Contacts of the helix formed by residues 73 - 85 (chain B) in PDB entry 3ER8
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 THR 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.6 16.5 + - - -
71B PRO* 3.4 13.6 - - - +
72B GLY* 1.3 75.5 - - - +
74B HIS* 1.3 65.8 + - - +
75B ILE 2.9 2.1 + - - -
76B ARG* 2.9 22.2 + - - +
100B ASP* 3.3 30.7 + - - +
102B ILE* 3.4 18.9 - - + +
293B PHE* 3.7 14.8 - - + -
294B LEU* 5.8 2.2 - - + -
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLN* 3.5 20.8 + - - +
42B LEU* 3.8 24.8 - - + +
43B LEU* 3.8 42.0 - - + +
46B GLU* 2.8 35.0 + - - -
66B TYR* 3.6 5.4 + - - -
69B SER* 5.4 0.7 - - - -
72B GLY* 3.7 14.8 - - - -
73B THR* 1.3 80.6 - - - +
75B ILE* 1.3 79.3 + - + +
77B TYR* 2.9 18.6 + - - +
78B LEU* 3.2 15.5 + - + +
293B PHE* 4.1 11.7 - - - -
294B LEU* 4.6 5.1 - - + +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 4.2 0.7 - - - +
66B TYR* 3.5 32.1 - - + -
69B SER* 3.8 27.6 - - - +
72B GLY* 3.5 14.1 - - - +
73B THR 2.9 0.8 + - - -
74B HIS* 1.3 98.2 - - + +
76B ARG* 1.3 56.5 + - - +
78B LEU* 4.2 5.6 - - + -
79B ARG* 2.7 30.3 + - + +
91B TRP* 4.2 31.0 - - + -
93B LEU* 4.1 21.3 - - + -
103B LEU* 4.4 6.5 - - + -
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Residues in contact with ARG 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR 2.9 14.8 + - - +
75B ILE* 1.3 78.0 - - - +
77B TYR* 1.3 60.2 + - - +
79B ARG* 3.1 7.4 + - - +
80B ASP* 2.5 64.5 + - - +
102B ILE* 2.6 60.1 + - + +
103B LEU* 3.8 12.9 - - + +
106B LEU* 4.1 30.7 - - - +
293B PHE* 3.8 13.5 - - + -
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.7 26.2 - - + -
47B LEU* 4.4 9.7 - - + +
74B HIS 2.9 10.0 + - - +
76B ARG* 1.3 77.0 - - - +
78B LEU* 1.3 60.4 + - + +
80B ASP* 2.9 8.5 + - + +
81B HIS* 2.7 56.0 + + + -
286B LEU* 4.7 9.4 + - - +
289B SER* 3.2 30.8 + - - -
290B ILE* 3.7 31.5 - - + +
293B PHE* 3.5 47.2 - + + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.2 30.3 - - + +
46B GLU* 3.1 40.8 - - + +
47B LEU* 3.6 34.3 - - + +
50B LEU* 4.7 3.6 - - + -
74B HIS* 3.2 15.0 + - + +
75B ILE* 3.5 11.7 - - + +
77B TYR* 1.3 80.9 - - - +
79B ARG* 1.3 64.7 + - - +
81B HIS* 3.3 3.3 + - - +
82B PHE* 3.2 33.3 + - + -
91B TRP* 4.0 22.4 - - + -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 2.7 17.9 + - + +
76B ARG* 3.1 15.8 - - - +
78B LEU* 1.3 73.8 - - - +
80B ASP* 1.3 79.7 + - - +
82B PHE* 4.2 2.1 - - - +
83B TYR* 3.2 55.8 + - - +
84B ASN* 6.0 0.2 - - - +
91B TRP* 4.0 23.9 + - + +
103B LEU* 5.8 0.9 - - + -
106B LEU* 3.8 37.8 - - + +
107B ARG 5.4 0.4 - - - +
108B ASP* 2.7 42.9 + - - +
109B VAL* 3.9 9.6 - - + -
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 2.5 49.5 + - - +
77B TYR* 2.9 9.8 + - + +
79B ARG* 1.3 102.4 + - - +
81B HIS* 1.3 68.3 + - - +
83B TYR* 4.2 3.4 - - - -
84B ASN* 3.0 36.4 + - - +
293B PHE* 5.0 1.4 - - - -
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.4 27.5 - - + +
51B SER* 4.6 2.0 + - - -
77B TYR* 2.7 39.6 + + + +
78B LEU 3.7 4.5 - - - +
80B ASP* 1.3 73.2 - - - +
82B PHE* 1.3 75.7 + + - +
84B ASN* 3.5 7.9 + - - +
85B LEU* 3.1 42.6 + - + +
270B VAL* 3.5 19.9 - - + +
271B TYR 2.9 23.9 + - - -
272B CYS* 4.9 6.6 - - + -
286B LEU* 5.0 10.2 - - + +
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Residues in contact with PHE 82 (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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47B LEU* 4.2 11.2 - - + -
50B LEU* 3.5 41.1 - - + -
51B SER* 4.0 9.9 - - - -
54B GLN* 3.4 26.2 - - - -
59B LEU* 3.5 22.9 - - + -
78B LEU* 3.2 31.6 + - + +
79B ARG 4.3 2.5 - - - +
80B ASP 3.2 0.2 - - - -
81B HIS* 1.3 92.2 - + - +
83B TYR* 1.3 70.4 + - - +
85B LEU* 2.9 13.3 + - + +
87B VAL* 3.3 35.6 + - + +
89B ILE* 4.5 10.5 - - + -
91B TRP* 4.2 13.0 - + + +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 3.2 52.5 + - - +
80B ASP* 3.2 7.9 + - - +
82B PHE* 1.3 77.2 - - - +
84B ASN* 1.3 71.5 + - - +
86B GLY* 2.8 24.4 + - - -
87B VAL 4.2 8.2 + - - +
108B ASP* 4.1 9.9 - - + +
99C GLU* 2.7 31.8 + - + +
211C ARG* 3.0 30.2 + - - -
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Residues in contact with ASN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 6.0 0.2 - - - +
80B ASP* 3.0 28.3 + - - +
81B HIS* 3.6 6.4 + - - +
83B TYR* 1.3 89.7 - - - +
85B LEU* 1.3 60.9 + - + +
86B GLY* 3.1 1.7 + - - -
273B ASN* 3.9 11.8 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN* 4.1 23.1 + - - +
81B HIS* 3.1 46.7 + - + +
82B PHE* 2.9 14.2 + - + +
84B ASN* 1.3 76.4 - - + +
86B GLY* 1.3 55.2 + - - +
87B VAL* 3.1 15.9 + - + +
271B TYR* 3.1 23.6 - - + +
272B CYS* 4.2 1.1 - - - +
273B ASN* 3.7 51.3 + - + +
256C ASN* 5.5 2.9 + - - +
258C ARG* 5.1 10.5 - - + +
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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