Contacts of the strand formed by residues 872 - 876 (chain E) in PDB entry 3EI4
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 SER 872 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723E LYS* 4.9 4.0 - - - -
817E VAL* 3.0 14.8 - - - -
870E VAL* 3.5 0.6 - - - +
871E TYR* 1.3 77.6 - - - +
873E MET* 1.3 72.8 + - - +
874E VAL* 5.8 0.2 - - - -
882E ALA* 3.4 0.5 - - - +
883E SER* 3.1 31.3 + - - +
912E LEU 3.6 11.8 + - - -
913E TYR* 4.8 0.7 - - - -
914E LEU* 3.2 40.5 + - - +
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Residues in contact with MET 873 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817E VAL* 3.5 21.5 - - + +
818E SER 4.2 2.4 - - - +
819E CYS* 4.0 19.7 - - + -
830E ILE* 3.2 46.4 - - + +
832E GLY* 3.7 30.5 - - - +
848E ILE* 4.3 9.0 - - - -
870E VAL* 3.8 15.0 - - + -
872E SER* 1.3 84.1 - - - +
874E VAL* 1.3 73.0 + - - +
880E LEU* 4.0 13.0 - - + -
881E LEU 3.1 8.7 - - - +
882E ALA* 4.0 8.5 - - + -
914E LEU* 4.6 0.7 - - - -
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Residues in contact with VAL 874 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819E CYS* 4.5 3.4 - - - -
872E SER* 5.6 0.9 - - - +
873E MET* 1.3 82.6 - - - +
875E GLU* 1.3 79.4 + - + +
876E PHE 3.3 0.7 + - - -
879E LYS 3.6 1.4 - - - +
880E LEU* 3.6 7.7 - - - -
881E LEU* 2.9 36.1 + - + +
914E LEU* 4.2 33.4 - - + +
915E LYS* 4.9 2.5 - - + +
916E THR* 3.8 31.4 - - + +
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Residues in contact with GLU 875 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819E CYS* 4.5 1.4 - - - -
820E LYS 5.0 3.6 - - - +
821E LEU* 3.6 41.3 - - + +
822E GLY 4.4 5.1 - - - +
874E VAL* 1.3 83.3 - - + +
876E PHE* 1.3 61.5 + - - +
877E ASN* 3.6 8.1 + - - -
878E GLY* 2.6 38.0 + - - -
879E LYS 3.7 3.8 - - - -
916E THR* 4.3 3.5 + - - -
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Residues in contact with PHE 876 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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874E VAL 3.3 6.5 + - - +
875E GLU* 1.3 75.6 + - - +
877E ASN* 1.3 74.6 + - + +
878E GLY 3.1 0.7 - - - -
879E LYS* 2.7 42.8 + - + +
881E LEU* 4.1 13.0 - - + +
890E LEU* 3.7 25.6 - - + -
916E THR* 3.6 31.4 - - + -
918E GLY 2.9 26.2 - - - -
919E ASP* 3.7 19.3 - - - -
921E ILE* 3.7 22.0 - - + -
935E TYR* 3.8 24.9 - + + -
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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