Contacts of the helix formed by residues 72 - 86 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 4.0 2.0 + - - -
71B VAL* 1.3 72.8 - - - +
73B LEU* 1.3 65.8 + - - +
74B ARG* 3.7 35.7 - - + -
75B GLY* 2.9 38.4 + - - -
76B VAL* 3.2 12.8 + - - +
97B GLY 3.8 22.9 - - - -
98B VAL* 4.1 11.4 - - + -
99B GLY 5.3 0.2 - - - -
100B ILE* 5.0 2.5 - - + -
226B PHE* 3.9 17.3 - + + -
2401B CB3 3.4 43.7 + - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B LEU* 4.5 7.9 - - + -
65B LEU* 4.1 31.6 - - + -
71B VAL 2.7 12.6 + - - +
72B PHE* 1.3 70.2 - - - +
74B ARG* 1.3 64.8 + - - +
76B VAL* 2.9 20.8 + - + +
77B ILE* 3.0 35.1 + - + +
233B LEU* 4.7 8.3 - - + -
300B PHE 5.9 0.4 - - - +
302B VAL* 3.5 40.4 - - + -
305B TYR* 5.4 6.7 - - + -
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 3.3 29.3 - - + -
73B LEU* 1.3 80.8 - - - +
75B GLY* 1.3 55.8 + - - +
77B ILE* 3.5 8.9 + - - +
78B ALA* 2.9 31.1 + - + +
96B GLN* 2.8 32.0 + - - +
97B GLY* 4.2 7.3 + - - -
98B VAL* 4.0 11.5 - - + +
297B VAL* 4.5 21.0 - - + +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 2.9 35.8 + - - -
74B ARG* 1.3 78.2 - - - +
76B VAL* 1.3 64.0 + - - +
78B ALA* 3.9 0.9 - - - +
79B GLU* 3.0 25.6 + - - +
98B VAL* 3.9 17.3 - - - +
100B ILE* 4.4 0.2 - - - +
226B PHE* 3.9 8.9 - - - -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 5.2 0.4 - - + -
71B VAL* 4.3 7.9 - - + -
72B PHE 3.2 15.7 + - - +
73B LEU* 2.9 12.4 + - + +
75B GLY* 1.3 76.6 - - - +
77B ILE* 1.3 63.6 + - - +
79B GLU* 3.3 4.2 + - - +
80B LEU* 3.0 22.1 + - - +
226B PHE* 3.5 42.0 - - + +
229B ALA* 4.0 9.0 - - + -
230B SER* 3.6 36.2 + - - +
233B LEU* 3.9 15.5 - - + -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.0 38.2 + - + +
74B ARG* 3.9 7.6 - - - +
76B VAL* 1.3 76.6 - - - +
78B ALA* 1.3 63.8 + - - +
80B LEU* 3.2 6.6 + - - +
81B LEU* 3.0 32.4 + - + +
233B LEU* 4.0 20.0 - - + -
297B VAL* 4.1 19.5 - - + +
300B PHE* 3.6 59.5 - - + +
302B VAL* 5.2 0.4 - - + -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 2.9 19.9 + - + +
75B GLY 3.9 1.1 - - - +
77B ILE* 1.3 79.6 - - - +
79B GLU* 1.3 62.2 + - - +
81B LEU* 3.4 3.8 + - - +
82B TRP* 3.0 23.4 + - - +
93B LEU* 3.6 6.7 - - + +
96B GLN* 3.7 31.2 - - - +
98B VAL* 3.9 20.0 - - + -
297B VAL* 4.7 9.1 - - + +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY 3.0 19.5 + - - +
76B VAL* 3.7 5.3 - - - +
78B ALA* 1.3 76.5 - - - +
80B LEU* 1.3 57.1 + - - +
82B TRP* 3.1 10.5 - - + +
83B PHE* 2.9 58.7 + - + -
93B LEU* 3.9 11.4 - - + +
100B ILE* 3.6 18.6 - - + +
101B TRP* 2.9 25.3 + - + +
188B HIS* 5.3 1.1 + - - -
226B PHE* 4.2 9.4 - - - +
230B SER* 4.7 8.3 + - - -
2401B CB3 3.0 25.2 - - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL 3.0 16.6 + - - +
77B ILE* 3.6 6.3 - - - +
