Contacts of the helix formed by residues 72 - 86 (chain J) in PDB entry 2AAZ
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 PHE 72 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J ARG* 4.0 2.2 + - - -
71J VAL* 1.3 72.8 - - - +
73J LEU* 1.3 66.3 + - - +
74J ARG* 3.7 40.4 - - + -
75J GLY* 3.0 36.8 + - - -
76J VAL* 3.1 14.2 + - - +
97J GLY 3.8 17.5 - - - -
98J VAL* 4.2 11.9 - - + -
99J GLY 5.3 1.3 - - - -
100J ILE* 5.0 6.5 - - + -
226J PHE* 3.9 18.3 - + + -
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Residues in contact with LEU 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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63J LEU* 4.6 7.6 - - + -
65J LEU* 4.1 31.0 - - + -
71J VAL 2.6 13.7 + - - +
72J PHE* 1.3 70.7 - - - +
74J ARG* 1.3 64.2 + - - +
76J VAL* 2.9 20.5 + - + +
77J ILE* 3.0 34.5 + - + +
229J ALA* 5.9 0.2 - - + -
233J LEU* 4.7 8.1 - - + -
300J PHE 5.9 0.7 - - - +
302J VAL* 3.5 41.1 - - + -
305J TYR* 5.3 6.3 - - + -
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Residues in contact with ARG 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J PHE* 3.4 28.9 - - + -
73J LEU* 1.3 81.0 - - - +
75J GLY* 1.3 55.9 + - - +
77J ILE* 3.5 8.6 + - - +
78J ALA* 2.9 30.7 + - + +
96J GLN* 2.8 31.4 + - - +
97J GLY* 4.2 7.7 + - - -
98J VAL* 4.0 12.4 - - + +
297J VAL* 4.4 21.4 - - + +
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Residues in contact with GLY 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72J PHE* 3.0 35.4 + - - -
74J ARG* 1.3 79.0 - - - +
76J VAL* 1.3 64.2 + - - +
78J ALA* 3.8 1.0 - - - +
79J GLU* 3.0 25.5 + - - +
98J VAL* 4.0 17.3 - - - +
226J PHE* 4.0 8.9 - - - -
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Residues in contact with VAL 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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65J LEU* 5.3 0.7 - - + -
71J VAL* 4.3 9.0 - - + -
72J PHE 3.1 16.8 + - - +
73J LEU* 2.9 12.2 + - + +
75J GLY* 1.3 77.4 - - - +
77J ILE* 1.3 63.9 + - - +
79J GLU* 3.7 4.9 - - - +
80J LEU* 3.0 22.5 + - - +
226J PHE* 3.5 40.2 - - + +
229J ALA* 4.0 9.0 - - + -
230J SER* 3.7 36.6 + - - +
233J LEU* 3.9 14.6 - - + -
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Residues in contact with ILE 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J LEU* 3.0 35.7 + - + +
74J ARG* 3.8 9.4 - - - +
76J VAL* 1.3 75.9 - - - +
78J ALA* 1.3 62.4 + - - +
80J LEU* 3.1 7.0 + - - +
81J LEU* 3.0 33.7 + - + +
233J LEU* 4.0 20.4 - - + -
297J VAL* 4.1 19.3 - - + +
300J PHE* 3.6 59.2 - - + +
302J VAL* 5.2 0.4 - - + -
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Residues in contact with ALA 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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74J ARG* 2.9 20.1 + - + +
75J GLY 3.8 3.4 - - - +
77J ILE* 1.3 79.3 - - - +
79J GLU* 1.3 63.3 + - - +
81J LEU* 3.4 4.0 + - - +
82J TRP* 3.0 23.2 + - - +
93J LEU* 3.7 7.0 - - + +
96J GLN* 3.7 30.7 - - - +
98J VAL* 3.9 17.7 - - + -
297J VAL* 4.7 8.7 - - + +
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Residues in contact with GLU 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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75J GLY 3.0 18.9 + - - +
76J VAL* 3.7 4.7 - - - +
78J ALA* 1.3 76.3 - - - +
80J LEU* 1.3 57.7 + - - +
82J TRP* 3.1 14.7 - - + +
83J PHE* 2.9 59.1 + - + -
93J LEU* 4.0 7.1 - - + +
100J ILE* 3.6 23.5 - - + +
101J TRP* 2.9 27.4 + - + +
188J HIS* 5.3 0.9 + - - -
226J PHE* 4.2 16.5 - - - +
230J SER* 4.8 8.0 + - - -
400J UMP 5.5 2.4 - - - +
