Contacts of the strand formed by residues 887 - 894 (chain B) in PDB entry 4E5W
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 GLY 887 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884B GLY* 2.7 34.5 + - - -
885B HIS 4.2 1.4 - - - +
886B PHE* 1.3 80.7 - - - +
888B LYS* 1.3 55.0 + - - +
908B LYS* 4.5 17.3 - - - +
909B SER 3.3 13.9 - - - -
910B LEU* 4.2 2.5 - - - -
911B LYS* 3.4 12.1 - - - +
922B LEU* 6.1 1.6 - - - -
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Residues in contact with LYS 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B ASP* 5.1 7.0 - - - +
882B GLY 3.6 10.3 - - - +
883B GLU* 4.3 17.3 - - + -
884B GLY 4.3 0.7 - - - +
887B GLY* 1.3 74.3 - - - +
889B VAL* 1.3 66.4 + - - +
890B GLU* 3.3 31.2 - - + +
907B VAL 3.5 1.6 - - - +
908B LYS* 3.3 2.0 - - - +
909B SER* 2.9 48.7 + - - +
910B LEU 3.7 13.9 + - - -
911B LYS* 4.4 12.1 - - + -
912B PRO* 4.0 18.3 - - + +
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Residues in contact with VAL 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880B ASP* 3.7 2.9 - - - +
881B LEU* 2.8 35.3 + - + -
882B GLY 2.8 14.8 + - - +
888B LYS* 1.3 76.7 - - - +
890B GLU* 1.3 62.4 + - - +
906B ALA* 3.9 26.7 - - + -
907B VAL 3.2 10.8 - - - +
908B LYS* 3.9 30.3 - - + -
956B MET* 4.2 10.1 - - + -
1021B ASP* 4.3 1.8 - - - +
1202B 0NT 3.6 42.6 - - + +
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Residues in contact with GLU 890 (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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877B ARG* 3.2 41.5 + - + +
879B ARG 3.4 8.1 - - - +
880B ASP* 3.3 18.1 - - - +
881B LEU* 3.9 5.6 - - - +
888B LYS* 3.3 33.3 - - + +
889B VAL* 1.3 76.8 - - - +
891B LEU* 1.3 65.7 + - - +
892B CYS* 3.6 10.5 + - - -
906B ALA* 3.6 1.0 - - - -
907B VAL* 2.8 42.0 + - + +
909B SER* 5.1 5.9 + - - +
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Residues in contact with LEU 891 (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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877B ARG* 3.9 0.3 - - - -
878B ILE* 2.8 49.9 + - + -
879B ARG* 2.7 43.8 + - + +
881B LEU* 3.7 20.9 - - + +
890B GLU* 1.3 71.8 - - - +
892B CYS* 1.3 63.8 + - - +
904B GLN* 3.8 26.7 - - + +
905B VAL 3.6 8.3 - - - +
958B PHE* 3.6 44.9 - - + -
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Residues in contact with CYS 892 (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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875B LEU* 3.9 20.6 - - + -
876B LYS 3.1 11.4 - - - +
877B ARG* 3.8 19.5 - - - -
878B ILE* 4.2 6.7 - - - +
890B GLU* 4.1 12.8 - - - -
891B LEU* 1.3 79.5 - - - +
893B ARG* 1.3 59.0 + - - +
904B GLN* 3.3 4.0 - - - -
905B VAL* 2.8 33.9 + - - +
907B VAL* 3.7 35.7 - - + -
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Residues in contact with ARG 893 (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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874B PHE 3.2 4.0 - - - +
875B LEU* 3.7 0.2 - - - -
876B LYS* 2.9 41.0 + - + +
878B ILE* 4.0 17.5 - - + +
892B CYS* 1.3 72.9 - - - +
894B TYR* 1.3 61.7 + - - +
895B ASP* 3.4 8.3 + - + -
900B ASN* 3.0 54.7 + - - +
901B THR* 3.8 3.8 + - - +
902B GLY* 2.7 47.9 + - - +
903B GLU 3.5 4.3 - - - +
904B GLN* 4.2 26.8 - - + +
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Residues in contact with TYR 894 (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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869B HIS 4.1 5.0 + - - -
870B PHE* 3.5 43.3 - + + -
871B GLU* 2.9 54.1 + - - +
874B PHE* 3.5 23.5 - + + -
875B LEU* 3.9 19.7 - - + +
892B CYS 4.1 1.2 + - - -
893B ARG* 1.3 70.9 - - - +
895B ASP* 1.3 57.0 + - - +
896B PRO* 3.4 32.2 - - + +
902B GLY* 3.2 19.8 - - - -
903B GLU* 2.8 22.2 + - + +
905B VAL* 4.5 6.2 - - + +
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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
------------------------------------------------------------
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