Contacts of the strand formed by residues 851 - 859 (chain A) in PDB entry 5EPG
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 TYR 851 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707A ILE* 3.9 4.8 - - - +
743A ILE 4.0 0.8 - - - +
744A HIS* 3.6 3.8 - - - +
745A MET* 2.8 44.3 + - + +
849A HIS* 4.0 4.0 - - + -
850A PRO* 1.3 81.5 - - - +
852A LEU* 1.3 60.1 + - - +
853A GLY 4.2 0.2 - - - -
872A HIS* 3.9 33.4 + + + -
873A TYR 3.2 7.2 - - - -
874A SER* 3.5 24.5 - - - -
886A VAL* 3.5 33.1 + - + +
887A ILE* 3.8 17.6 - - + +
890A GLY* 4.2 7.8 - - - -
924A GLY 4.6 2.4 + - - -
927A GLN* 3.6 44.9 - - + -
928A ALA* 4.4 6.1 - - - -
931A ILE* 4.6 10.8 - - + -
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Residues in contact with LEU 852 (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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707A ILE* 3.5 27.6 - - + -
708A GLU* 3.5 26.0 - - + +
742A GLU* 4.0 13.0 - - + +
743A ILE 3.7 8.1 - - - +
744A HIS* 3.7 28.5 - - + +
851A TYR* 1.3 75.5 - - - +
853A GLY* 1.3 77.7 + - - +
854A LYS* 4.1 22.4 - - + -
872A HIS* 3.5 2.8 - - - -
873A TYR* 2.8 53.8 + - + -
931A ILE* 4.4 2.0 - - - -
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Residues in contact with GLY 853 (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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742A GLU* 3.0 24.4 - - - +
743A ILE 3.0 19.2 + - - -
852A LEU* 1.3 74.0 - - - +
854A LYS* 1.3 61.8 + - - -
855A TYR* 4.5 4.7 - - - -
871A GLU 3.3 7.0 - - - -
872A HIS* 4.8 0.2 - - - -
931A ILE* 3.5 29.8 - - - +
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Residues in contact with LYS 854 (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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708A GLU* 5.7 6.7 - - - +
741A GLY 3.5 7.6 - - - +
742A GLU* 3.7 25.3 + - - +
852A LEU* 4.1 21.3 - - + +
853A GLY* 1.3 78.6 - - - +
855A TYR* 1.3 62.7 + - - +
856A LYS* 4.4 11.8 - - - +
870A MET* 3.6 2.8 - - - +
871A GLU* 2.7 55.3 + - + +
873A TYR* 4.2 24.0 - - + -
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Residues in contact with TYR 855 (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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739A LEU* 3.8 22.7 - - + -
740A GLU* 3.4 5.2 - - - +
741A GLY* 3.0 47.2 + - - +
742A GLU* 3.7 14.1 + - - -
743A ILE* 4.4 4.0 - - + -
853A GLY 4.3 2.5 - - - -
854A LYS* 1.3 80.0 - - - +
856A LYS* 1.3 67.7 + - - +
857A ALA* 4.9 0.9 - - + -
868A LEU* 4.0 9.2 - - + -
869A ASP 3.3 11.0 - - - +
870A MET* 3.9 12.1 - - + -
931A ILE* 4.4 15.0 - - + -
934A SER* 3.2 20.8 + - - -
935A CYS* 3.2 43.5 - - + -
938A GLU* 3.1 24.4 + - - +
1301A THR* 4.2 1.9 - - - +
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Residues in contact with LYS 856 (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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732A PHE* 3.6 27.4 - - + -
738A ILE* 5.3 2.9 - - + -
739A LEU 3.3 6.7 - - - +
740A GLU* 3.7 30.7 + - + +
854A LYS* 4.4 14.3 - - - +
855A TYR* 1.3 81.1 - - - +
857A ALA* 1.3 59.8 + - - +
868A LEU* 3.3 3.5 - - - +
869A ASP* 2.8 73.9 + - + +
871A GLU* 4.1 24.0 + - - +
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Residues in contact with ALA 857 (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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732A PHE* 4.4 2.4 - - - -
738A ILE* 3.5 3.5 - - - -
739A LEU* 2.9 36.9 + - + +
856A LYS* 1.3 71.9 - - - +
858A GLY* 1.3 59.3 + - - +
859A PHE* 3.6 6.8 - - - -
865A ILE* 4.5 7.0 - - + -
867A ALA 3.6 7.0 - - - +
868A LEU* 4.2 4.0 - - + -
935A CYS* 3.6 30.3 - - - -
939A VAL* 4.3 16.8 - - + -
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Residues in contact with GLY 858 (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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732A PHE* 3.8 7.1 - - - -
735A VAL* 3.4 21.7 - - - +
737A GLN 3.4 9.0 - - - -
738A ILE* 4.1 6.1 - - - -
857A ALA* 1.3 70.9 - - - +
859A PHE* 1.3 61.3 + - - +
865A ILE* 3.7 1.8 - - - +
866A LEU 3.2 5.9 + - - -
867A ALA* 2.9 37.9 + - - +
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Residues in contact with PHE 859 (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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735A VAL* 3.5 2.2 - - - +
736A ASP 3.2 20.1 + - - -
737A GLN* 3.1 58.5 + - + -
738A ILE 4.4 0.4 - - - -
739A LEU* 3.9 23.6 - - + -
857A ALA 3.6 11.2 - - - -
858A GLY* 1.3 74.3 - - - +
860A MET* 1.3 84.1 + - - +
863A GLY 4.7 0.2 - - - +
864A ARG 3.2 18.4 - - - +
865A ILE* 4.1 11.2 - - + -
939A VAL* 3.7 26.7 - - + -
942A LYS* 3.7 18.8 - - + -
943A CYS* 3.5 26.2 - - - -
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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