Contacts of the helix formed by residues 72 - 80 (chain A) in PDB entry 5JEI
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 ASN 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASP* 3.2 12.3 - - - +
60A LYS* 3.1 30.7 - - + +
62A GLY* 3.3 14.4 + - - -
63A ALA* 2.9 40.4 + - - +
70A ILE* 3.8 1.7 + - + +
71A TRP* 1.3 73.9 - - - +
73A GLY* 1.3 65.7 + - - +
75A VAL* 4.1 0.9 - - - +
76A GLY* 2.9 19.1 + - - -
140A SER* 4.6 6.9 + - - -
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Residues in contact with GLY 73 (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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56A VAL* 3.5 6.6 - - - +
58A ASP* 2.9 26.2 + - - -
60A LYS* 3.0 24.7 - - - -
61A TYR 4.0 2.0 - - - -
72A ASN* 1.3 71.8 - - - +
74A MET* 1.3 67.1 + - - -
76A GLY* 3.1 1.4 + - - -
77A GLU* 3.1 23.9 + - - +
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Residues in contact with MET 74 (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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9A THR* 3.5 31.2 - - + +
10A THR* 3.6 20.0 - - - +
11A ILE* 3.6 17.3 - - + -
56A VAL* 3.9 13.7 - - + -
60A LYS 3.1 3.4 + - - +
61A TYR* 3.0 47.6 + - + +
73A GLY* 1.3 67.9 - - - -
75A VAL* 1.3 67.3 + - - +
77A GLU* 3.1 12.4 + - - +
78A LEU* 3.2 18.9 + - - +
86A ALA* 4.6 7.9 - - + -
88A ALA* 3.4 28.9 - - + -
90A LEU* 4.1 12.6 - - + -
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Residues in contact with VAL 75 (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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61A TYR 3.2 12.2 + - - +
62A GLY* 3.9 6.7 - - - -
71A TRP* 3.4 35.0 - - + -
73A GLY 3.2 0.4 - - - -
74A MET* 1.3 75.1 - - - +
76A GLY* 1.3 58.8 + - - +
78A LEU* 3.1 8.3 + - - +
79A VAL* 2.9 36.8 + - + +
90A LEU* 4.2 9.0 - - + -
96A ARG* 3.8 31.4 - - + +
99A VAL* 4.3 6.3 - - + -
100A ILE* 4.1 23.6 - - + -
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Residues in contact with GLY 76 (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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71A TRP* 3.7 25.7 - - - +
72A ASN 2.9 17.6 + - - -
73A GLY 3.1 4.5 + - - -
75A VAL* 1.3 77.4 - - - +
77A GLU* 1.3 63.8 + - - +
79A VAL* 4.4 0.9 - - - -
80A TYR* 2.9 37.3 + - - +
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Residues in contact with GLU 77 (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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9A THR* 3.8 22.4 - - - +
54A THR* 6.2 0.3 - - - +
56A VAL* 4.1 12.7 - - + +
57A GLY 5.4 4.4 + - - -
73A GLY 3.1 19.4 + - - +
74A MET 3.1 7.4 + - - +
76A GLY* 1.3 77.4 - - - +
78A LEU* 1.3 59.9 + - - +
81A GLY 3.5 0.2 + - - -
82A LYS* 2.9 59.4 + - - +
83A ALA* 3.1 18.3 + - + +
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Residues in contact with LEU 78 (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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9A THR* 4.5 0.9 - - + -
74A MET 3.2 11.7 + - - +
75A VAL* 3.1 7.2 + - - +
77A GLU* 1.3 75.5 - - - +
79A VAL* 1.3 65.3 + - - +
81A GLY* 3.2 12.6 + - - -
83A ALA* 3.6 23.1 - - + +
84A ASP 4.0 2.5 - - - -
85A ILE* 3.6 31.2 - - - +
86A ALA* 4.0 10.8 - - + -
90A LEU* 5.1 0.7 - - + -
100A ILE* 4.0 23.6 - - + -
223A ALA* 3.6 35.2 - - + +
224A THR 4.2 2.5 - - - +
225A PRO* 4.0 28.9 - - + +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A TRP* 4.3 12.8 - - + -
75A VAL* 2.9 34.3 + - + +
76A GLY* 4.0 5.4 - - - +
78A LEU* 1.3 72.8 - - - +
80A TYR* 1.3 85.9 + - + +
81A GLY* 3.3 1.1 + - - -
99A VAL* 4.1 21.3 - - + +
100A ILE* 3.7 21.5 - - + -
225A PRO* 6.0 0.7 - - - -
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Residues in contact with TYR 80 (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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69A LYS 4.1 3.5 + - - -
70A ILE* 3.3 21.8 - - + +
71A TRP* 3.0 53.1 + - + +
76A GLY* 2.9 28.5 + - - +
79A VAL* 1.3 93.8 - - + +
81A GLY* 1.3 60.9 + - - +
82A LYS* 3.4 19.5 + - + +
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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