Contacts of the strand formed by residues 887 - 894 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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884A GLY* 2.7 33.3 + - - -
885A HIS 4.2 0.8 - - - +
886A PHE* 1.3 82.1 - - - +
888A LYS* 1.3 54.9 + - - +
908A LYS* 4.5 17.9 - - - +
909A SER 3.1 15.5 - - - -
910A LEU* 4.2 1.6 - - - -
911A LYS* 3.4 11.1 - - - +
922A LEU* 6.1 1.6 - - - -
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Residues in contact with LYS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880A ASP* 5.1 6.8 + - - +
882A GLY 3.6 10.1 - - - +
883A GLU* 4.3 16.4 - - + -
884A GLY 4.3 0.4 - - - +
887A GLY* 1.3 75.2 - - - +
889A VAL* 1.3 65.4 + - - +
890A GLU* 3.4 32.4 + - + +
907A VAL 3.5 1.6 - - - +
908A LYS* 3.3 1.6 - - - +
909A SER* 2.9 43.6 + - - +
910A LEU 5.0 7.0 - - - +
911A LYS* 4.4 15.5 - - + +
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Residues in contact with VAL 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ASP* 3.7 3.1 - - - +
881A LEU* 2.8 35.2 + - + -
882A GLY 2.8 11.7 + - - +
884A GLY 6.2 0.2 - - - +
888A LYS* 1.3 78.2 - - - +
890A GLU* 1.3 61.9 + - - +
906A ALA* 3.9 26.9 - - + -
907A VAL 3.2 9.6 - - - +
908A LYS* 3.8 30.3 - - + -
956A MET* 4.2 10.8 - - + -
1021A ASP* 4.4 1.6 - - - +
1201A 0NT 3.6 42.0 - - + +
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Residues in contact with GLU 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A ARG* 3.3 40.4 + - + +
879A ARG 3.4 7.4 - - - +
880A ASP* 3.3 20.5 - - - +
881A LEU* 3.9 5.4 - - - +
888A LYS* 3.4 33.9 + - + +
889A VAL* 1.3 76.9 - - - +
891A LEU* 1.3 66.9 + - - +
892A CYS* 3.5 11.6 + - - -
906A ALA* 3.6 1.2 - - - -
907A VAL* 2.8 37.7 + - + +
909A SER* 5.6 4.1 + - - -
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Residues in contact with LEU 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A ARG* 3.9 0.2 - - - -
878A ILE* 2.8 56.5 + - + -
879A ARG* 2.7 44.2 + - + +
881A LEU* 3.7 20.7 - - + +
890A GLU* 1.3 72.8 - - - +
892A CYS* 1.3 63.0 + - - +
904A GLN* 4.0 14.4 - - + +
905A VAL 3.6 8.3 - - - +
958A PHE* 3.5 49.1 - - + -
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Residues in contact with CYS 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875A LEU* 4.1 21.1 - - + -
876A LYS 3.2 11.4 - - - +
877A ARG* 3.8 18.8 - - - -
878A ILE* 4.2 5.8 - - - +
890A GLU* 4.1 12.8 - - - -
891A LEU* 1.3 80.1 - - - +
893A ARG* 1.3 57.3 + - - +
894A TYR 4.0 0.2 - - - -
904A GLN* 3.3 3.8 - - - -
905A VAL* 2.8 35.2 + - + +
907A VAL* 3.7 35.2 - - + -
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Residues in contact with ARG 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874A PHE 3.2 3.8 - - - +
876A LYS* 2.9 37.5 + - + +
878A ILE* 4.0 19.3 - - + +
892A CYS* 1.3 73.3 - - - +
894A TYR* 1.3 58.9 + - - +
895A ASP* 3.2 9.8 + - + +
900A ASN* 2.7 58.0 + - - +
901A THR* 3.6 6.3 + - - +
902A GLY* 2.6 54.0 + - - +
903A GLU 3.5 4.5 - - - +
904A GLN* 4.3 21.6 + - + +
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Residues in contact with TYR 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869A HIS 4.3 4.2 + - - -
870A PHE* 3.6 36.0 - + + -
871A GLU* 2.9 54.5 + - - +
874A PHE* 3.4 23.9 - + + -
875A LEU* 3.6 24.9 - - + -
892A CYS 4.0 1.6 - - - -
893A ARG* 1.3 70.3 - - - +
895A ASP* 1.3 56.0 + - - +
896A PRO* 3.3 26.4 - - + +
902A GLY* 3.3 17.8 - - - -
903A GLU* 2.9 20.2 + - + +
905A 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
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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