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Residues in contact with LEU 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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76J VAL 3.0 14.1 + - - +
77J ILE* 3.5 9.0 - - - +
79J GLU* 1.3 74.9 + - - +
81J LEU* 1.3 59.9 + - + +
83J PHE* 3.1 18.5 + - + +
84J VAL* 3.0 35.1 + - + +
131J TRP* 4.6 7.0 - - + -
230J SER* 3.6 24.5 - - - +
233J LEU* 3.6 31.2 - - + -
234J LEU* 3.7 26.2 - - + +
237J MET* 3.5 30.1 - - - -
300J PHE* 5.0 3.6 - - + -
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Residues in contact with LEU 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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77J ILE* 3.0 23.0 + - + +
78J ALA* 3.9 3.8 - - - +
80J LEU* 1.3 76.2 - - + +
82J TRP* 1.3 57.3 + - - +
84J VAL* 3.6 7.4 + - + +
85J SER* 3.0 27.7 + - - -
237J MET* 3.7 19.1 - - + -
292J ILE 5.9 0.4 - - - +
295J PHE* 3.7 30.3 - - + +
296J LYS* 3.6 11.4 - - - -
297J VAL* 3.5 44.2 - - + +
300J PHE* 4.0 8.7 - - + -
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Residues in contact with TRP 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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78J ALA 3.0 14.1 + - - +
79J GLU* 3.1 14.8 - - + +
81J LEU* 1.3 75.9 - - - +
83J PHE* 1.3 98.2 - + - +
85J SER* 2.6 22.1 + - - -
86J GLY 3.4 3.1 + - - -
87J CYS* 3.4 42.5 + - + +
88J THR* 3.7 23.3 - - - -
89J ASP 3.1 25.7 + - - -
90J ALA* 4.0 4.9 - - - -
92J MET* 4.1 12.8 - - + +
93J LEU* 3.7 26.0 - - + +
96J GLN* 5.9 0.7 - - - +
101J TRP* 3.8 22.4 - + - -
123J LEU* 3.5 25.4 - - + -
126J VAL* 4.7 7.6 - - + -
127J TYR* 5.3 0.4 - + - -
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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
----------------------------------------------------------
79J GLU* 2.9 50.5 + - + -
80J LEU* 3.4 17.0 - - + +
82J TRP* 1.3 101.9 - + - +
84J VAL* 1.3 54.4 + - - +
86J GLY* 2.8 23.0 + - - -
87J CYS 5.7 0.2 - - - -
101J TRP* 4.7 0.2 - - - -
127J TYR* 3.4 44.6 - + + -
128J GLY* 3.1 21.4 - - - +
131J TRP* 3.5 35.1 - + + -
132J ARG* 4.5 0.9 - - - +
188J HIS* 3.7 22.0 - + - -
230J SER* 4.5 9.9 - - - -
231J TYR* 6.1 0.2 - + - -
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Residues in contact with VAL 84 (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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80J LEU* 3.0 27.3 + - + +
81J LEU* 3.7 8.3 - - + +
82J TRP 3.3 0.2 - - - -
83J PHE* 1.3 80.8 - - - +
85J SER* 1.3 59.2 + - - +
86J GLY 3.1 1.2 + - - -
131J TRP* 4.6 5.6 - - + -
132J ARG* 2.7 32.3 + - - +
153J LEU* 3.8 27.6 - - + -
234J LEU* 4.6 7.6 - - + -
237J MET* 4.3 18.8 - - + -
292J ILE* 3.4 26.9 - - + +
293J ASP* 3.8 12.1 - - - +
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Residues in contact with SER 85 (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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81J LEU 3.0 13.8 + - - -
82J TRP* 2.6 24.7 + - - -
84J VAL* 1.3 77.5 - - - +
86J GLY* 1.3 58.9 + - - +
87J CYS* 3.1 18.8 + - - +
132J ARG* 4.6 3.2 - - - +
133J HIS* 5.2 4.0 + - - -
293J ASP* 4.7 5.8 - - - -
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Residues in contact with GLY 86 (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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83J PHE 2.8 10.0 + - - -
84J VAL 3.0 1.2 - - - -
85J SER* 1.3 79.9 + - - +
87J CYS* 1.3 63.0 + - - +
88J THR* 3.8 3.8 + - - +
128J GLY 3.2 26.0 - - - -
129J PHE* 3.6 18.2 + - - +
132J ARG* 4.0 9.6 - - - -
133J HIS* 4.8 8.2 - - - -
145J TYR* 5.9 1.6 - - - -
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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