Contacts of the strand formed by residues 917 - 927 (chain B) in PDB entry 5IY8
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 LYS 917 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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817B GLN* 4.0 0.7 - - - -
818B GLU* 3.1 54.9 + - + +
829B PHE* 3.8 39.7 + - + +
851B ASP 5.9 0.2 + - - -
909B VAL* 4.1 23.3 - - + -
910B THR 3.6 9.6 - - - +
911B LEU* 4.4 2.9 - - - -
915B GLY 4.0 0.6 + - - -
916B TYR* 1.3 73.3 - - - +
918B PHE* 1.3 63.2 + - - +
31L ARG* 4.9 10.9 - - - +
34L ILE* 4.7 14.4 - - + -
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Residues in contact with PHE 918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 4.3 4.3 - - - -
116B ARG 5.2 0.2 - - - -
117B ASN* 3.0 32.5 - - - -
815B LYS* 3.7 37.9 - - + -
816B GLU 3.8 13.7 - - - -
817B GLN* 4.2 13.2 - - + -
829B PHE* 5.1 1.1 - - - -
908B MET* 4.6 0.2 - - + -
909B VAL* 3.6 3.6 - - - +
910B THR* 2.7 53.3 + - + +
912B ASN* 3.5 42.6 - - + +
917B LYS* 1.3 76.1 - - - +
919B CYS* 1.3 65.6 + - - +
920B LYS* 3.6 26.2 - - + -
56Y G 5.1 1.3 - - - -
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Residues in contact with CYS 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815B LYS* 3.4 5.1 - - - +
816B GLU* 3.2 40.4 + - - +
829B PHE* 3.9 14.1 - - + -
853B LEU* 3.9 20.0 - - + -
867B ILE* 3.8 23.8 - - - -
908B MET* 3.1 16.2 - - - +
909B VAL* 4.6 4.0 - - + -
918B PHE* 1.3 79.5 - - - +
920B LYS* 1.3 66.9 + - - +
921B ILE* 4.3 3.4 - - + -
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Residues in contact with LYS 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ARG 3.5 20.8 + - - -
115B LEU* 3.3 20.9 + - - +
117B ASN* 3.6 13.3 + - - +
189B GLY 5.6 1.2 + - - -
744B MET* 3.6 50.2 + - + +
746B THR* 6.1 2.4 - - - +
813B SER* 5.0 5.4 - - - -
814B TYR 3.4 7.2 - - - +
815B LYS* 4.2 12.9 - - + +
907B VAL* 3.9 0.5 - - - -
908B MET* 3.0 41.5 + - + +
918B PHE* 3.6 19.1 - - + -
919B CYS* 1.3 78.8 - - - +
921B ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812B ARG 3.8 0.9 - - - +
813B SER* 3.4 1.7 - - - -
814B TYR* 2.7 44.5 + - + +
853B LEU* 4.2 10.5 - - + -
854B ILE* 4.1 15.3 - - + +
866B ILE* 3.7 39.5 - - + +
867B ILE* 3.9 22.4 - - + -
904B VAL* 4.6 6.3 - - + -
906B GLN 3.5 8.1 - - - +
907B VAL* 3.7 25.6 - - + +
919B CYS* 4.3 3.6 - - - -
920B LYS* 1.3 78.4 - - - +
922B ARG* 1.3 60.5 + - - +
923B VAL* 4.4 12.1 - - + -
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Residues in contact with ARG 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B PHE* 3.9 5.4 + - - -
741B HIS* 3.5 22.2 + - - +
743B ARG 2.7 33.3 + - - -
744B MET* 4.1 10.0 - - - +
745B ASP 5.4 1.1 - - - -
811B TYR* 3.8 38.8 + - + -
812B ARG 3.5 5.4 - - - +
813B SER* 3.2 23.3 - - - +
904B VAL* 3.4 4.4 - - - +
905B ASP* 2.2 62.4 + - - -
906B GLN* 2.7 50.8 + - + +
920B LYS 4.2 0.4 + - - -
921B ILE* 1.3 71.7 - - - +
923B VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 923 (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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810B PHE 3.1 12.5 - - - +
811B TYR* 3.2 14.7 - - - -
812B ARG* 2.8 16.7 + - + +
814B TYR* 3.8 32.5 - - + -
860B VAL* 4.1 18.8 - - + -
866B ILE* 5.3 0.7 - - + -
896B LEU* 5.0 7.2 - - + -
899B SER* 5.4 7.0 - - - -
901B THR 5.3 1.8 - - - +
902B GLY* 4.5 4.9 - - - -
903B ILE 3.3 23.3 - - - +
904B VAL* 4.1 6.7 - - + +
921B ILE* 4.4 11.9 - - + -
922B ARG* 1.3 78.7 - - - +
924B ARG* 1.3 60.1 + - - +
925B SER* 5.3 1.7 - - - -
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Residues in contact with ARG 924 (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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809B VAL* 3.4 31.2 - - + -
810B PHE 3.3 3.1 - - - -
811B TYR* 3.6 17.0 - - + -
857B GLY* 5.9 0.2 - - - -
902B GLY* 3.5 1.7 - - - -
903B ILE* 2.5 68.4 + - + +
904B VAL 4.3 1.2 + - - -
905B ASP* 3.0 33.7 + - + +
923B VAL* 1.3 73.1 - - - +
925B SER* 1.3 60.4 + - - +
60C HIS* 3.7 28.9 + - - +
61C ASP* 3.3 23.2 + - - +
62C GLU* 2.8 45.8 + - - +
48L ARG* 5.3 2.8 - - - +
55L PHE* 5.1 0.2 - - - -
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Residues in contact with SER 925 (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 SER 3.9 0.2 - - - +
809B VAL* 3.3 4.2 - - - +
810B PHE* 2.7 58.1 + - - +
899B SER* 5.8 2.9 - - - -
901B THR* 4.0 21.6 + - - +
902B GLY* 4.4 3.7 - - - -
923B VAL* 5.9 1.3 - - - -
924B ARG* 1.3 76.9 - - - +
926B VAL* 1.3 68.6 + - - +
927B ARG* 3.7 16.6 + - - -
62C GLU* 5.0 1.3 - - - -
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Residues in contact with VAL 926 (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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752B TYR* 3.1 28.5 - - + +
807B ARG* 5.6 8.3 - - + +
808B SER 3.5 5.8 - - - +
809B VAL* 4.7 3.1 - - + -
925B SER* 1.3 80.6 + - - +
927B ARG* 1.3 64.5 + - - +
928B ILE* 3.6 12.8 + - + +
60C HIS* 4.5 1.8 - - + -
62C GLU* 3.1 39.8 + - + +
1K MET* 5.9 3.1 - - - +
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Residues in contact with ARG 927 (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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749B HIS* 4.7 1.0 + - + -
807B ARG* 4.1 1.4 - - - -
808B SER* 3.1 32.3 + - - +
810B PHE* 2.8 53.1 - - + -
899B SER* 4.9 3.2 + - - +
925B SER* 3.7 15.3 + - - -
926B VAL* 1.3 72.5 - - - +
928B ILE* 1.3 60.5 + - - +
929B PRO* 3.8 0.3 - - - +
1050B ARG* 2.9 29.7 + - - +
1054B MET* 3.8 32.8 - - + +
1056B ASP* 5.9 7.4 - - - +
1057B ASP* 3.3 34.0 + - - +
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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