Contacts of the helix formed by residues 67 - 82 (chain G) in PDB entry 2EHO
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 67 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G GLU 4.7 2.7 - - - +
65G TRP 2.6 10.6 + - - -
66G MSE 1.3 72.2 - - - +
68G VAL* 1.3 62.2 + - - +
69G GLU* 3.2 17.7 + - - +
70G LYS* 2.5 73.9 + - + +
71G LEU* 2.8 13.6 + - - +
113G ILE* 3.9 1.3 - - - -
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Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G MSE 3.9 0.2 + - - -
67G ASP* 1.3 74.9 - - - +
69G GLU* 1.3 67.9 + - + +
72G GLU* 3.3 16.7 + - - +
108G PRO 5.4 0.4 + - - +
109G LYS* 3.7 25.8 - - + -
112G GLU* 3.2 33.7 - - + +
113G ILE* 3.1 27.5 - - + +
116G LEU* 3.0 33.0 - - + +
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Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ASP* 3.0 17.1 + - - +
68G VAL* 1.3 84.8 - - + +
70G LYS* 1.3 57.1 + - - +
72G GLU* 3.9 14.2 - - - +
73G LYS* 3.4 29.2 + - - +
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Residues in contact with LYS 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU 3.4 17.7 - - - +
65G TRP* 3.2 30.8 + - - +
67G ASP* 2.5 48.4 + - + +
69G GLU* 1.3 70.5 - - + +
71G LEU* 1.3 56.8 + - - +
72G GLU 2.9 5.4 - - - -
73G LYS* 2.9 43.6 + - + +
74G MSE 3.3 19.2 + - - +
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G TRP* 3.4 44.9 - - + +
66G MSE 4.5 0.9 - - - -
67G ASP 2.8 13.2 + - - +
70G LYS* 1.3 71.9 - - - +
72G GLU* 1.3 56.5 + - - +
73G LYS 3.3 0.2 - - - -
74G MSE 3.8 19.9 - - - +
75G ARG* 2.8 29.5 + - - +
88G PRO* 4.8 1.3 - - + -
113G ILE* 3.8 21.1 - - + -
116G LEU* 3.3 21.4 - - + +
117G VAL* 3.5 32.5 - - + -
120G MSE 3.5 23.2 - - + +
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Residues in contact with GLU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G VAL* 3.3 25.1 + - - +
69G GLU* 3.9 11.7 - - - +
70G LYS 2.9 0.2 - - - -
71G LEU* 1.3 78.3 - - - +
73G LYS* 1.3 63.8 + - - +
75G ARG* 3.4 26.5 + - - +
76G ASP* 2.7 32.3 + - - +
116G LEU* 3.5 9.8 - - + +
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Residues in contact with LYS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLU* 3.4 31.5 + - - +
70G LYS* 2.9 24.3 + - + +
72G GLU* 1.3 79.1 - - + +
74G MSE 1.3 54.1 + - + +
76G ASP* 3.3 4.3 + - - +
77G HIS* 2.8 35.5 + - - +
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Residues in contact with MSE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G LYS* 3.3 19.7 + - - +
71G LEU* 3.9 26.7 - - - +
72G GLU 3.2 0.2 - - - -
73G LYS* 1.3 74.8 - - + +
75G ARG* 1.3 59.5 + - - +
76G ASP 2.9 2.1 + - - -
77G HIS* 3.9 11.7 - - + -
78G GLU* 2.7 35.7 + - - +
85G THR* 5.2 4.9 - - + +
86G PRO 3.5 24.7 - - - +
87G MSE 4.1 7.2 - - + -
88G PRO* 3.6 33.0 - - + -
120G MSE 3.8 17.7 - - - -
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Residues in contact with ARG 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LEU 2.8 24.2 + - - +
72G GLU* 3.6 19.9 + - - +
74G MSE 1.3 73.0 - - - +
76G ASP* 1.3 89.1 + - - +
78G GLU* 3.9 3.7 - - - +
79G ARG* 3.3 51.0 + - - +
116G LEU* 3.7 28.6 - - - +
119G ASP* 2.8 42.2 + - + +
120G MSE 3.8 19.7 - - + +
123G THR* 5.3 2.0 + - + +
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Residues in contact with ASP 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 2.7 22.6 + - - +
73G LYS* 3.6 7.4 - - - +
74G MSE 3.0 0.4 - - - -
75G ARG* 1.3 107.8 + - - +
77G HIS* 1.3 59.6 + - - +
78G GLU 3.0 1.8 - - - -
79G ARG* 2.7 35.7 + - - +
80G LYS* 3.1 14.3 + - - +
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Residues in contact with HIS 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G LYS 2.8 23.3 + - - +
74G MSE 3.6 11.0 - - + +
76G ASP* 1.3 72.3 - - - +
78G GLU* 1.3 62.6 + - - +
80G LYS* 4.0 25.1 + - - +
81G GLU* 3.2 59.7 + - + +
85G THR* 3.4 32.0 - - + +
86G PRO* 5.1 3.8 - - + +
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Residues in contact with GLU 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G MSE 2.7 19.7 + - - +
75G ARG* 3.9 7.9 - - - +
77G HIS* 1.3 75.5 - - - +
79G ARG* 1.3 66.0 + - - +
81G GLU* 3.6 5.0 + - - +
84G PHE* 3.6 2.0 - - - -
85G THR* 2.6 47.7 + - - -
87G MSE 4.1 13.5 - - + -
120G MSE 4.9 8.3 - - + -
123G THR* 4.1 9.4 + - - +
124G ARG* 3.3 32.4 + - + +
127G LYS* 3.0 53.8 + - - +
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Residues in contact with ARG 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G ARG* 3.3 44.7 - - - +
76G ASP* 2.7 17.5 + - - +
78G GLU* 1.3 67.6 - - - +
80G LYS* 1.3 69.7 + - - +
81G GLU 2.8 1.9 + - - -
82G GLU* 2.9 15.9 + - - -
119G ASP* 5.3 2.0 - - - -
123G THR* 4.7 23.3 - - + +
127G LYS* 4.3 3.6 + - - +
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Residues in contact with LYS 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G ASP 3.1 9.8 + - - +
77G HIS* 4.0 30.6 + - - +
79G ARG* 1.3 78.0 - - - +
81G GLU* 1.3 71.9 + - - +
82G GLU* 3.2 5.4 + - - +
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Residues in contact with GLU 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G HIS* 3.2 50.4 + - + +
78G GLU 3.6 6.7 - - - +
79G ARG 2.8 4.4 + - - -
80G LYS* 1.3 80.6 - - - +
82G GLU* 1.3 58.7 + - - +
83G THR* 2.6 53.5 + - - +
84G PHE 5.2 1.6 - - - +
85G THR* 3.9 8.5 - - - +
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Residues in contact with GLU 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G ARG 2.9 17.0 + - - -
80G LYS 3.2 4.9 + - - +
81G GLU* 1.3 73.9 - - - +
83G THR* 1.3 66.1 + - - +
127G LYS* 3.0 28.1 - - - +
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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
------------------------------------------------------------
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