Contacts of the strand formed by residues 884 - 894 (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 SER 884 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718B ILE* 4.6 8.1 - - - +
722B ASP 5.0 1.9 + - - -
723B ILE* 3.7 30.0 - - - +
790B LYS* 3.3 19.4 + - - -
792B PHE* 4.2 7.0 - - - +
876B ALA 3.4 13.5 - - - -
877B SER* 3.9 7.6 - - - +
882B LEU 3.5 6.1 + - - -
883B TRP* 1.3 77.5 - - - +
885B ASP* 1.3 64.8 + - - +
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Residues in contact with ASP 885 (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* 3.9 6.0 - - - +
726B ARG* 3.0 29.2 + - - -
790B LYS* 2.7 27.6 + - - +
792B PHE* 3.7 18.4 - - + +
793B PHE* 3.7 15.0 - - - -
794B ILE* 2.9 31.2 + - + +
875B LYS* 3.5 0.7 - - - -
876B ALA* 2.7 40.2 + - - +
884B SER* 1.3 77.0 - - - +
886B GLY* 1.3 60.2 + - - +
887B VAL* 3.7 2.8 - - - +
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Residues in contact with GLY 886 (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* 3.9 5.5 - - - +
724B ILE 5.0 2.0 + - - -
725B SER* 3.5 22.0 - - - +
726B ARG* 2.8 27.1 + - - +
790B LYS* 5.1 0.2 - - - +
794B ILE* 4.3 0.9 - - - -
874B ILE 3.1 11.0 - - - -
875B LYS* 4.0 5.8 - - - -
885B ASP* 1.3 77.5 + - - +
887B VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 887 (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* 3.9 3.1 + - - -
726B ARG* 3.1 38.8 - - - +
729B PHE* 4.3 9.2 - - + -
794B ILE* 3.8 23.5 - - + +
796B LEU* 4.5 15.3 - - + +
872B VAL 3.5 2.1 - - - +
873B GLU* 3.2 1.4 - - - -
874B ILE* 2.8 40.8 + - + +
885B ASP* 3.7 6.5 - - - +
886B GLY* 1.3 77.9 - - - +
888B ARG* 1.3 61.2 + - - +
889B LYS* 3.8 31.9 - - + +
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Residues in contact with ARG 888 (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* 4.1 12.9 + - - -
726B ARG 3.0 17.5 + - - +
727B SER* 3.8 30.9 + - - +
729B PHE* 3.8 7.3 - - - -
871B ASP* 3.5 44.5 + - + +
872B VAL 3.4 3.1 - - - -
873B GLU* 3.1 42.5 + - + +
887B VAL* 1.3 72.7 - - - +
889B LYS* 1.3 67.4 + - - +
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Residues in contact with LYS 889 (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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729B PHE* 3.8 29.4 - - + +
796B LEU* 3.2 42.1 + - + +
797B GLN* 4.8 7.3 + - - +
798B MET* 4.5 17.0 - - + +
871B ASP* 3.6 2.8 - - - -
872B VAL* 2.7 44.3 + - - +
887B VAL* 3.8 14.8 - - + +
888B ARG* 1.3 78.2 - - - +
890B LYS* 1.3 63.0 + - - +
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Residues in contact with LYS 890 (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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798B MET* 4.4 7.6 - - - +
869B LEU* 4.1 41.0 - - + +
870B HIS 3.4 7.9 - - - +
871B ASP* 3.2 22.9 - - - +
889B LYS* 1.3 74.5 - - - +
891B LEU* 1.3 60.3 + - - +
892B LYS 3.9 1.6 + - - -
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Residues in contact with LEU 891 (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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798B MET* 3.8 35.2 - - + -
799B PRO* 4.1 8.7 - - + +
802B VAL* 3.6 42.8 - - + -
808B VAL* 5.3 1.1 - - + -
810B ILE* 4.2 7.4 - - + -
834B PHE* 4.4 15.5 - - + -
862B ILE* 4.1 26.5 - - + -
864B PRO* 4.6 2.9 - - + -
868B GLY 3.4 3.8 - - - +
869B LEU* 3.7 1.7 - - - -
870B HIS* 2.8 33.9 + - - +
872B VAL* 4.3 5.4 - - + -
889B LYS 3.8 0.6 + - - -
890B LYS* 1.3 73.1 - - - +
892B LYS* 1.3 63.7 + - - +
893B VAL* 3.4 7.1 + - + +
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Residues in contact with LYS 892 (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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168A ASP* 5.7 5.2 - - - -
799B PRO 5.3 1.4 + - - -
800B TYR* 3.2 55.5 + - + +
801B SER* 3.2 7.2 - - - +
802B VAL* 2.9 27.8 + - - +
868B GLY* 3.8 3.6 - - - +
869B LEU* 3.7 25.3 - - + +
890B LYS 3.9 2.6 + - - -
891B LEU* 1.3 72.3 - - - +
893B VAL* 1.3 65.1 + - - +
894B VAL* 3.9 19.6 - - - +
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Residues in contact with VAL 893 (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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802B VAL* 3.4 12.8 - - + +
804B LYS* 3.9 20.0 - - - +
834B PHE* 4.9 4.0 - - + -
864B PRO* 3.7 32.3 - - + -
866B GLU 3.2 26.7 - - - +
867B GLN* 3.4 8.3 - - - +
868B GLY* 2.7 42.7 + - - +
870B HIS* 4.2 6.5 - - + -
891B LEU* 3.9 12.6 - - + +
892B LYS* 1.3 76.8 - - - +
894B VAL* 1.3 66.0 + - - +
895B PRO* 4.5 0.2 - - - +
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Residues in contact with VAL 894 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801B SER* 4.2 19.5 - - - +
802B VAL 2.9 18.3 + - - +
803B VAL* 3.6 8.0 - - + -
804B LYS* 2.9 26.5 + - - +
867B GLN* 4.3 3.6 - - - -
892B LYS* 3.9 24.0 - - - +
893B VAL* 1.3 77.8 - - - +
895B PRO* 1.3 78.1 - - + +
1308C ASN* 6.0 0.4 - - - +
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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