Contacts of the helix formed by residues 83 - 92 (chain A) in PDB entry 4H3E
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 SER 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 5.4 6.0 - - - +
23A LEU 5.1 4.0 - - - -
24A PRO* 4.9 6.5 - - - -
26A LEU 3.6 13.2 - - - -
27A LEU* 3.8 15.3 - - - +
81A GLY 4.0 1.0 + - - -
82A LYS* 1.3 76.4 - - - +
84A ILE* 1.3 65.6 + - - +
85A GLU* 3.5 9.4 + - - +
86A GLU* 2.9 50.0 + - - +
87A ILE* 3.1 12.7 + - - +
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.0 38.8 + - + +
27A LEU 3.8 19.3 - - - +
28A LYS* 3.9 6.7 - - + +
34A ALA* 4.8 1.6 - - + -
71A LEU* 3.9 14.6 - - + -
82A LYS 3.8 0.2 + - - -
83A SER* 1.3 71.4 - - - +
85A GLU* 1.3 58.1 + - + +
87A ILE* 3.1 17.2 + - + +
88A ILE* 3.0 33.1 + - + +
104A ALA* 3.4 31.0 - - + +
107A HIS* 3.7 31.0 - - + +
108A PHE* 4.2 8.5 - - + +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR 4.5 3.2 - - - +
21A ALA* 3.6 13.2 - - + +
22A THR* 2.7 30.6 + - - -
23A LEU* 2.7 39.3 + - - +
26A LEU* 4.7 0.9 + - - +
83A SER* 3.1 7.2 + - - +
84A ILE* 1.3 75.5 - - - +
86A GLU* 1.3 64.3 + - + +
88A ILE* 3.3 8.9 + - - +
89A LEU* 3.1 25.0 + - - +
108A PHE* 3.5 30.4 - - + -
183A LEU* 3.8 23.2 - - + +
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLY 4.6 1.2 - - - +
82A LYS* 3.6 34.9 - - + +
83A SER* 2.9 49.6 + - - +
85A GLU* 1.3 76.6 - - + +
87A ILE* 1.3 58.0 + - - +
89A LEU* 3.8 6.1 - - - +
90A ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 4.1 20.4 - - + -
71A LEU* 5.0 9.2 - - + -
75A ALA* 5.7 1.3 - - + -
79A TYR* 3.7 45.1 - - + +
82A LYS* 4.2 6.7 - - + -
83A SER 3.1 15.0 + - - +
84A ILE* 3.1 20.2 + - + +
86A GLU* 1.3 73.3 - - - +
88A ILE* 1.3 66.7 + - - +
90A ALA* 3.2 7.1 + - - +
91A VAL* 2.9 29.0 + - + +
100A LEU* 4.5 21.1 - - + -
104A ALA* 4.0 18.6 - - + -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.0 23.7 + - + +
85A GLU* 3.3 10.5 + - - +
87A ILE* 1.3 75.3 - - - +
89A LEU* 1.3 58.8 + - - +
91A VAL* 3.3 4.4 + - - -
92A ALA* 3.0 28.4 + - - +
101A PHE* 3.7 24.0 - - + +
104A ALA* 3.7 22.2 - - + +
105A ALA* 3.7 28.0 - - + +
108A PHE* 3.7 21.3 - - + -
181A CYS* 4.4 5.8 - - + -
183A LEU* 4.2 15.9 - - + -
184A THR* 4.1 13.7 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU 3.1 13.4 + - - +
86A GLU* 3.8 6.7 - - - +
88A ILE* 1.3 78.2 - - - +
90A ALA* 1.3 66.4 + - - +
91A VAL 3.1 1.0 + - - -
92A ALA* 3.4 16.4 + - + +
93A ASN 5.1 0.2 + - - -
183A LEU* 3.8 31.0 - - + +
184A THR* 4.5 10.1 - - + +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 4.9 9.4 - - + -
82A LYS* 6.5 0.9 - - + -
86A GLU 2.9 19.5 + - - +
87A ILE* 3.6 7.6 - - - +
89A LEU* 1.3 76.8 - - - +
91A VAL* 1.3 65.8 + - + +
92A ALA 3.8 0.2 + - - -
93A ASN 5.2 0.7 + - - -
94A ASP* 4.8 4.9 - - - +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A TYR* 3.5 31.9 - - + +
87A ILE* 2.9 29.8 + - + +
88A ILE* 3.9 3.8 - - - +
90A ALA* 1.3 80.7 - - + +
92A ALA* 1.3 65.1 + - - +
93A ASN 3.2 4.3 + - - -
94A ASP* 3.2 21.4 + - + +
97A LYS* 3.6 26.5 - - + -
98A LYS* 5.6 0.7 - - - +
100A LEU* 4.3 4.0 - - + -
101A PHE* 3.7 39.5 - - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE 3.0 16.2 + - - +
89A LEU* 3.4 13.3 + - + +
90A ALA 3.6 0.2 - - - -
91A VAL* 1.3 77.5 - - - +
93A ASN* 1.3 76.5 + - - +
94A ASP 3.5 0.6 + - - -
98A LYS* 5.5 6.4 - - - +
101A PHE* 3.6 17.6 - - + -
184A THR* 3.7 29.6 - - + -
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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