Contacts of the strand formed by residues 808 - 817 (chain B) in PDB entry 5IYB
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 808 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733B MET* 4.1 14.2 - - - -
750B VAL 3.2 16.2 - - - -
751B LEU* 3.4 18.8 - - - -
752B TYR* 3.7 11.9 - - - -
807B ARG* 1.3 74.9 - - - +
809B VAL* 1.3 57.9 + - - +
926B VAL* 3.3 4.0 - - - +
927B ARG* 2.7 43.2 + - - +
1050B ARG* 2.8 25.6 + - - -
1054B MET* 4.1 1.9 - - - +
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Residues in contact with VAL 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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733B MET* 5.8 0.3 - - - +
740B PHE* 5.6 1.8 - - + -
748B ALA 4.3 0.3 - - - +
749B HIS* 3.9 2.1 + - - +
750B VAL* 3.1 49.1 + - + +
752B TYR* 3.6 7.4 - - + -
808B SER* 1.3 75.5 - - - +
810B PHE* 1.3 63.5 + - - +
811B TYR* 3.8 24.4 - - + -
924B ARG* 3.6 32.5 - - + -
925B SER 3.2 10.1 - - - +
926B VAL* 4.2 1.3 - - + +
927B ARG* 5.1 0.2 - - - -
60C HIS* 3.5 26.0 - - + +
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Residues in contact with PHE 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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747B LEU* 3.3 38.8 - - + -
748B ALA 3.7 9.2 - - - -
749B HIS* 3.1 32.5 - + - +
809B VAL* 1.3 70.8 - - - +
811B TYR* 1.3 65.7 + - - +
812B ARG* 4.6 16.8 - - + -
923B VAL 3.4 1.8 - - - +
924B ARG* 3.2 2.0 - - - -
925B SER* 2.4 70.2 + - - +
927B ARG* 3.9 37.2 - - + -
1057B ASP* 4.9 8.1 - - - -
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Residues in contact with TYR 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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740B PHE* 4.6 22.1 - + - -
745B ASP 5.5 1.8 - - - +
747B LEU* 3.5 5.2 - - - +
748B ALA* 2.9 51.3 + - + +
750B VAL* 4.9 5.4 - - + -
809B VAL* 3.8 25.4 - - + -
810B PHE* 1.3 77.8 - - - +
812B ARG* 1.3 60.1 + - - +
813B SER* 5.4 0.9 - - - +
905B ASP* 3.7 16.6 - - + -
922B ARG* 3.5 47.8 + - + +
923B VAL 3.1 4.0 - - - -
924B ARG* 3.3 46.4 + - + -
60C HIS* 3.8 17.0 - - - +
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Residues in contact with ARG 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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746B THR* 2.6 51.7 + - - +
747B LEU* 4.4 18.9 - - - +
810B PHE* 4.6 16.5 - - + -
811B TYR* 1.3 75.3 - - - +
813B SER* 1.3 77.0 + - - +
814B TYR* 3.2 46.3 + - + +
898B THR* 5.6 3.0 - - - +
921B ILE 3.9 0.7 - - - +
922B ARG* 3.4 1.7 - - - -
923B VAL* 2.7 39.6 + - + +
56Y G 5.3 13.7 + - - -
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Residues in contact with SER 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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744B MET* 3.8 24.0 + - - +
745B ASP 3.2 20.6 + - - -
746B THR* 3.1 15.7 + - - +
811B TYR* 5.4 0.2 - - - +
812B ARG* 1.3 92.4 + - - +
814B TYR* 1.3 66.4 + - - +
815B LYS* 4.1 1.6 + - - +
920B LYS* 5.4 5.2 - - - -
921B ILE 3.4 7.9 - - - -
922B ARG* 3.7 19.8 - - - +
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Residues in contact with TYR 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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812B ARG* 3.2 51.4 - - + +
813B SER* 1.3 77.4 - - - +
815B LYS* 1.3 61.3 + - - +
866B ILE* 3.6 34.1 - - + -
867B ILE* 5.2 0.9 - - + -
894B THR* 5.3 8.1 - - + -
895B PHE 5.9 1.1 - - - -
896B LEU* 3.7 24.3 - - + +
898B THR* 3.7 29.3 + - + +
901B THR* 6.1 0.3 - - - -
920B LYS* 3.2 4.4 - - - +
921B ILE* 2.8 40.0 + - + +
923B VAL* 3.7 29.2 - - + +
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Residues in contact with LYS 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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117B ASN* 4.5 12.8 - - - +
813B SER 4.1 1.8 + - - +
814B TYR* 1.3 76.5 - - - +
816B GLU* 1.3 70.8 + - - +
817B GLN* 6.2 1.0 - - - +
867B ILE* 5.1 0.4 - - - -
894B THR* 5.7 2.1 - - - +
918B PHE* 4.1 28.4 - - + -
919B CYS 3.1 12.1 - - - +
920B LYS* 4.1 15.5 - - + +
58Y C 4.5 30.7 - - - -
59Y G 4.8 8.7 + - - -
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Residues in contact with GLU 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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815B LYS* 1.3 81.8 - - - +
817B GLN* 1.3 61.6 + - - +
829B PHE* 3.9 12.4 - - + -
867B ILE* 3.8 30.2 - - + +
869B LYS* 2.5 49.9 + - + -
892B CYS 4.7 3.1 - - - +
894B THR* 2.7 29.3 + - + +
918B PHE* 3.7 5.5 - - - -
919B CYS* 2.9 33.4 + - - +
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Residues in contact with GLN 817 (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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815B LYS* 6.2 0.9 - - - +
816B GLU* 1.3 79.4 + - - +
818B GLU* 1.3 76.5 + - - +
819B SER* 3.5 17.6 - - - -
827B GLU* 3.5 2.3 - - - +
829B PHE* 4.4 0.4 - - - -
869B LYS* 3.0 30.1 + - - +
912B ASN* 3.1 31.1 + - - +
914B GLU* 4.7 5.1 - - - +
916B TYR* 3.5 14.4 - - + -
917B LYS 4.2 4.9 - - - +
918B PHE* 4.0 15.2 - - + -
59Y G 4.5 15.8 + - - -
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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