Contacts of the strand formed by residues 916 - 925 (chain B) in PDB entry 5WRZ
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 916 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675B MET* 4.3 16.2 - - + -
834B ILE* 5.3 5.2 - - + -
866B THR* 3.9 12.5 - - - +
910B THR* 3.8 8.8 - - - +
914B ASP* 3.3 20.8 - - - +
915B PRO* 1.3 82.5 - - + +
917B GLY* 1.3 62.0 + - - +
1004B LYS* 3.6 37.0 - - + -
1005B LEU 3.3 4.7 - - - +
1006B LYS* 3.4 37.7 - - + +
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Residues in contact with GLY 917 (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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866B THR* 4.2 5.8 - - - -
908B CYS* 4.6 2.2 - - - -
910B THR* 3.8 8.5 - - - -
916B ILE* 1.3 75.7 - - - +
918B LEU* 1.3 65.2 + - - +
1004B LYS* 3.5 6.1 - - - +
1005B LEU* 2.8 36.9 + - - +
1007B PHE* 3.6 21.5 - - - -
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Residues in contact with LEU 918 (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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672B LEU* 3.9 25.1 - - + -
675B MET* 4.4 9.2 - - - -
676B ILE* 3.6 31.2 - - + -
864B SER 3.4 19.1 + - - +
866B THR* 4.3 19.3 - - + +
869B PHE* 3.4 38.4 - - + -
908B CYS* 3.4 11.4 - - - -
917B GLY* 1.3 83.8 - - - +
919B ILE* 1.3 60.7 + - - +
1002B LEU* 4.1 7.2 - - + -
1003B LEU 3.4 11.9 - - - +
1004B LYS* 3.9 16.8 - - + -
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Residues in contact with ILE 919 (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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861B TRP* 3.4 28.0 - - + -
862B HIS 3.4 16.4 - - - +
863B GLY* 3.9 2.9 - - - +
869B PHE* 4.4 1.1 - - - -
901B VAL* 3.9 13.7 - - + +
904B SER* 3.4 28.0 - - - -
905B ALA* 4.3 7.2 - - + +
908B CYS* 4.6 3.8 - - - -
918B LEU* 1.3 75.2 - - - +
920B LEU* 1.3 72.6 + - - +
1002B LEU* 3.7 3.1 - - - +
1003B LEU* 2.8 44.0 + - + +
1005B LEU* 3.2 30.1 - - + -
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Residues in contact with LEU 920 (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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839B ILE* 3.6 23.3 - - + -
861B TRP* 3.4 11.3 - - - -
862B HIS* 2.9 45.7 + - + +
869B PHE* 3.7 17.5 - - + -
872B ILE* 3.9 24.7 - - + -
873B LEU* 4.8 4.5 - - + -
877B LEU* 4.2 13.9 - - + -
919B ILE* 1.3 73.7 - - - +
921B LEU* 1.3 65.8 + - - +
999B LEU* 4.2 25.6 - - + -
1001B TYR 3.4 13.7 - - - +
1002B LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 921 (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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814B ILE* 4.0 27.6 - - + -
817B TYR* 3.6 24.5 - - + -
859B LEU* 4.0 22.4 - - + -
860B LEU 3.4 12.1 - - - +
861B TRP* 3.4 48.0 - - + -
919B ILE 4.1 0.2 + - - -
920B LEU* 1.3 76.5 - - - +
922B GLY* 1.3 57.1 + - - +
999B LEU* 4.1 1.6 - - - -
1000B LYS* 3.1 21.5 + - - -
1001B TYR* 2.8 31.5 + - + +
1003B LEU* 4.3 8.5 - - + +
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Residues in contact with GLY 922 (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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858B ARG 3.3 1.9 - - - +
859B LEU* 3.4 5.9 - - - -
860B LEU 2.9 33.5 + - - +
897B PHE* 5.1 5.0 - - - -
920B LEU* 4.1 1.0 - - - +
921B LEU* 1.3 74.3 - - - +
923B GLU* 1.3 64.4 + - - -
924B VAL* 3.4 10.4 + - - +
997B VAL* 5.2 0.7 - - - -
998B ASN 3.5 10.3 - - - -
999B LEU* 4.2 11.9 - - - -
1000B LYS 4.3 0.4 - - - -
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Residues in contact with GLU 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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848B TYR* 2.7 39.0 + - - +
852B LYS* 4.7 0.9 - - - +
857B ARG* 3.1 26.4 + - + -
858B ARG 3.5 3.6 - - - -
859B LEU* 3.9 8.6 - - + +
922B GLY* 1.3 70.9 - - - -
924B VAL* 1.3 62.5 + - - +
925B ALA 4.2 0.2 - - - -
967B VAL* 3.7 36.0 - - + +
996B GLN 3.9 0.7 - - - +
997B VAL* 3.5 3.1 - - - -
998B ASN* 2.8 43.6 + - + +
1000B LYS* 4.2 25.7 + - + +
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Residues in contact with VAL 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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848B TYR* 4.3 2.7 - - - -
856B ASN 3.9 0.2 - - - +
857B ARG* 3.4 1.7 - - - -
858B ARG 2.8 36.1 + - - +
860B LEU* 4.2 10.8 - - + -
897B PHE* 3.6 48.2 - - + -
922B GLY 3.6 11.9 - - - +
923B GLU* 1.3 78.5 - - - +
925B ALA* 1.3 60.3 + - - +
926B LEU* 3.3 31.3 + - + +
991B VAL* 3.7 20.2 - - + -
996B GLN 3.5 5.6 - - - +
997B VAL* 4.8 2.7 - - + -
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Residues in contact with ALA 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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848B TYR* 3.8 12.5 + - - +
851B PHE* 3.7 35.2 - - + +
854B LEU* 4.0 12.1 - - + +
857B ARG* 4.1 11.2 - - + -
924B VAL* 1.3 67.9 - - - +
926B LEU* 1.3 57.0 + - - +
927B GLY 3.6 1.6 - - - -
991B VAL* 4.1 1.7 - - - +
996B GLN* 2.7 52.3 + - + +
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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