Contacts of the strand formed by residues 829 - 841 (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 TYR 829 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822B HIS* 3.2 42.3 + + - -
826B HIS* 3.5 11.7 - - + +
827B ASN 3.1 0.8 - - - -
828B ALA* 1.3 92.5 - - + +
830B ASP* 1.3 71.5 + - - +
831B LEU* 3.6 12.8 - - + -
902B SER* 3.1 21.9 + - - -
905B ALA* 3.5 9.0 - - - +
906B ASN* 2.8 30.6 + - - -
1007B PHE* 3.5 34.5 - + + -
1008B ASN 3.3 17.0 - - - +
1009B PHE* 3.9 22.0 - + + -
1010B LYS* 3.6 13.0 + - - +
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Residues in contact with ASP 830 (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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822B HIS* 3.8 9.6 - - + +
829B TYR* 1.3 76.4 - - - +
831B LEU* 1.3 65.9 + - - +
1006B LYS 3.6 0.2 - - - +
1007B PHE* 3.5 5.2 - - - -
1008B ASN* 2.9 53.9 + - - +
1010B LYS* 3.4 28.6 - - - +
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Residues in contact with LEU 831 (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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818B VAL* 4.4 18.5 - - + +
822B HIS* 3.9 20.0 + - + +
829B TYR* 3.6 29.8 - - + -
830B ASP* 1.3 81.2 - - - +
832B GLU* 1.3 62.2 + - - +
901B VAL* 4.1 32.1 - - + -
902B SER* 4.8 1.8 - - - -
905B ALA* 4.3 8.3 - - + -
1005B LEU* 4.2 13.9 - - + -
1006B LYS 3.5 3.8 - - - +
1007B PHE* 3.7 34.8 - - + -
1008B ASN* 5.3 0.4 - - - -
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Residues in contact with GLU 832 (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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818B VAL* 5.9 0.2 - - - -
831B LEU* 1.3 74.8 - - - +
833B VAL* 1.3 65.9 + - - +
834B ILE* 3.5 15.9 + - + +
1005B LEU* 3.3 5.8 - - - -
1006B LYS* 2.8 60.5 + - + +
1008B ASN* 3.3 24.4 + - - +
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Residues in contact with VAL 833 (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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806B ARG* 4.8 4.0 + - - -
814B ILE* 5.7 0.2 - - + -
815B ARG* 4.5 23.1 - - + -
818B VAL* 4.1 26.9 - - + -
832B GLU* 1.3 77.2 - - - +
834B ILE* 1.3 68.3 + - - +
835B ASP 3.8 11.0 - - - +
836B ILE* 3.5 34.3 - - + -
1003B LEU* 4.4 7.9 - - + -
1004B LYS 3.9 4.5 - - - +
1005B LEU* 3.9 15.0 - - + -
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Residues in contact with ILE 834 (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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806B ARG* 2.8 31.1 + - - +
832B GLU* 3.9 16.4 - - + +
833B VAL* 1.3 82.3 - - - +
835B ASP* 1.3 69.0 + - - +
916B ILE* 5.3 4.9 - - + -
1004B LYS* 2.8 49.2 + - + +
1005B LEU 4.4 1.8 - - - -
1006B LYS* 3.9 33.7 - - + +
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Residues in contact with ASP 835 (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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668B PRO* 3.6 32.4 - - + +
803B VAL* 5.1 6.3 - - + +
806B ARG* 4.5 9.5 + - - +
833B VAL* 3.8 1.4 - - - +
834B ILE* 1.3 89.8 - - - +
836B ILE* 1.3 67.6 + - - +
837B PHE* 3.5 26.4 - - + -
1003B LEU* 3.4 4.5 - - - -
1004B LYS* 2.9 56.6 + - + +
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Residues in contact with ILE 836 (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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803B VAL* 3.7 7.1 - - - +
804B VAL* 2.8 46.1 + - + +
806B ARG* 6.3 0.4 - - - -
811B ALA* 4.2 26.9 - - + +
814B ILE* 3.7 43.3 - - + -
815B ARG* 4.5 9.9 - - + +
833B VAL* 3.5 27.4 - - + -
835B ASP* 1.3 73.8 - - - +
837B PHE* 1.3 67.3 + - - +
1001B TYR* 4.3 1.8 - - + -
1002B LEU 3.7 2.5 - - - -
1003B LEU* 4.2 14.4 - - + +
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Residues in contact with PHE 837 (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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668B PRO* 3.4 40.8 - - + -
669B VAL* 3.9 12.6 - - + -
672B LEU* 3.9 29.2 - - + -
801B ILE* 3.7 26.9 - - + -
802B LYS 3.1 11.4 - - - +
803B VAL* 4.1 10.5 - - + -
804B VAL* 4.1 3.1 - - - -
835B ASP* 3.5 31.4 - - + -
836B ILE* 1.3 76.8 - - - +
838B LYS* 1.3 58.9 + - - +
839B ILE* 4.4 1.1 - - + -
1001B TYR* 3.1 10.7 - - - +
1002B LEU* 2.7 58.6 + - + +
1004B LYS* 4.6 9.6 - - + -
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Residues in contact with LYS 838 (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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800B ASP* 3.7 1.7 - - - +
801B ILE* 3.4 4.7 - - - -
802B LYS* 2.6 50.5 + - + +
804B VAL* 3.8 15.0 - - + +
810B GLU* 4.0 11.4 - - - +
837B PHE* 1.3 72.6 - - - +
839B ILE* 1.3 67.4 + - - +
840B GLU* 6.4 0.4 - - + +
1000B LYS* 3.6 30.4 + - - +
1001B TYR* 3.8 25.7 + - + -
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Residues in contact with ILE 839 (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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799B THR* 4.2 7.9 - - + -
800B ASP 3.3 3.4 - - - +
801B ILE* 4.1 26.2 - - + -
837B PHE* 4.4 1.3 - - + -
838B LYS* 1.3 86.2 + - - +
840B GLU* 1.3 62.2 + - - +
841B ARG* 4.1 2.0 - - + +
873B LEU* 4.2 14.1 - - + -
920B LEU* 3.6 30.5 - - + -
999B LEU* 3.4 32.6 - - + +
1000B LYS* 2.9 25.5 + - - +
1001B TYR 3.9 8.3 - - - +
1002B LEU* 4.1 21.8 - - + +
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Residues in contact with GLU 840 (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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799B THR* 3.4 3.5 - - - -
800B ASP* 2.9 48.4 + - + +
838B LYS* 6.4 0.4 - - + -
839B ILE* 1.3 73.9 - - - +
841B ARG* 1.3 72.2 + - - +
842B GLU* 3.4 2.4 + - - -
845B CYS* 4.2 30.1 - - - +
998B ASN* 6.2 1.1 - - - +
999B LEU 5.1 1.3 - - - -
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Residues in contact with ARG 841 (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 LYS 3.9 2.5 - - - +
799B THR* 3.7 14.1 - - + +
839B ILE* 4.1 2.3 - - + +
840B GLU* 1.3 80.4 - - - +
842B GLU* 1.3 74.6 + - - +
843B GLY 3.3 0.3 + - - -
844B GLU* 3.0 57.6 + - + +
845B CYS* 4.5 1.2 + - - -
847B ARG* 3.4 27.3 - - - +
872B ILE 3.6 8.3 - - - -
873B LEU* 2.8 36.1 - - + +
874B SER 3.1 22.8 + - - -
875B GLN* 3.3 4.2 - - - +
876B GLY* 3.3 21.9 - - - +
998B ASN* 6.1 0.4 - - - +
999B LEU* 4.5 15.5 + - + -
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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