Contacts of the helix formed by residues 72 - 86 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ARG* 4.0 2.9 + - - +
71A VAL* 1.3 74.2 - - - +
73A LEU* 1.3 64.4 + - - +
74A ARG* 3.7 40.8 - - + -
75A GLY* 3.0 37.7 + - - -
76A VAL* 3.1 13.9 + - - +
97A GLY 3.9 17.5 - - - -
98A VAL* 4.1 12.1 - - + -
99A GLY 5.3 0.2 - - - -
100A ILE* 5.0 2.0 - - + -
226A PHE* 3.8 16.2 - + + -
2351A CB3 3.2 46.2 + - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 4.5 7.9 - - + -
65A LEU* 4.1 31.2 - - + -
71A VAL 2.7 13.8 + - - +
72A PHE* 1.3 71.8 - - - +
74A ARG* 1.3 65.4 + - - +
76A VAL* 2.9 21.4 + - + +
77A ILE* 3.0 34.9 + - + +
233A LEU* 4.6 8.1 - - + -
300A PHE 5.9 0.7 - - - +
302A VAL* 3.6 40.4 - - + -
305A TYR* 5.4 5.6 - - + -
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Residues in contact with ARG 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.3 29.7 - - + -
73A LEU* 1.3 80.5 - - - +
75A GLY* 1.3 57.5 + - - +
77A ILE* 3.5 9.1 + - - +
78A ALA* 2.9 30.6 + - + +
96A GLN* 2.8 31.2 + - - +
97A GLY* 4.3 7.7 + - - -
98A VAL* 4.0 11.8 - - + +
297A VAL* 4.5 19.9 - - + +
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.0 35.9 + - - -
74A ARG* 1.3 77.8 - - - +
76A VAL* 1.3 64.1 + - - +
78A ALA* 3.9 1.0 - - - +
79A GLU* 3.0 25.6 + - - +
98A VAL* 4.0 18.2 - - - +
100A ILE* 4.5 0.2 - - - +
226A PHE* 3.9 8.7 - - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 5.2 0.4 - - + -
71A VAL* 4.3 8.1 - - + -
72A PHE 3.1 15.0 + - - +
73A LEU* 2.9 11.5 + - + +
75A GLY* 1.3 77.4 - - - +
77A ILE* 1.3 64.7 + - - +
79A GLU* 3.3 5.4 + - - +
80A LEU* 3.0 21.7 + - - +
226A PHE* 3.5 42.6 - - + +
229A ALA* 4.0 8.5 - - + -
230A SER* 3.6 36.7 + - - +
233A LEU* 3.9 14.6 - - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LEU* 3.0 36.2 + - + +
74A ARG* 3.8 9.0 - - - +
76A VAL* 1.3 76.3 - - - +
78A ALA* 1.3 63.7 + - - +
80A LEU* 3.1 8.1 + - - +
81A LEU* 2.9 26.2 + - + +
233A LEU* 4.0 21.1 - - + -
297A VAL* 4.1 26.2 - - + +
300A PHE* 3.6 58.6 - - + +
302A VAL* 5.3 0.9 - - + -
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Residues in contact with ALA 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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74A ARG* 2.9 23.7 + - + +
75A GLY 3.9 0.9 - - - +
77A ILE* 1.3 72.5 - - - +
79A GLU* 1.3 63.5 + - - +
81A LEU* 3.4 3.9 + - - +
82A TRP* 3.0 23.4 + - - +
93A LEU* 3.7 5.5 - - + +
96A GLN* 3.7 32.1 - - - +
98A VAL* 3.8 20.9 - - + -
297A VAL* 4.8 8.7 - - + +
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Residues in contact with GLU 79 (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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75A GLY 3.0 18.1 + - - +
76A VAL* 3.7 4.2 - - - +
78A ALA* 1.3 76.8 - - - +
80A LEU* 1.3 57.5 + - - +
82A TRP* 3.1 15.3 - - + +
83A PHE* 2.9 60.4 + - + -
93A LEU* 4.0 7.3 - - + +
100A ILE* 3.6 18.7 - - + +
101A TRP* 2.8 26.0 + - + +
188A HIS* 5.3 1.1 + - - -
226A PHE* 4.2 9.2 - - - +
230A SER* 4.8 7.6 + - - -
350A UMP 5.5 0.2 - - - +
2351A CB3 3.3 25.0 - - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL 3.0 18.1 + - - +
77A ILE* 3.1 4.9 + - - +
79A GLU* 1.3 77.8 - - - +
81A LEU* 1.3 58.0 + - + +
83A PHE* 3.1 16.6 + - + +
84A VAL* 3.0 36.1 + - + +
