Contacts of the helix formed by residues 846 - 859 (chain B) in PDB entry 2EYQ
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 ARG 846 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685A ARG* 3.0 24.7 + - - +
686A PHE* 3.3 25.2 - - - -
660B LEU* 4.6 2.6 + - - +
663B GLN* 3.3 15.2 - - - +
664B GLN* 3.6 19.7 - - - +
667B ASP* 2.5 47.2 + - + +
668B ASN* 3.8 13.0 - - - +
844B GLN* 2.6 35.4 + - - +
845B MET* 1.3 74.8 - - - +
847B GLU* 1.3 60.4 + - - +
848B ARG* 3.9 32.1 - - - +
849B GLU* 2.5 47.3 + - + +
850B LEU* 3.0 5.0 + - - +
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Residues in contact with GLU 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B PHE* 5.6 3.4 - - + -
631B GLY 4.1 5.0 - - - +
632B PHE* 3.6 26.2 - - + -
633B GLY* 3.0 26.8 + - - +
634B LYS 4.4 0.3 + - - -
635B THR* 3.2 41.4 + - + +
668B ASN* 3.1 24.3 + - - +
845B MET 3.7 1.5 + - - +
846B ARG* 1.3 68.6 - - - +
848B ARG* 1.3 66.3 + - - +
850B LEU* 2.8 26.0 + - - +
851B GLU 3.0 9.4 + - - -
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Residues in contact with ARG 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685A ARG 2.7 29.7 + - - -
686A PHE* 4.2 1.4 - - - +
687A ARG* 3.3 16.8 + - - +
688A SER* 3.3 26.3 - - - +
689A ALA 5.5 0.7 - - - +
667B ASP* 4.4 10.3 - - - +
670B ARG* 5.5 1.8 - - - +
671B ASP* 2.7 50.5 - - + -
846B ARG* 3.9 22.1 - - + +
847B GLU* 1.3 78.0 - - - +
849B GLU* 1.3 73.0 + - + +
851B GLU* 3.6 18.6 - - - +
852B ARG* 3.2 29.4 + - - +
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Residues in contact with GLU 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685A ARG* 2.7 50.3 + - - +
842B HIS* 4.3 5.4 - - - -
845B MET* 3.0 20.7 - - - +
846B ARG* 2.5 53.4 + - + +
848B ARG* 1.3 84.1 + - + +
850B LEU* 1.3 63.8 + - - +
852B ARG* 3.3 6.1 + - - +
853B VAL* 3.0 26.1 + - + +
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Residues in contact with LEU 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B VAL* 4.4 17.7 - - + +
631B GLY 4.6 1.8 - - - +
632B PHE* 3.7 27.8 - - + +
845B MET* 3.6 42.2 - - + +
846B ARG 3.0 18.7 + - - +
847B GLU* 2.8 18.6 + - - +
849B GLU* 1.3 73.4 - - - +
851B GLU* 1.3 66.0 + - - +
853B VAL* 3.1 1.9 + - - +
854B MET* 2.7 53.3 + - + +
875B ILE* 4.5 12.8 - - + -
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Residues in contact with GLU 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B GLU* 4.3 5.7 - - - +
454B VAL* 4.6 9.0 - - + -
599B PHE* 3.1 35.5 - - + -
632B PHE* 3.9 16.7 - - + -
847B GLU 3.0 7.7 + - - +
848B ARG* 3.6 19.3 - - - +
850B LEU* 1.3 78.9 - - - +
852B ARG* 1.3 69.0 + - - +
854B MET* 3.8 1.0 - - - +
855B ASN* 2.9 37.6 + - - +
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Residues in contact with ARG 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A ALA* 4.4 20.6 - - - +
712A LYS* 4.9 12.1 - - - +
848B ARG* 3.2 17.3 + - - +
849B GLU* 3.7 8.7 - - - +
850B LEU 3.3 0.2 - - - -
851B GLU* 1.3 82.8 - - - +
853B VAL* 1.3 68.2 + - + +
855B ASN* 3.3 4.9 - - - +
856B ASP* 2.8 45.4 + - - +
