Contacts of the strand formed by residues 903 - 911 (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 ILE 903 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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857B GLY* 3.2 37.5 - - - +
858B VAL 3.4 7.2 - - - +
859B ARG* 4.6 9.4 - - + +
902B GLY* 1.3 73.4 - - - -
904B VAL* 1.3 66.6 + - - +
905B ASP 3.2 0.2 + - - -
923B VAL* 3.6 2.6 - - - +
924B ARG* 2.9 64.2 + - + +
62C GLU* 3.7 19.9 + - - +
48L ARG* 5.2 4.9 - - - +
53L VAL* 4.7 5.2 - - + -
55L PHE* 3.7 29.8 - - + -
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Residues in contact with VAL 904 (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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854B ILE* 3.5 28.5 - - + -
855B ALA 4.6 3.4 - - - +
856B PRO* 4.2 7.4 - - + -
857B GLY* 2.7 33.7 + - - +
858B VAL* 3.1 18.9 + - + +
860B VAL* 4.1 15.0 - - + -
866B ILE* 5.3 0.2 - - + -
902B GLY 4.2 0.2 + - - -
903B ILE* 1.3 71.2 - - - +
905B ASP* 1.3 62.7 + - - +
906B GLN 3.9 9.0 - - - +
907B VAL* 3.9 10.3 - - + -
921B ILE* 3.6 27.8 - - + -
922B ARG 3.7 9.2 - - - +
923B VAL* 4.3 7.0 - - + +
924B ARG* 5.5 0.7 + - - -
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Residues in contact with ASP 905 (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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811B TYR* 3.7 9.0 - - + -
856B PRO* 3.9 8.1 - - - +
903B ILE 3.2 3.2 + - - -
904B VAL* 1.3 74.3 - - - +
906B GLN* 1.3 72.5 + - - +
922B ARG* 2.5 60.1 + - - +
924B ARG* 2.5 47.2 + - + +
45L TYR* 3.3 10.0 + - - -
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Residues in contact with GLN 906 (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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741B HIS* 3.5 22.0 + - - +
742B VAL* 5.5 1.6 - - - +
743B ARG 5.1 0.3 - - - +
744B MET* 3.1 29.7 - - + +
856B PRO* 4.3 3.1 - - - -
904B VAL 3.7 1.0 - - - -
905B ASP* 1.3 101.3 + - - +
907B VAL* 1.3 66.1 + - - +
920B LYS 4.5 0.7 - - - -
921B ILE* 3.3 3.0 - - - +
922B ARG* 2.8 47.7 + - + +
67J LYS* 5.8 6.9 - - - +
45L TYR* 3.3 29.5 + - + +
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Residues in contact with VAL 907 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B LEU* 3.7 30.3 - - + -
854B ILE 3.1 23.3 - - - +
856B PRO* 3.8 15.9 - - + +
904B VAL* 3.9 13.0 - - + -
906B GLN* 1.3 79.8 - - - +
908B MET* 1.3 65.3 + - - +
909B VAL* 4.3 1.1 - - + -
919B CYS* 4.1 11.9 - - - -
920B LYS 3.5 4.7 - - - +
921B ILE* 3.9 9.4 - - + -
45L TYR* 3.2 28.0 - - - -
46L LYS* 3.3 20.2 + - + -
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Residues in contact with MET 908 (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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115B LEU* 3.5 56.8 - - - +
744B MET* 4.3 12.6 - - + +
907B VAL* 1.3 77.2 - - - +
909B VAL* 1.3 68.6 + - - +
910B THR* 3.8 15.0 - - + -
918B PHE 3.8 0.3 - - - +
919B CYS* 3.3 7.4 - - - -
920B LYS* 2.8 61.0 + - + +
43L ILE* 4.7 7.2 - - + -
44L MET 3.7 26.5 - - - +
45L TYR* 5.7 1.3 - - + -
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Residues in contact with VAL 909 (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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853B LEU* 4.3 22.0 - - + -
907B VAL* 4.3 3.7 + - + -
908B MET* 1.3 78.1 - - - +
910B THR* 1.3 64.2 + - - +
917B LYS* 3.6 34.8 - - + -
918B PHE 3.7 4.0 - - - +
919B CYS* 4.6 7.4 - - + -
17L TYR* 3.7 34.1 - - + +
34L ILE* 3.8 21.3 - - + +
44L MET* 3.0 35.9 + - - +
45L TYR 4.5 0.4 - - - +
46L LYS* 4.8 1.6 - - + +
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Residues in contact with THR 910 (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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115B LEU 4.3 0.7 - - - +
116B ARG* 3.5 21.7 + - + +
908B MET* 3.8 24.2 - - + -
909B VAL* 1.3 76.4 - - - +
911B LEU* 1.3 70.5 + - - +
917B LYS* 3.7 0.5 - - - -
918B PHE* 2.8 46.6 + - + +
34L ILE* 3.5 18.3 - - - +
42L ARG* 3.3 9.6 + - - +
43L ILE* 3.1 29.6 - - - +
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Residues in contact with LEU 911 (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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100B GLU* 4.2 15.5 - - - +
101B ARG* 4.9 15.5 - - - +
116B ARG* 2.8 55.2 + - - +
910B THR* 1.3 87.4 + - - +
912B ASN* 1.3 68.6 + - - +
915B GLY* 3.6 25.6 - - - +
916B TYR 3.1 17.3 - - - +
917B LYS* 4.4 2.5 - - - +
918B PHE* 4.2 0.9 - - - -
34L ILE* 4.1 14.1 - - + +
35L ARG* 5.7 7.0 - - + -
42L ARG* 4.6 12.9 + - + -
131M PRO* 6.4 0.2 - - + -
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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