Contacts of the helix formed by residues 72 - 83 (chain J) in PDB entry 7C97
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 72 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21J TYR* 4.1 12.3 - - - -
24J GLN* 3.4 19.4 + - - -
25J VAL* 3.8 23.3 - - - -
60J PRO* 4.3 14.2 - - - +
70J TRP 3.7 0.2 - - - -
71J GLU* 1.3 70.0 + - - +
73J ARG* 1.3 58.2 + - - +
74J ILE 3.1 0.7 - - - -
75J ILE* 3.4 15.2 - - - +
76J MET* 2.6 47.4 + - - +
160J TYR* 5.0 0.3 + - - -
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Residues in contact with ARG 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I ARG* 3.3 47.2 - - - +
74I ILE* 3.2 34.4 - - - +
100I ARG* 5.8 0.9 - - - -
71J GLU* 2.6 35.6 + - - +
72J SER* 1.3 77.2 + - - +
74J ILE* 1.3 59.0 + - + -
76J MET* 4.1 6.3 - - - +
77J GLU* 3.5 38.1 + - - +
100J ARG* 4.3 5.4 + - - +
103J MET* 3.6 30.2 - - - +
104J HIS* 3.8 24.3 + - - +
107J GLU* 6.2 2.0 - - - +
160J TYR* 4.6 2.9 + - - +
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Residues in contact with ILE 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I GLY* 3.9 22.8 - - - +
100I ARG* 3.2 38.8 - - + +
101I LEU* 3.3 26.7 - - + -
104I HIS* 3.8 14.6 - - + -
69J LEU* 4.0 19.7 - - + -
70J TRP 3.7 9.6 - - - +
71J GLU* 2.5 27.4 + - - +
73J ARG* 1.3 73.4 - - + +
75J ILE* 1.3 66.2 + - - +
77J GLU* 3.8 2.5 + - - +
78J TYR* 3.3 18.0 + - - +
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Residues in contact with ILE 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LEU* 5.7 0.9 - - + -
25J VAL* 4.1 16.8 - - + -
60J PRO* 4.3 18.4 - - + +
61J THR* 4.3 1.8 - - - +
62J LEU* 4.0 29.6 - - + +
69J LEU* 3.5 43.5 - - + +
70J TRP* 4.1 9.0 - - - +
71J GLU 3.8 0.2 + - - -
72J SER* 3.0 19.4 + - - +
74J ILE* 1.3 77.2 - - - +
76J MET* 1.3 60.4 + - - +
78J TYR* 2.9 29.2 + - - +
79J LEU* 3.2 24.5 + - + +
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Residues in contact with MET 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J GLN* 3.5 11.7 - - + +
25J VAL* 4.6 13.0 - - + -
28J VAL* 3.5 25.5 - - + +
72J SER* 2.6 44.1 + - - +
73J ARG* 4.6 1.3 - - - +
75J ILE* 1.3 75.7 - - - +
77J GLU* 1.3 62.6 + - + +
79J LEU* 3.5 7.5 + - - +
80J ASP* 3.1 22.3 + - - +
156J LEU* 4.2 19.0 - - + +
159J CYS* 3.9 27.8 - - - -
160J TYR* 3.0 39.3 - - + +
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Residues in contact with GLU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I ARG* 4.0 23.2 + - - +
73J ARG* 3.5 37.9 + - - +
74J ILE* 4.4 2.5 - - - +
75J ILE 3.3 0.8 - - - -
76J MET* 1.3 77.0 - - + +
78J TYR* 1.3 60.3 + - - +
80J ASP* 3.8 7.4 - - - +
81J GLU* 2.9 34.7 + - - +
89J MET* 4.8 15.9 - - + +
100J ARG* 2.7 48.6 + - - +
103J MET* 5.0 6.4 - - + +
156J LEU* 5.8 5.2 - - + -