79B GLU* 1.3 75.3 + - - +
81B LEU* 1.3 60.5 + - + +
83B PHE* 3.1 18.3 + - + +
84B VAL* 3.0 36.0 + - + +
131B TRP* 4.5 6.7 - - + -
230B SER* 3.6 25.1 - - - +
233B LEU* 3.6 30.3 - - + -
234B LEU* 3.7 26.0 - - + +
237B MET* 3.6 29.8 - - - -
300B PHE* 5.0 3.6 - - + -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 3.0 22.3 + - + +
78B ALA* 4.0 3.8 - - - +
80B LEU* 1.3 76.8 - - + +
82B TRP* 1.3 57.0 + - - +
84B VAL* 3.5 6.7 + - + +
85B SER* 3.0 28.8 + - - -
237B MET* 3.7 30.3 - - + -
292B ILE 5.8 0.4 - - - +
295B PHE* 3.7 19.7 - - + +
296B LYS* 3.6 11.7 - - - +
297B VAL* 3.5 44.2 - - + +
300B PHE* 4.1 8.7 - - + -
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Residues in contact with TRP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA 3.0 14.6 + - - +
79B GLU* 3.1 14.6 - - + +
81B LEU* 1.3 75.4 - - - +
83B PHE* 1.3 97.8 - + - +
85B SER* 2.6 22.9 + - - -
86B GLY 3.4 3.5 + - - -
87B CYS* 3.4 41.5 + - + +
88B THR* 3.8 22.9 - - - -
89B ASP 3.1 25.2 + - - -
90B ALA* 4.0 5.4 - - - -
92B MET* 4.0 13.0 - - + +
93B LEU* 3.7 24.6 - - + +
96B GLN* 5.8 0.7 - - - +
101B TRP* 3.7 23.6 - + - -
123B LEU* 3.5 24.5 - - + -
126B VAL* 4.8 8.3 - - + -
127B TYR* 5.4 0.4 - + - -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 2.9 51.1 + - + -
80B LEU* 3.4 16.8 - - + +
82B TRP* 1.3 102.4 - + - +
84B VAL* 1.3 59.3 + - - +
86B GLY* 2.8 18.7 + - - -
87B CYS 5.1 0.4 - - - -
101B TRP* 4.7 0.2 - - - -
127B TYR* 3.5 43.5 - + + -
128B GLY* 3.1 21.4 - - - +
131B TRP* 3.5 35.3 - + + -
132B ARG* 4.6 0.7 - - - +
188B HIS* 3.7 22.4 - + - -
230B SER* 4.4 9.9 - - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.0 27.5 + - + +
81B LEU* 3.7 9.2 - - + +
82B TRP 3.3 0.2 - - - -
83B PHE* 1.3 80.3 - - - +
85B SER* 1.3 58.8 + - - +
86B GLY 3.1 1.2 + - - -
131B TRP* 4.6 8.3 - - + -
132B ARG* 2.7 32.8 + - - +
153B LEU* 3.8 27.4 - - + -
234B LEU* 4.6 5.4 - - + -
237B MET* 4.3 19.1 - - + -
292B ILE* 3.4 26.5 - - + +
293B ASP* 3.8 12.3 - - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU 3.0 14.8 + - - -
82B TRP* 2.6 23.8 + - - -
84B VAL* 1.3 76.2 - - - +
86B GLY* 1.3 58.3 + - - +
87B CYS* 3.1 19.5 + - - +
132B ARG* 4.6 3.1 - - - +
133B HIS* 5.3 2.9 + - - -
293B ASP* 4.7 6.5 - - - -
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Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE 2.8 10.7 + - - -
84B VAL 3.0 1.4 - - - -
85B SER* 1.3 78.5 + - - +
87B CYS* 1.3 62.3 + - - +
88B THR* 3.8 3.5 + - - +
128B GLY 3.2 25.7 - - - -
129B PHE* 3.7 17.9 + - - +
132B ARG* 4.0 9.6 - - - -
133B HIS* 4.8 8.4 + - - -
145B TYR* 5.9 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
------------------------------------------------------------
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