Contacts of the strand formed by residues 872 - 879 (chain A) in PDB entry 5E3H
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 ASP 872 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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861A LYS* 4.4 6.9 - - - +
862A ILE 3.7 15.1 - - - +
863A PHE* 4.1 19.7 - - + -
870A SER 3.7 1.6 + - - -
871A HIS* 1.3 80.3 + - + +
873A TRP* 1.3 53.2 + - - +
874A GLY* 3.4 15.6 + - - +
888A LYS* 2.7 35.4 + - - +
891A SER* 2.2 26.9 + - - -
1B C 5.7 0.2 - - - -
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Residues in contact with TRP 873 (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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810A CYS* 3.8 22.7 - - + -
815A ALA* 5.6 3.1 - - + -
816A LEU 4.8 1.6 - - - -
817A ALA* 4.0 14.8 - - + -
838A PHE* 3.4 41.3 - + - -
841A CYS* 3.2 35.7 - - + -
842A PHE* 3.8 13.9 - - + -
862A ILE* 3.4 17.2 + - + -
864A CYS* 3.5 39.6 - - + +
871A HIS* 3.3 16.9 + + + -
872A ASP* 1.3 76.4 - - - +
874A GLY* 1.3 59.2 + - - +
887A ILE* 3.8 8.4 - - + +
888A LYS* 3.3 29.1 + - - +
891A SER* 3.5 11.8 - - - -
892A PHE* 3.3 28.6 - + + -
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Residues in contact with GLY 874 (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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861A LYS* 3.7 1.2 - - - -
862A ILE* 2.7 36.2 + - - +
872A ASP* 3.4 13.9 + - - +
873A TRP* 1.3 80.6 - - - +
875A ILE* 1.3 60.6 + - - +
886A VAL 3.3 11.4 - - - -
888A LYS* 4.6 0.9 - - - -
1B C 3.8 13.7 - - - -
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Residues in contact with ILE 875 (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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847A HIS* 4.7 13.5 - - + +
853A PHE* 3.6 23.1 - - + -
858A LYS* 5.5 1.8 - - + -
860A ALA 3.6 11.9 - - - +
861A LYS* 4.6 7.2 - - + -
862A ILE* 3.1 8.1 - - - +
874A GLY* 1.3 77.0 - - - +
876A HIS* 1.3 55.9 - - - +
877A VAL* 3.5 26.5 - - + -
886A VAL* 2.7 41.8 + - + +
1B C 3.1 44.6 - - + +
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Residues in contact with HIS 876 (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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842A PHE* 4.7 12.7 - + - -
844A SER* 5.0 7.2 - - - -
859A ARG* 3.5 14.9 + - + +
860A ALA* 2.8 46.5 + - + +
862A ILE* 3.7 12.0 - - + +
875A ILE* 1.3 71.7 - - - +
877A VAL* 1.3 65.7 + - - +
883A GLU* 3.9 26.5 + - + +
884A ILE 3.8 4.0 - - - -
885A PRO* 3.4 38.4 - - + +
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Residues in contact with VAL 877 (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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853A PHE* 4.4 7.2 - - + -
856A PHE* 3.5 22.7 - - + -
857A GLU 3.2 22.4 - - - +
858A LYS* 4.1 6.1 - - - +
859A ARG* 4.5 4.3 - - - -
875A ILE* 3.5 33.0 - - + -
876A HIS* 1.3 81.2 - - - +
878A LYS* 1.3 63.8 - - - +
879A TYR 4.1 1.1 - - - +
883A GLU* 3.6 7.8 - - - +
884A ILE* 3.3 32.4 + - + +
886A VAL* 3.5 26.2 - - + -
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Residues in contact with LYS 878 (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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855A SER 3.9 2.9 - - - +
856A PHE* 3.6 6.8 - - - -
857A GLU* 3.2 47.8 + - + +
859A ARG* 3.6 44.1 - - - +
877A VAL* 1.3 74.8 - - - +
879A TYR* 1.3 61.7 + - - +
880A LYS 4.0 9.3 + - - +
881A THR 5.9 0.4 - - - +
882A PHE 3.8 2.9 - - - +
883A GLU* 3.3 42.1 + - + +
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Residues in contact with TYR 879 (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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826A ILE* 3.7 27.8 - - + +
827A GLU* 3.2 33.4 + - - +
855A SER* 3.9 20.6 - - - -
856A PHE* 4.1 28.7 - + + -
877A VAL* 4.1 1.8 + - + -
878A LYS* 1.3 71.4 - - - +
880A LYS* 1.3 80.0 + - + +
882A PHE* 2.8 46.7 + + + +
884A ILE* 4.7 13.0 - - + +
918A PHE* 4.4 21.1 - + - -
920A PRO* 6.5 0.2 - - + -
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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