Contacts of the helix formed by residues 82 - 92 (chain B) in PDB entry 3E4E
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 GLY 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B HIS* 1.3 76.5 - - - +
83B TYR* 1.3 62.0 + - - -
84B LYS 3.4 2.2 - - - -
85B ALA 3.7 1.1 + - - -
86B VAL* 2.9 31.8 + - - +
395B SER* 2.9 30.8 + - - -
396B VAL* 4.3 1.1 - - - -
399B ASP* 5.9 1.1 - - - -
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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
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82B GLY* 1.3 70.9 - - - -
84B LYS* 1.3 67.1 + - + +
87B LYS* 2.8 62.5 + - + +
395B SER 4.9 0.6 + - - -
396B VAL* 3.9 30.5 - - + +
399B ASP* 4.7 6.3 + - - +
425B ASP* 2.3 50.8 + - - +
426B TYR* 3.6 51.8 - + + -
428B LYS* 5.4 3.6 - - + -
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 3.4 0.4 - - - -
83B TYR* 1.3 88.9 - - + +
85B ALA* 1.3 65.0 + - - +
87B LYS* 3.7 2.8 - - - +
88B GLU* 3.1 32.1 + - + +
379B ARG* 3.6 19.5 - - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO* 3.7 34.9 - - + +
67B VAL* 4.6 2.0 - - + -
80B MET* 3.7 14.9 - - + +
81B HIS 3.8 12.3 - - - +
82B GLY 3.7 2.0 + - - -
83B TYR 3.4 0.2 - - - -
84B LYS* 1.3 79.2 - - - +
86B VAL* 1.3 61.8 + - - +
88B GLU* 3.5 3.2 + - - +
89B ALA* 3.1 24.6 + - - +
378B PHE* 4.2 2.2 - - + -
379B ARG* 3.4 19.5 - - - +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 3.3 32.8 - - + +
82B GLY 2.9 28.9 + - - +
83B TYR* 4.1 0.4 - - + +
85B ALA* 1.3 70.9 - - - +
87B LYS* 1.3 64.6 + - - +
89B ALA* 3.2 3.7 + - - +
90B LEU* 3.0 48.4 + - + +
391B PRO* 4.2 6.7 - - + +
392B THR 3.4 23.1 - - - +
393B LEU* 4.7 5.2 - - + -
396B VAL* 3.7 20.2 - - + -
428B LYS* 6.3 1.6 - - + -
432B THR* 6.1 0.2 - - + -
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.8 62.2 + - + +
84B LYS* 3.7 3.1 - - - +
86B VAL* 1.3 72.2 - - - +
88B GLU* 1.3 54.7 + - + +
90B LEU* 3.1 3.7 + - - -
91B LEU* 2.6 69.5 + - + +
92B ASP* 4.9 1.1 - - - +
425B ASP* 3.7 15.9 + - - -
428B LYS* 5.9 3.6 - - + +
432B THR* 5.5 4.3 - - + -
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Residues in contact with GLU 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 LYS* 3.1 27.3 + - + +
85B ALA 3.8 4.0 - - - +
87B LYS* 1.3 77.7 - - + +
89B ALA* 1.3 58.5 + - - +
92B ASP* 3.0 49.2 + - - +
93B TYR* 3.2 20.1 + - + -
378B PHE* 4.1 14.1 - - + -
379B ARG* 2.5 45.3 + - - +
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Residues in contact with ALA 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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80B MET* 4.0 33.0 - - + -
85B ALA 3.1 17.0 + - - +
86B VAL* 3.6 4.7 - - - +
87B LYS 3.1 0.6 - - - -
88B GLU* 1.3 76.8 - - - +
90B LEU* 1.3 63.9 + - - +
93B TYR 3.5 10.9 - - - +
94B LYS* 4.7 0.3 - - - -
97B PHE* 3.3 33.6 - - + +
378B PHE* 4.2 4.5 - - + -
389B VAL* 5.0 2.0 - - + -
391B PRO* 4.7 9.2 - - + -
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Residues in contact with LEU 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 VAL* 3.0 40.9 + - + +
87B LYS 3.9 0.4 - - - +
89B ALA* 1.3 83.8 - - - +
91B LEU* 1.3 58.7 + - - +
92B ASP 3.8 0.2 - - - -
94B LYS* 3.7 14.5 - - - +
97B PHE* 6.0 0.4 - - + -
367B ASN* 4.1 3.1 - - - +
370B HIS* 3.7 26.2 - - + +
391B PRO* 3.6 31.2 - - + -
393B LEU* 4.8 2.9 - - + -
431B SER* 4.0 14.4 - - - +
432B THR* 3.4 38.8 - - + +
433B GLY* 3.5 19.8 - - - -
434B LYS 4.4 0.7 + - - -
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Residues in contact with LEU 91 (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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87B LYS* 2.6 54.0 + - + +
90B LEU* 1.3 82.5 - - - +
92B ASP* 1.3 69.2 + - - +
94B LYS* 3.3 30.7 + - - +
428B LYS* 6.3 1.3 - - - -
432B THR* 3.8 25.6 - - + +
433B GLY* 3.8 20.0 - - - +
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Residues in contact with ASP 92 (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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87B LYS* 4.4 1.4 - - - +
88B GLU* 3.0 36.2 + - - +
91B LEU* 1.3 90.8 - - - +
93B TYR* 1.3 71.1 + - + +
94B LYS* 3.2 12.4 + - - +
96B GLU* 4.1 6.2 - - - +
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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