Contacts of the helix formed by residues 84 - 92 (chain C) in PDB entry 1EFU
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 HIS 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C GLY* 1.3 69.1 - - - +
85C ALA* 1.3 67.9 + - - +
87C TYR* 3.2 4.2 + - - +
88C VAL* 3.0 39.0 + - + +
121C LEU* 3.4 38.6 - - + +
124C GLN* 2.8 31.6 + - + -
80D ASP* 2.9 21.5 + - - +
81D PHE* 3.6 18.7 - + + -
84D LYS* 3.2 35.0 + - + +
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C HIS* 1.3 85.9 + - - +
86C ASP* 1.3 57.7 + - - +
88C VAL* 3.3 2.9 + - - -
89C LYS* 2.9 27.3 + - - +
355C ASN* 3.0 24.2 + - - +
80D ASP* 3.1 13.2 + - - +
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Residues in contact with ASP 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C THR* 5.4 2.3 + - - -
82C PRO* 4.1 20.7 - - + +
83C GLY* 3.7 16.9 - - - +
85C ALA* 1.3 79.5 - - - +
87C TYR* 1.3 63.7 + - - +
89C LYS* 3.3 13.9 + - - +
90C ASN* 3.1 42.4 + - - +
80D ASP* 4.7 0.4 + - - -
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Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 4.8 8.5 - - + -
80C ASP 5.2 1.6 - - - -
81C CYS* 3.8 22.0 - - + -
82C PRO* 6.3 0.4 - - - +
83C GLY 2.9 20.1 + - - +
84C HIS 3.2 3.3 + - - +
86C ASP* 1.3 75.9 + - - +
88C VAL* 1.3 52.8 + - - +
90C ASN* 3.2 11.1 + - + +
91C MET* 2.8 43.0 + - + +
96C ALA* 3.5 26.3 - - + +
97C GLN* 3.7 2.1 + - - -
98C MET* 3.3 54.5 + - + +
121C LEU* 4.0 19.3 - - + -
125C VAL* 3.6 43.4 - - + +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C HIS* 3.0 36.6 + - + +
85C ALA* 3.5 7.9 - - - +
87C TYR* 1.3 74.9 - - - +
89C LYS* 1.3 64.0 + - - +
91C MET* 3.3 12.6 + - + +
92C ILE* 2.9 48.2 + - + +
121C LEU* 3.9 10.8 - - + -
124C GLN* 6.3 0.9 - - + -
125C VAL* 4.2 9.9 - - + -
307C GLU* 4.9 11.4 - - + +
355C ASN* 4.0 15.5 - - + +
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Residues in contact with LYS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ALA 2.9 17.2 + - - +
86C ASP* 3.5 13.4 + - - +
87C TYR 3.2 0.2 - - - -
88C VAL* 1.3 76.3 - - - +
90C ASN* 1.3 68.0 + - - +
92C ILE* 3.2 5.5 + - - +
93C THR* 2.9 35.8 + - + +
309C TYR* 3.4 41.9 + - + +
315C GLU* 2.9 25.4 + - - -
353C GLY 5.5 0.4 - - - +
355C ASN* 3.7 16.4 - - - +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C THR* 3.8 31.5 + - - +
86C ASP* 3.1 32.5 + - - +
87C TYR* 3.6 11.1 - - + +
89C LYS* 1.3 83.6 - - - +
91C MET* 1.3 65.6 + - - +
93C THR* 3.1 13.6 + - - -
94C GLY 3.2 0.7 + - - -
95C ALA* 2.8 49.1 + - + +
96C ALA* 4.2 2.7 - - + -
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Residues in contact with MET 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C TYR* 2.8 39.7 + - + +
88C VAL* 3.6 11.7 - - + +
90C ASN* 1.3 72.6 - - - +
92C ILE* 1.3 68.0 + - + +
96C ALA* 3.4 18.3 - - + +
97C GLN* 3.9 21.3 - - - +
125C VAL* 3.7 38.1 - - + +
307C GLU* 5.3 11.9 - - + -
373C ARG* 2.7 32.4 + - - -
387C VAL* 4.5 13.0 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL* 2.9 39.2 + - + +
89C LYS* 3.6 4.3 - - - +
91C MET* 1.3 77.1 - - - +
93C THR* 1.3 57.0 + - - +
94C GLY 2.9 5.1 + - - -
307C GLU* 3.8 24.9 - - + +
308C VAL 3.7 24.2 - - - +
309C TYR* 3.8 13.2 - - + +
355C ASN* 4.8 2.2 - - + +
373C ARG* 2.7 19.4 + - - +
385C ALA* 3.4 31.9 - - + +
386C GLY* 3.7 18.0 - - - +
387C VAL* 3.7 11.4 - - + +
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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