Contacts of the helix formed by residues 72 - 86 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 3.4 46.2 - - - -
70F ARG* 4.0 1.4 + - - -
71F VAL* 1.3 72.8 - - - +
73F LEU* 1.3 66.9 + - - +
74F ARG* 3.7 30.7 - - + -
75F GLY* 3.0 37.9 + - - -
76F VAL* 3.2 14.2 + - - +
97F GLY 3.8 8.1 - - - -
98F VAL* 4.1 11.0 - - + -
100F ILE* 5.0 2.0 - - + -
226F PHE* 3.8 17.3 - + + -
2601F CB3 3.4 37.0 + - + +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F LEU* 4.5 7.6 - - + -
65F LEU* 4.1 30.7 - - + -
71F VAL 2.7 14.1 + - - +
72F PHE* 1.3 71.2 - - - +
74F ARG* 1.3 64.2 + - - +
76F VAL* 3.0 19.2 + - + +
77F ILE* 3.0 35.5 + - + +
233F LEU* 4.7 7.6 - - + -
300F PHE 5.9 0.4 - - - +
302F VAL* 3.5 41.1 - - + -
305F TYR* 5.4 6.3 - - + -
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 3.4 40.0 - - - +
305C TYR* 5.7 3.5 + - - -
307C PRO* 4.0 18.2 - - - +
72F PHE* 3.3 16.4 - - + -
73F LEU* 1.3 77.9 - - - +
75F GLY* 1.3 58.4 + - - +
77F ILE* 3.5 10.9 + - - +
78F ALA* 2.9 30.2 + - + +
96F GLN* 2.8 31.3 + - - +
97F GLY 4.2 3.6 + - - -
98F VAL* 4.0 11.2 - - + +
297F VAL* 4.5 19.3 - - + -
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F PHE* 3.0 35.5 + - - -
74F ARG* 1.3 80.1 - - - +
76F VAL* 1.3 61.8 + - - +
78F ALA* 3.8 0.9 - - - +
79F GLU* 3.0 26.7 + - - +
98F VAL* 3.9 17.5 - - - +
226F PHE* 3.9 8.4 - - - -
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Residues in contact with VAL 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 5.2 0.2 - - + -
71F VAL* 4.3 9.2 - - + -
72F PHE 3.2 14.7 + - - +
73F LEU* 3.0 11.3 + - + +
75F GLY* 1.3 77.4 - - - +
77F ILE* 1.3 62.5 + - - +
79F GLU* 3.8 5.0 - - - +
80F LEU* 3.0 21.7 + - - +
226F PHE* 3.5 39.9 - - + +
229F ALA* 3.9 9.4 - - + -
230F SER* 3.6 38.2 + - - +
233F LEU* 3.8 16.2 - - + -
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Residues in contact with ILE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU* 3.0 38.4 + - + +
74F ARG* 3.8 7.6 - - - +
76F VAL* 1.3 76.6 - - - +
78F ALA* 1.3 64.3 + - - +
80F LEU* 3.1 7.5 + - - +
81F LEU* 3.0 25.1 + - + +
233F LEU* 4.0 20.6 - - + -
297F VAL* 4.0 24.9 - - + +
300F PHE* 3.6 58.6 - - + +
302F VAL* 5.2 0.7 - - + -
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Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 2.9 19.9 + - + +
75F GLY 3.8 3.4 - - - +
77F ILE* 1.3 77.8 - - - +
79F GLU* 1.3 64.3 + - - +
81F LEU* 3.4 4.1 + - - +
82F TRP* 3.0 23.2 + - - +
93F LEU* 3.7 6.7 - - + +
96F GLN* 3.7 31.0 - - - +
98F VAL* 3.9 17.3 - - + -
297F VAL* 4.7 9.4 - - + +
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F GLY 3.0 17.9 + - - +
76F VAL* 3.8 4.2 - - - +
78F ALA* 1.3 76.6 - - - +
80F LEU* 1.3 57.3 + - - +
82F TRP* 3.1 10.7 - - + +
83F PHE* 2.9 59.5 + - + -
93F LEU* 3.9 12.3 - - + +
100F ILE* 3.6 20.9 - - + +
101F TRP* 2.8 25.7 + - + +
188F HIS* 5.3 1.1 + - - -
226F PHE* 4.2 9.7 - - - +
230F SER* 4.7 8.3 + - - -
600F UMP 5.4 0.2 - - - +
