870 (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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831B ASN* 4.4 3.2 + - - +
833B ALA* 3.4 20.6 - - + +
834B PHE* 3.8 21.1 - + + -
866B GLU* 3.5 42.6 + - - +
867B GLN 3.4 19.4 + - - -
868B GLY 3.4 23.5 - - - -
869B LEU* 1.3 82.0 + - - +
871B ASP* 1.3 67.7 + - - +
872B VAL 3.5 0.5 + - - -
890B LYS* 4.2 2.0 - - - +
891B LEU* 2.8 39.8 + - - +
893B VAL* 4.2 5.8 - - + -
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Residues in contact with ASP 871 (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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831B ASN* 2.9 31.5 + - - +
834B PHE* 3.3 7.6 - - - -
870B HIS* 1.3 71.7 - - - +
872B VAL* 1.3 61.1 + - - +
873B GLU* 3.9 3.0 + - + +
888B ARG* 3.5 38.7 + - - +
889B LYS 3.6 2.9 - - - -
890B LYS* 3.2 26.3 - - - +
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Residues in contact with VAL 872 (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* 4.4 8.9 - - + +
798B MET* 3.3 33.2 - - + -
810B ILE* 4.3 15.3 - - + -
828B LEU* 4.2 21.5 - - + -
834B PHE* 3.6 28.9 - - + -
862B ILE* 4.5 5.2 - - + -
871B ASP* 1.3 72.8 - - - +
873B GLU* 1.3 59.7 + - - +
874B ILE* 4.1 7.6 + - + -
887B VAL 3.5 2.8 - - - +
888B ARG* 3.4 1.5 - - - -
889B LYS* 2.7 32.8 + - - +
891B LEU* 4.3 11.9 - - + -
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Residues in contact with GLU 873 (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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725B SER* 3.0 27.9 + - - +
828B LEU* 4.0 3.4 - - - +
829B LEU* 3.1 60.5 + - + +
871B ASP* 3.9 3.4 + - + -
872B VAL* 1.3 75.0 - - - +
874B ILE* 1.3 64.1 + - - +
875B LYS* 3.6 13.0 + - - -
887B VAL 3.2 7.2 - - - +
888B ARG* 3.1 42.4 + - + -
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Residues in contact with ILE 874 (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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725B SER* 4.2 0.3 + - - -
794B ILE* 3.7 25.6 - - + +
796B LEU* 4.1 20.6 - - + -
810B ILE* 5.2 1.1 - - + -
812B ALA* 3.8 17.7 - - + -
826B VAL* 3.7 22.4 - - + -
827B GLU 3.6 7.0 - - - +
828B LEU* 4.3 11.9 - - + -
860B PHE* 3.6 32.8 - - + -
872B VAL* 4.4 8.7 - - + -
873B GLU* 1.3 79.4 - - - +
875B LYS* 1.3 67.1 + - - +
886B GLY* 3.1 2.6 - - - -
887B VAL* 2.8 36.1 + - + +
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Residues in contact with LYS 875 (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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720B ASP* 3.0 54.1 + - - +
721B SER* 4.9 2.0 - - - +
723B ILE* 3.0 34.9 + - + -
725B SER* 3.4 24.0 - - - +
794B ILE* 4.3 0.4 - - - -
825B ARG 3.8 0.5 - - - +
826B VAL* 3.3 5.8 - - - +
827B GLU* 2.9 37.4 + - + +
829B LEU* 3.9 22.5 - - + +
873B GLU* 3.6 12.8 + - - +
874B ILE* 1.3 80.5 - - - +
876B ALA* 1.3 61.0 + - - +
885B ASP 3.5 4.7 - - - +
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Residues in contact with ALA 876 (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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723B ILE* 4.0 4.1 - - - +
792B PHE* 3.8 21.5 - - + -
794B ILE* 4.1 13.5 - - + -
814B LEU* 4.5 7.2 - - + -
824B VAL* 5.7 0.2 - - + -
825B ARG 3.2 11.4 - - - +
826B VAL* 4.0 13.5 - - + -
875B LYS* 1.3 77.3 - - - +
877B SER* 1.3 62.9 + - - +
884B SER* 3.4 1.9 - - - -
885B ASP 2.7 35.0 + - - +
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Residues in contact with SER 877 (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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717B PHE* 3.4 21.7 - - - +
718B ILE* 3.6 20.6 + - - -
723B ILE* 4.0 12.6 - - - -
792B PHE* 4.2 2.5 - - - -
824B VAL* 3.4 4.1 - - - -
825B ARG* 3.1 33.3 + - - +
876B ALA* 1.3 76.2 - - - +
878B VAL* 1.3 63.8 + - - +
883B TRP 3.7 6.3 - - - -
884B SER* 3.9 15.7 - - - +
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Residues in contact with VAL 878 (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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716B GLY 4.5 1.6 - - - +
717B PHE* 4.0 5.3 - - - -
718B ILE* 5.1 1.6 - - - +
792B PHE* 3.9 36.8 - - + -
822B ILE* 3.5 41.5 - - + -
823B TYR 3.8 6.1 - - - +
824B VAL* 4.3 1.3 - - + +
877B SER* 1.3 76.8 + - - +
879B GLN* 1.3 75.2 + - - +
880B GLU 3.6 1.0 + - - -
881B ALA* 3.6 30.0 + - + +
883B TRP* 3.1 25.9 + - + +
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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