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Residues in contact with VAL 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839B ALA* 6.0 3.1 - - + -
840B ILE 4.6 9.2 - - - +
845B MET* 4.3 16.2 - - + -
849B GLU* 3.0 16.3 + - + +
850B LEU* 3.5 4.9 - - - +
852B ARG* 1.3 79.7 - - + +
854B MET* 1.3 61.0 + - - +
856B ASP* 3.4 6.0 + - - -
857B PHE* 2.9 45.8 + - + +
865B LEU* 4.5 27.1 - - + -
875B ILE* 4.5 19.1 - - + -
877B ILE* 4.9 4.0 - - + -
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Residues in contact with MET 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B VAL* 3.5 34.5 - - + -
455B ALA* 4.9 6.5 + - - +
632B PHE* 3.9 16.8 - - + +
850B LEU* 2.7 65.8 + - + +
851B GLU 3.9 2.9 - - - +
853B VAL* 1.3 76.0 - - - +
855B ASN* 1.3 64.3 + - - +
857B PHE* 3.6 5.0 + - - +
858B HIS* 3.2 19.4 + - - +
875B ILE* 4.1 17.7 - - + -
876B ASP 4.0 22.4 - - - +
877B ILE* 4.8 5.9 - - + +
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Residues in contact with ASN 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452B GLU* 3.0 42.0 - - - +
453B ARG 3.6 26.9 + - - -
454B VAL* 4.2 9.7 - - - +
455B ALA 5.3 0.2 - - - +
851B GLU* 2.9 29.3 + - - +
852B ARG* 2.8 11.4 + - - +
854B MET* 1.3 74.7 + - - +
856B ASP* 1.3 62.1 + - - +
857B PHE 2.9 0.9 - - - -
858B HIS* 2.6 31.3 + - - +
859B HIS* 2.9 16.2 + - + +
861B ARG* 5.1 1.8 - - - +
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Residues in contact with ASP 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B ARG* 2.8 43.1 + - - +
853B VAL* 3.8 5.7 + - - +
855B ASN* 1.3 74.1 - - - +
857B PHE* 1.3 62.0 + - + +
859B HIS 3.4 0.7 + - - -
860B GLN 3.3 2.4 + - - -
861B ARG* 2.7 71.9 + - + +
862B PHE* 3.6 32.8 + - + -
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Residues in contact with PHE 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B GLN* 3.2 62.2 + - + +
812B VAL 4.7 1.1 - - - -
813B TYR* 6.2 0.2 - + - -
839B ALA* 3.9 12.3 - - + -
853B VAL* 2.9 28.2 + - + +
854B MET* 4.0 4.3 - - - +
855B ASN 2.7 3.6 + - - -
856B ASP* 1.3 75.6 - - + +
858B HIS* 1.3 63.9 + - - +
860B GLN* 3.5 7.3 + - - -
862B PHE* 3.5 26.0 - - + -
863B ASN 3.9 0.4 - - - -
864B VAL 3.3 24.7 - - - -
865B LEU* 3.4 33.7 - - + -
877B ILE* 3.5 33.0 - - + -
879B THR* 4.7 1.3 + - - -
880B ALA* 5.7 0.2 - - + -
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Residues in contact with HIS 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B ARG 5.8 3.6 - - - -
455B ALA* 3.8 33.0 - - + +
854B MET 3.2 13.2 + - - +
855B ASN* 2.6 18.4 + - - +
857B PHE* 1.3 73.9 - - - +
859B HIS* 1.3 71.9 + + + +
860B GLN* 3.2 11.7 + - - +
877B ILE* 6.3 1.1 - - - -
878B PRO* 6.1 2.6 - - + +
879B THR* 5.3 10.6 + - + +
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Residues in contact with HIS 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B GLU* 2.7 36.2 + - + +
855B ASN* 2.9 12.6 + - + +
858B HIS* 1.3 97.5 - + + +
860B GLN* 1.3 62.3 + - - +
861B ARG* 2.8 46.3 + - + +
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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