Contacts of the helix formed by residues 82 - 90 (chain B) in PDB entry 1E2R
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LEU 3.8 16.6 - - - +
73B ARG* 3.5 16.8 - - + +
74B LYS* 3.8 20.0 - - + -
80B ALA* 3.6 3.9 - - - +
81B LEU* 1.3 78.0 - - - +
83B PRO* 1.3 64.0 - - + +
84B ASP* 2.7 22.3 + - - -
85B LEU* 2.8 37.8 + - - +
86B THR* 3.0 10.5 + - - -
131B PRO* 4.7 3.8 - - + -
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Residues in contact with PRO 83 (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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38A ALA* 3.9 10.3 - - + -
73B ARG* 3.8 3.8 - - - +
82B THR* 1.3 87.6 - - - +
84B ASP* 1.3 62.2 + - - +
85B LEU 3.0 1.4 + - - -
86B THR* 3.2 11.6 - - - +
87B ARG* 3.0 58.1 + - - +
128B LEU 4.2 1.1 - - - +
129B LEU 3.4 26.7 - - - +
130B ASP* 4.1 1.8 - - - +
131B PRO* 3.6 27.4 - - + -
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Residues in contact with ASP 84 (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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36A ASP 5.2 7.6 - - - +
37A VAL* 5.7 0.4 - - - -
38A ALA* 3.7 23.5 - - + +
82B THR* 2.7 32.0 + - - -
83B PRO* 1.3 74.8 - - - +
85B LEU* 1.3 74.1 + - - +
87B ARG* 5.5 0.2 - - - -
88B ASP* 3.0 23.8 - - - +
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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
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80B ALA* 3.6 44.0 - - + +
82B THR* 2.8 14.8 + - - +
84B ASP* 1.3 100.0 - - - +
86B THR* 1.3 65.5 + - + +
87B ARG 3.3 1.1 - - - -
88B ASP* 3.2 17.3 + - - +
89B LEU* 3.3 20.2 + - + +
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Residues in contact with THR 86 (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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80B ALA 5.2 0.2 - - - +
81B LEU* 3.4 42.8 - - + +
82B THR 3.0 0.8 + - - -
83B PRO* 3.2 13.9 - - - +
85B LEU* 1.3 76.5 - - + +
87B ARG* 1.3 57.7 + - - +
89B LEU* 3.1 13.6 + - + +
90B GLY 2.9 25.1 + - - -
94B LEU* 4.1 25.8 - - + +
127B LEU* 2.8 28.0 + - + +
128B LEU* 3.5 9.4 - - - +
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Residues in contact with ARG 87 (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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38A ALA* 3.5 19.4 - - - +
39A ALA* 2.8 25.1 + - - +
51A ASP* 5.4 2.8 + - - -
43B PRO* 3.4 27.2 - - - +
44B GLU 5.3 2.5 - - - -
46B VAL* 4.0 14.0 - - + +
83B PRO* 3.0 34.6 + - - +
84B ASP* 5.4 0.4 - - - -
86B THR* 1.3 76.7 + - - +
88B ASP* 1.3 65.5 + - - +
90B GLY* 3.5 9.9 + - - -
128B LEU* 2.8 44.9 + - + +
130B ASP* 3.0 28.3 + - - +
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Residues in contact with ASP 88 (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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84B ASP 3.0 20.7 - - - +
85B LEU* 3.2 10.6 + - - +
86B THR 3.2 0.8 - - - -
87B ARG* 1.3 79.2 - - - +
89B LEU* 1.3 67.3 + - + +
90B GLY* 4.6 0.3 - - - -
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Residues in contact with LEU 89 (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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81B LEU* 5.9 0.7 - - + -
85B LEU* 3.4 18.2 - - + +
86B THR* 3.1 13.1 + - + +
88B ASP* 1.3 81.1 - - + +
90B GLY* 1.3 59.9 + - - +
93B TYR* 3.2 60.9 + - + +
94B LEU* 4.1 13.2 - - + -
601B HEC 3.5 26.2 - - + +
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Residues in contact with GLY 90 (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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86B THR 2.9 10.5 + - - -
87B ARG 3.5 8.9 + - - -
88B ASP 3.3 2.0 - - - -
89B LEU* 1.3 78.4 - - - +
91B PHE* 1.3 65.8 + - - -
92B ASP 3.3 2.9 - - - -
93B TYR 3.2 11.3 + - - -
94B LEU* 3.2 19.3 + - - +
128B LEU* 4.6 3.1 - - - -
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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
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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