Contacts of the strand formed by residues 997 - 1009 (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 VAL 997 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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844B GLU* 3.8 16.8 - - - +
847B ARG* 4.1 3.9 + - - +
848B TYR* 3.9 7.4 - - - +
877B LEU* 4.6 7.4 - - + +
895B ILE* 4.1 14.8 - - + -
897B PHE* 3.8 33.2 - - + -
922B GLY* 5.2 0.9 - - - -
923B GLU 3.5 7.0 - - - +
924B VAL* 4.8 1.3 - - + -
991B VAL* 3.8 19.5 - - + -
993B ASP 4.7 0.2 - - - +
994B ILE 3.3 17.4 + - - +
995B ALA 3.3 1.5 - - - +
996B GLN* 1.3 83.1 - - - +
998B ASN* 1.3 62.9 + - - +
999B LEU* 3.7 29.2 - - + -
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Residues in contact with ASN 998 (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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840B GLU* 6.2 1.0 - - - +
841B ARG 6.1 0.4 - - - +
844B GLU* 2.9 33.8 + - - +
845B CYS* 4.2 17.5 - - - -
848B TYR* 3.8 33.4 - - + +
923B GLU* 2.8 46.0 + - + +
997B VAL* 1.3 75.2 - - - +
999B LEU* 1.3 67.4 + - - +
1000B LYS* 3.0 29.6 + - - +
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Residues in contact with LEU 999 (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* 3.4 29.9 - - + +
840B GLU* 5.1 1.7 - - - -
841B ARG* 4.5 16.5 + - + +
844B GLU* 2.6 31.0 + - - +
872B ILE* 4.1 28.5 - - + +
873B LEU* 4.9 1.8 - - + -
877B LEU* 4.0 25.1 - - + +
897B PHE* 5.4 1.1 - - + -
920B LEU* 4.2 20.9 - - + -
921B LEU 4.2 2.5 - - - -
922B GLY* 4.7 7.6 - - - -
997B VAL* 3.7 23.6 - - + -
998B ASN* 1.3 74.5 + - - +
1000B LYS* 1.3 64.8 + - - +
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Residues in contact with LYS1000 (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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838B LYS* 3.6 23.9 - - - +
839B ILE* 2.9 29.7 + - - +
845B CYS* 5.6 3.8 - - - -
859B LEU* 4.5 8.3 - - + -
921B LEU 3.1 9.4 + - - +
923B GLU* 4.2 25.5 + - + +
965B ASP* 6.1 3.6 - - - +
967B VAL* 6.2 0.4 - - - +
998B ASN* 3.0 39.2 + - - +
999B LEU* 1.3 81.9 - - - +
1001B TYR* 1.3 90.1 + - + +
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Residues in contact with TYR1001 (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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804B VAL* 4.0 11.9 - - + -
810B GLU* 2.8 35.3 + - + +
814B ILE* 3.9 27.4 - - + -
836B ILE* 4.3 1.1 - - + -
837B PHE 3.1 16.2 - - - +
838B LYS* 3.8 25.2 + - + +
839B ILE* 4.1 4.5 - - - -
859B LEU* 4.8 6.7 - - + -
920B LEU* 3.4 9.0 - - - +
921B LEU* 2.8 51.4 + - + +
964B LEU* 4.0 21.6 - - + +
965B ASP* 4.4 8.7 + - - -
1000B LYS* 1.3 93.1 - - + +
1002B LEU* 1.3 59.3 + - - +
1003B LEU* 4.2 12.8 - - + -
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Residues in contact with LEU1002 (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* 3.8 35.4 - - + -
676B ILE* 6.1 0.4 - - + -
836B ILE* 3.7 0.3 - - - -
837B PHE* 2.7 47.7 + - + -
839B ILE* 4.1 17.4 - - + +
869B PHE* 3.4 35.9 - - + -
873B LEU* 4.3 24.0 - - + -
918B LEU* 4.1 15.3 - - + -
919B ILE 3.7 9.0 - - - +
920B LEU* 4.0 7.6 - - + -
1001B TYR* 1.3 73.0 - - - +
1003B LEU* 1.3 63.0 + - - +
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Residues in contact with LEU1003 (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* 3.7 28.5 - - + -
