Contacts of the strand formed by residues 857 - 864 (chain C) 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 LYS 857 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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805C HIS* 5.0 0.2 - - - -
852C GLN 3.9 1.9 - - - +
853C TYR* 3.4 3.8 - - - -
854C SER* 2.8 38.5 + - - +
855C ASP* 2.8 7.3 + - + +
856C GLY* 1.3 76.6 - - - +
858C LEU* 1.3 60.0 + - - +
859C GLN* 4.1 2.7 - - + -
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Residues in contact with LEU 858 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764C SER* 4.2 11.9 + - - +
793C ILE* 4.3 9.2 - - + -
795C ASP* 4.6 8.1 - - - +
805C HIS* 3.2 31.5 - - + +
807C PHE* 3.8 32.9 - - + -
829C PHE* 4.9 6.5 - - + -
851C PHE* 3.6 47.3 - - + -
852C GLN 3.8 2.5 - - - +
853C TYR* 3.8 25.6 - - + -
856C GLY 3.6 2.2 + - - -
857C LYS* 1.3 72.7 - - - +
859C GLN* 1.3 59.9 - - - +
860C THR* 4.0 1.6 + - - -
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Residues in contact with GLN 859 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851C PHE* 3.5 5.7 - - - -
852C GLN* 3.0 40.1 + - - +
857C LYS* 4.1 2.9 - - + -
858C LEU* 1.3 74.1 - - - +
860C THR* 1.3 69.3 + - - +
861C VAL* 3.0 27.2 + - - +
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Residues in contact with THR 860 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C SER* 3.6 18.8 - - - -
768C SER* 4.6 8.1 - - - +
807C PHE* 4.3 2.6 - - - -
849C VAL* 3.7 25.1 - - + -
851C PHE* 3.4 21.3 - - - -
858C LEU 4.0 2.9 + - - -
859C GLN* 1.3 75.0 - - - +
861C VAL* 1.3 64.8 + - - +
862C ALA 4.1 4.9 - - - +
863C GLU* 4.1 14.1 - - - +
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Residues in contact with VAL 861 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828C TYR* 3.8 21.5 - - + +
850C VAL* 2.8 15.8 + - + +
851C PHE 3.7 4.3 - - - -
852C GLN* 3.4 31.0 - - + +
859C GLN* 3.3 25.8 - - - +
860C THR* 1.3 76.9 - - - +
862C ALA* 1.3 61.5 + - + +
893C TRP* 4.2 15.7 - - + -
897C LYS* 4.8 11.6 - - + +
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Residues in contact with ALA 862 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849C VAL* 3.7 9.5 - - - +
850C VAL* 3.4 25.6 + - + +
860C THR* 4.1 3.9 - - - +
861C VAL* 1.3 80.1 - - - +
863C GLU* 1.3 68.1 + - - +
893C TRP* 3.5 23.6 - - + -
897C LYS 3.4 25.6 - - - +
898C ASP* 4.2 11.0 - - - +
899C VAL 4.8 1.6 - - - +
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Residues in contact with GLU 863 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768C SER* 3.1 24.3 + - - -
770C LEU* 3.1 33.7 - - + +
847C ARG* 3.5 28.8 + - + +
848C ILE 3.4 8.5 - - - -
849C VAL* 4.0 10.9 - - + +
850C VAL* 4.4 1.0 - - - +
860C THR* 4.1 9.9 - - + +
862C ALA* 1.3 79.6 - - - +
864C LYS* 1.3 69.5 + - - +
898C ASP* 4.4 10.7 + - - +
899C VAL* 4.3 7.9 + - - +
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Residues in contact with LYS 864 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847C ARG* 3.4 1.9 - - - -
848C ILE* 2.8 40.7 + - + +
863C GLU* 1.3 80.2 - - - +
865C GLU* 1.3 73.0 + - - +
866C VAL* 3.6 1.9 + - - +
891C TYR* 3.8 27.4 - - + +
899C VAL* 3.4 35.6 + - + +
900C ARG* 5.0 1.2 - - - +
901C THR* 3.1 27.8 + - - +
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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