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Residues in contact with TYR 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I PRO* 3.3 33.7 - - + -
94I VAL* 4.4 5.5 - - - +
97I GLY* 4.9 8.7 - - - -
11J MET* 5.0 4.7 - - + +
62J LEU* 4.5 8.5 - - + -
64J ASP* 2.6 23.0 + - - -
67J LEU* 4.5 8.8 - - + +
69J LEU* 4.1 20.6 - - + -
74J ILE 3.3 13.6 + - - +
75J ILE 2.9 10.6 + - - +
77J GLU* 1.3 73.2 - - - +
79J LEU* 1.3 92.9 + - + +
81J GLU* 2.9 7.9 + - - +
82J ARG* 2.4 78.0 + - + +
83J PHE* 5.1 0.2 - + - -
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Residues in contact with LEU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J MET* 4.6 9.4 - - - -
25J VAL* 4.4 2.0 - - + -
28J VAL* 3.9 22.0 - - + -
29J LEU* 3.2 35.4 - - + +
32J LYS* 2.8 23.6 + - + +
34J VAL* 5.6 3.4 - - + -
62J LEU* 4.1 12.6 - - + -
75J ILE* 3.2 27.9 + - + +
76J MET* 3.5 2.2 + - - +
78J TYR* 1.3 98.4 - - + +
80J ASP* 1.3 56.7 + - - +
82J ARG 4.0 0.2 - - - -
83J PHE* 3.2 36.9 + - + +
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Residues in contact with ASP 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J VAL* 5.1 1.5 - - + +
32J LYS* 3.6 12.5 + - - +
76J MET 3.1 16.6 + - - +
77J GLU* 3.9 7.4 - - - +
78J TYR 3.1 0.6 - - - -
79J LEU* 1.3 77.2 - - - +
81J GLU* 1.3 68.0 + - - +
83J PHE 3.5 11.6 - - - +
84J PRO* 4.3 5.5 - - - +
87J PRO* 4.2 5.5 - - - +
88J LEU* 3.5 31.8 + - + +
89J MET* 3.2 33.8 - - - +
156J LEU* 4.3 9.0 - - + +
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Residues in contact with GLU 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D VAL* 3.7 16.8 - - - +
81I GLU* 4.4 2.6 - - - +
93I PRO* 3.7 18.4 - - + +
96I ARG* 2.3 43.4 + - - +
100I ARG* 5.0 2.6 + - - +
77J GLU* 2.9 20.1 + - - +
78J TYR* 2.9 5.7 + - - +
80J ASP* 1.3 84.6 - - - +
82J ARG* 1.3 59.2 - - - +
83J PHE 5.1 0.2 - - - -
84J PRO* 5.2 1.1 - - - +
96J ARG* 3.9 24.1 + - - -
100J ARG* 5.6 1.5 + - - -
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Residues in contact with ARG 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLY 3.7 14.3 + - - +
83D VAL* 3.2 17.2 - - - +
84D ILE* 3.4 20.5 + - + +
91D GLU* 2.3 34.4 + - - -
93I PRO* 4.0 16.3 - - + +
94I VAL* 3.8 25.9 - - - +
11J MET* 5.7 2.2 - - - +
64J ASP* 3.9 5.3 + - - -
66J GLU* 5.1 5.9 + - - -
78J TYR* 2.4 58.7 + - + +
81J GLU* 1.3 79.6 - - - +
83J PHE* 1.3 82.7 + - + +
84J PRO* 3.0 14.4 - - - +
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Residues in contact with PHE 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ILE* 3.3 34.3 - - + -
11J MET* 4.5 13.9 - - + -
32J LYS* 2.2 56.5 + - + +
33J GLY 5.7 0.9 - - - -
34J VAL* 4.1 35.2 - - + -
79J LEU* 3.2 37.4 + - + +
80J ASP 3.5 3.9 - - - +
82J ARG* 1.3 97.3 - - + +
84J PRO* 1.3 62.8 - - - +
85J HIS 3.6 3.1 - - - +
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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