818B VAL* 3.9 12.3 - - + -
833B VAL* 4.4 6.3 - - + -
835B ASP 3.4 4.3 - - - +
836B ILE* 4.2 14.8 - - + -
861B TRP* 3.8 29.6 - - + -
917B GLY 3.8 0.2 - - - +
918B LEU* 3.4 10.2 - - - +
919B ILE* 2.8 47.5 + - + +
921B LEU* 4.3 4.3 - - + -
1001B TYR* 4.2 18.8 - - + -
1002B LEU* 1.3 79.1 - - - +
1004B LYS* 1.3 58.0 + - - +
1005B LEU* 3.9 16.7 + - + -
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Residues in contact with LYS1004 (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* 5.2 2.0 + - - +
671B ASP* 4.3 18.6 + - - +
672B LEU* 5.3 0.9 - - + +
675B MET* 3.5 32.1 - - + +
833B VAL* 3.8 2.3 - - - -
834B ILE* 2.8 48.8 + - + +
835B ASP* 2.9 43.7 + - + +
837B PHE* 4.6 8.9 - - + -
916B ILE* 3.6 23.1 - - + -
917B GLY 3.5 3.4 - - - -
918B LEU* 3.9 11.9 - - + -
1002B LEU 4.2 0.4 + - - -
1003B LEU* 1.3 71.7 - - - +
1005B LEU* 1.3 62.5 + - - +
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Residues in contact with LEU1005 (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* 4.9 8.1 - - + -
831B LEU* 4.2 29.2 - - + -
832B GLU 3.3 5.6 - - - +
833B VAL* 3.9 31.4 - - + -
834B ILE* 4.4 3.1 - - - -
901B VAL* 4.7 7.2 - - + -
905B ALA* 5.0 2.0 - - + -
916B ILE* 3.3 6.5 - - - +
917B GLY 2.8 41.8 + - - +
919B ILE* 3.2 34.3 - - + +
1003B LEU* 4.1 15.7 - - + -
1004B LYS* 1.3 76.4 - - - +
1006B LYS* 1.3 59.7 + - - +
1007B PHE* 3.7 15.8 - - + -
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Residues in contact with LYS1006 (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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830B ASP 3.6 0.5 - - - +
831B LEU* 3.5 6.6 - - - +
832B GLU* 2.8 56.6 + - + +
834B ILE* 3.9 16.0 - - + +
915B PRO* 3.7 21.1 - - + +
916B ILE* 3.4 23.8 - - + -
1005B LEU* 1.3 72.9 - - - +
1007B PHE* 1.3 66.4 + - - +
1008B ASN* 3.7 25.3 + - - +
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Residues in contact with PHE1007 (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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829B TYR* 3.5 35.9 - + + -
830B ASP 3.5 4.9 - - - +
831B LEU* 3.7 17.3 - - + -
905B ALA* 3.7 32.3 - - + -
908B CYS* 4.1 7.2 - - - -
910B THR* 3.1 37.5 - - + +
915B PRO* 2.8 40.1 + - - +
917B GLY* 3.6 17.7 - - - -
1005B LEU* 3.7 12.6 - - + -
1006B LYS* 1.3 78.2 - - - +
1008B ASN* 1.3 66.2 + - - +
1009B PHE* 3.7 22.6 + + + -
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Residues in contact with ASN1008 (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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829B TYR* 3.3 1.4 - - - -
830B ASP* 2.9 55.9 + - - +
832B GLU* 3.3 36.8 + - - +
1006B LYS* 3.7 26.4 + - - +
1007B PHE* 1.3 72.7 - - - +
1009B PHE* 1.3 65.1 + - - +
1010B LYS* 3.6 2.1 + - - +
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Residues in contact with PHE1009 (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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828B ALA* 3.4 20.4 - - + +
829B TYR* 3.9 16.8 - + + +
910B THR* 3.9 32.8 - - - -
911B SER* 3.6 25.4 - - - -
912B GLN* 3.7 43.2 + - + +
915B PRO* 4.2 3.4 - - + -
1007B PHE* 3.7 28.7 - + + -
1008B ASN* 1.3 73.7 - - - +
1010B LYS* 1.3 63.1 + - - +
1011B THR* 4.3 7.5 - - - +
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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