131A TRP* 4.4 7.4 - - + -
230A SER* 3.5 36.8 + - - +
233A LEU* 3.7 14.6 - - + -
234A LEU* 3.7 29.8 - - + +
237A MET* 3.6 30.3 - - - -
300A PHE* 5.2 3.4 - - + -
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Residues in contact with LEU 81 (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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77A ILE* 2.9 22.1 + - + +
78A ALA* 4.0 3.4 - - - +
80A LEU* 1.3 76.4 - - + +
82A TRP* 1.3 56.5 + - - +
84A VAL* 3.6 6.6 + - + +
85A SER* 3.0 28.6 + - - -
237A MET* 3.8 30.1 - - + -
295A PHE* 3.8 19.5 - - + +
296A LYS* 3.7 11.9 - - - -
297A VAL* 3.5 42.6 - - + +
300A PHE* 4.1 8.5 - - + -
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Residues in contact with TRP 82 (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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78A ALA 3.0 14.6 + - - +
79A GLU* 3.1 13.9 - - + +
81A LEU* 1.3 76.2 - - - +
83A PHE* 1.3 100.5 + + - +
85A SER* 2.6 22.7 + - - -
86A GLY 3.4 2.9 + - - -
87A CYS* 3.4 44.0 + - + +
88A THR* 3.8 22.9 - - - -
89A ASP 3.1 25.2 + - - -
90A ALA* 4.0 5.6 - - - -
92A MET* 4.0 12.8 - - + +
93A LEU* 3.7 24.6 - - + +
96A GLN* 5.8 0.7 - - - +
101A TRP* 3.7 22.9 - + - -
123A LEU* 3.6 24.9 - - + -
126A VAL* 4.7 8.1 - - + -
127A TYR* 5.4 0.4 - + - -
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Residues in contact with PHE 83 (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 GLU* 2.9 49.1 + - + -
80A LEU* 3.4 15.3 - - + +
82A TRP* 1.3 103.7 - + - +
84A VAL* 1.3 55.4 + - - +
86A GLY* 2.8 23.0 + - - -
87A CYS 5.1 0.2 - - - -
101A TRP* 4.7 0.2 - - - -
127A TYR* 3.4 43.5 - + + -
128A GLY* 3.1 22.4 - - - +
131A TRP* 3.5 35.6 - + + -
132A ARG* 4.4 0.7 - - - +
188A HIS* 3.7 21.8 - + - -
230A SER* 4.5 9.4 - - - -
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Residues in contact with VAL 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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80A LEU* 3.0 27.7 + - + +
81A LEU* 3.7 8.1 - - + +
83A PHE* 1.3 80.7 - - - +
85A SER* 1.3 60.2 + - - +
86A GLY 3.1 1.2 + - - -
131A TRP* 4.6 5.8 - - + -
132A ARG* 2.6 38.5 + - - +
153A LEU* 3.8 28.0 - - + -
234A LEU* 4.6 7.2 - - + -
237A MET* 4.3 18.4 - - + -
292A ILE* 3.4 26.7 - - + +
293A ASP* 3.8 5.6 - - - +
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Residues in contact with SER 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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81A LEU 3.0 13.9 + - - -
82A TRP* 2.6 24.6 + - - -
84A VAL* 1.3 78.1 - - - +
86A GLY* 1.3 58.6 + - - +
87A CYS* 3.2 18.5 + - - +
132A ARG* 4.6 1.9 - - - +
133A HIS* 5.1 3.6 + - - -
293A ASP* 4.7 6.1 - - - -
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Residues in contact with GLY 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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83A PHE 2.8 10.4 + - - -
84A VAL 3.0 1.6 + - - -
85A SER* 1.3 78.0 + - - +
87A CYS* 1.3 63.4 + - - +
88A THR* 3.7 3.3 + - - +
128A GLY 3.2 25.8 - - - -
129A PHE* 3.6 19.2 + - - +
132A ARG* 4.0 9.4 - - - -
133A HIS* 4.7 8.9 - - - -
145A TYR* 5.8 1.7 - - - -
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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