Contacts of the helix formed by residues 101 - 109 (chain F) in PDB entry 3E2A
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 CYS 101 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F CYS* 3.8 5.4 - - - -
44F ASP* 3.0 4.9 - - - -
67F ALA* 4.3 7.4 - - - -
68F ASN* 5.0 2.0 - - - -
98F HIS* 3.5 21.1 - - - +
99F THR 3.2 0.6 - - - -
100F ASN* 1.3 74.6 - - - +
102F GLY* 1.3 64.0 + - - +
103F GLY* 3.7 2.7 - - - -
104F ILE* 3.6 36.4 - - + +
105F HIS* 3.0 29.0 + - - -
147F THR* 4.6 4.8 + - + +
230F ZN 2.3 37.5 - - - -
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Residues in contact with GLY 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D HIS* 6.1 2.0 - - - -
83D TYR* 3.8 11.2 + - - -
44F ASP* 2.8 18.8 + - - +
100F ASN 3.5 5.3 + - - -
101F CYS* 1.3 68.5 - - - +
103F GLY* 1.3 53.9 + - - -
105F HIS* 3.3 6.3 + - - +
106F ALA* 2.7 36.6 + - - +
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D TYR* 4.2 1.7 + - - -
44F ASP* 3.1 14.2 + - - -
66F VAL* 3.7 28.9 - - - -
67F ALA* 4.5 8.5 - - - -
101F CYS* 4.2 3.1 - - - -
102F GLY* 1.3 75.6 - - - +
104F ILE* 1.3 50.8 + - - +
106F ALA* 3.2 7.8 + - - +
107F ALA* 2.7 35.0 + - - +
120F LEU* 4.1 4.3 - - - +
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Residues in contact with ILE 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ALA* 4.4 6.7 - - + -
68F ASN* 6.1 0.2 - - - +
101F CYS* 3.4 28.2 + - + +
102F GLY 3.3 0.2 - - - -
103F GLY* 1.3 74.8 - - - +
105F HIS* 1.3 63.8 + - + +
107F ALA* 3.2 6.8 + - - +
108F MET* 3.1 29.7 + - - +
123F ILE* 4.1 19.5 - - + -
143F ALA* 3.8 13.9 - - + +
146F LEU* 4.1 16.8 - - + +
147F THR* 3.6 33.4 - - + +
150F ASN* 3.9 31.9 - - + +
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ASN* 4.7 9.4 + - - -
101F CYS 3.0 35.0 + - - +
102F GLY* 3.8 6.5 - - - +
104F ILE* 1.3 74.6 - - + +
106F ALA* 1.3 65.6 + - - +
108F MET* 3.2 9.0 + - - +
109F ALA* 3.1 23.6 + - - +
143F ALA* 3.4 31.4 - - + +
144F ASP* 5.6 2.0 + - - -
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D TYR* 4.0 15.9 - - + +
102F GLY 2.7 22.3 + - - +
103F GLY* 3.4 6.3 - - - +
105F HIS* 1.3 75.2 - - - +
107F ALA* 1.3 61.4 + - - +
108F MET 3.3 0.5 + - - -
109F ALA* 3.4 19.7 + - - +
111F LYS 5.4 1.2 - - - +
113F LEU* 4.0 23.7 - - + +
117F ASN* 5.4 1.0 - - - +
120F LEU* 4.0 18.4 - - + +
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Residues in contact with ALA 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLY 2.7 19.6 + - - +
104F ILE 3.2 6.7 + - - +
106F ALA* 1.3 74.1 - - - +
108F MET* 1.3 57.0 + - + +
109F ALA 4.0 0.6 - - - +
120F LEU* 3.9 23.5 - - + +
123F ILE* 3.7 36.3 - - + -
124F ARG* 3.1 35.9 + - + +
127F TRP* 4.2 0.6 - - - -
146F LEU* 5.4 0.2 - - + -
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Residues in contact with MET 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F ILE* 3.1 18.2 + - - +
105F HIS* 3.2 8.9 + - - +
107F ALA* 1.3 74.7 - - - +
109F ALA* 1.3 67.5 + - - +
110F ASP* 3.6 7.3 + - - +
124F ARG* 3.7 2.1 + - - -
127F TRP* 3.7 45.5 - - + +
134F LEU* 6.0 0.4 - - + -
142F ARG* 3.8 32.5 - - + +
143F ALA* 3.6 32.8 - - - +
146F LEU* 3.7 28.3 - - + -
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F HIS 3.1 12.6 + - - +
106F ALA* 3.4 19.5 + - - +
107F ALA 4.0 0.2 - - - +
108F MET* 1.3 81.5 - - - +
110F ASP* 1.3 63.4 + - - +
111F LYS* 3.2 17.3 + - + +
113F LEU* 5.9 3.1 - - + -
117F ASN* 5.8 0.3 + - - -
124F ARG* 3.3 12.3 + - - -
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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