2601F CB3 3.2 24.9 - - - +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F VAL 3.0 18.9 + - - +
77F ILE* 3.5 4.7 - - - +
79F GLU* 1.3 75.1 + - - +
81F LEU* 1.3 62.1 + - + +
83F PHE* 3.1 17.9 + - + +
84F VAL* 2.9 36.0 + - + +
131F TRP* 4.5 6.7 - - + -
230F SER* 3.7 24.7 - - - +
233F LEU* 3.6 31.4 - - + -
234F LEU* 3.7 27.6 - - + +
237F MET* 3.6 28.9 - - - -
300F PHE* 5.0 3.8 - - + -
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ILE* 3.0 23.4 + - + +
78F ALA* 4.0 3.8 - - - +
80F LEU* 1.3 76.2 - - + +
82F TRP* 1.3 56.9 + - - +
84F VAL* 3.6 6.7 + - + +
85F SER* 3.0 28.1 + - - -
237F MET* 3.8 19.5 - - + -
292F ILE 5.9 0.2 - - - +
295F PHE* 3.8 30.7 - - + +
296F LYS* 3.6 11.9 - - - +
297F VAL* 3.4 44.4 - - + +
300F PHE* 4.0 9.0 - - + -
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Residues in contact with TRP 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ALA 3.0 14.2 + - - +
79F GLU* 3.1 14.4 - - + +
81F LEU* 1.3 75.2 - - - +
83F PHE* 1.3 99.6 + + - +
85F SER* 2.6 22.5 + - - -
86F GLY 3.3 3.3 + - - -
87F CYS* 3.4 43.2 + - + +
88F THR* 3.8 22.9 - - - -
89F ASP 3.1 25.1 + - - -
90F ALA* 4.0 3.8 - - - -
92F MET* 4.1 13.4 - - + +
93F LEU* 3.7 25.1 - - + +
96F GLN* 5.8 0.4 - - - +
101F TRP* 3.7 23.1 - + - -
123F LEU* 3.5 26.0 - - + -
126F VAL* 4.7 7.4 - - + -
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Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F GLU* 2.9 48.0 + - + -
80F LEU* 3.4 15.7 - - + +
82F TRP* 1.3 104.2 - + - +
84F VAL* 1.3 55.1 + - - +
86F GLY* 2.8 22.3 + - - -
87F CYS 5.1 0.4 - - - -
101F TRP* 4.7 0.2 - - - -
127F TYR* 3.5 35.9 - + + -
128F GLY* 3.1 22.6 - - - +
131F TRP* 3.5 34.1 - + + -
132F ARG* 4.6 0.9 - - - +
188F HIS* 3.6 30.3 - + - -
230F SER* 4.4 9.9 - - - -
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU* 2.9 28.8 + - + +
81F LEU* 3.7 8.7 - - + +
83F PHE* 1.3 80.4 - - - +
85F SER* 1.3 60.3 + - - +
86F GLY 3.1 1.2 + - - -
131F TRP* 4.6 4.9 - - + -
132F ARG* 3.0 30.6 + - - +
153F LEU* 3.9 28.0 - - + -
234F LEU* 4.6 8.5 - - + -
237F MET* 4.3 18.6 - - + -
292F ILE* 3.4 26.2 - - + +
293F ASP* 3.8 11.7 - - - +
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Residues in contact with SER 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU 3.0 14.0 + - - -
82F TRP* 2.6 24.1 + - - -
84F VAL* 1.3 77.1 - - - +
86F GLY* 1.3 57.6 + - - +
87F CYS* 3.1 19.4 + - - +
132F ARG* 4.8 1.7 - - - +
133F HIS* 5.2 3.5 + - - -
293F ASP* 4.7 5.4 - - - -
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Residues in contact with GLY 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE 2.8 11.0 + - - -
84F VAL 3.1 2.3 - - - -
85F SER* 1.3 79.1 + - - +
87F CYS* 1.3 63.1 + - - +
88F THR* 3.8 3.8 + - - +
128F GLY 3.3 25.4 - - - -
129F PHE* 3.6 18.2 + - - +
132F ARG* 4.2 8.1 - - - -
133F HIS* 4.7 9.5 - - - -
145F TYR* 5.9 1.2 - - - -
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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