Contacts of the helix formed by residues 72 - 86 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70O ARG* 4.0 2.4 + - - -
71O VAL* 1.3 72.0 - - - +
73O LEU* 1.3 66.1 + - - +
74O ARG* 3.7 40.4 - - + -
75O GLY* 3.0 36.5 + - - -
76O VAL* 3.1 14.7 + - - +
97O GLY 3.8 17.7 - - - -
98O VAL* 4.2 12.1 - - + -
99O GLY 5.3 1.3 - - - -
100O ILE* 5.0 6.7 - - + -
226O PHE* 3.9 18.8 - + + -
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Residues in contact with LEU 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O LEU* 4.6 7.0 - - + -
65O LEU* 4.1 30.3 - - + -
71O VAL 2.7 13.9 + - - +
72O PHE* 1.3 70.4 - - - +
74O ARG* 1.3 65.1 + - - +
76O VAL* 2.9 20.2 + - + +
77O ILE* 3.0 34.1 + - + +
233O LEU* 4.7 9.0 - - + -
300O PHE 5.9 0.4 - - - +
302O VAL* 3.5 41.7 - - + -
305O TYR* 5.3 6.5 - - + -
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Residues in contact with ARG 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O PHE* 3.4 28.4 - - + -
73O LEU* 1.3 80.3 - - - +
75O GLY* 1.3 57.2 + - - +
77O ILE* 3.8 8.9 - - - +
78O ALA* 2.9 31.2 + - + +
96O GLN* 2.9 31.0 + - - +
97O GLY* 4.2 8.1 + - - -
98O VAL* 4.0 12.0 - - + +
297O VAL* 4.4 20.6 - - + +
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Residues in contact with GLY 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72O PHE* 3.0 34.5 + - - -
74O ARG* 1.3 78.4 - - - +
76O VAL* 1.3 63.8 + - - +
78O ALA* 3.8 0.9 - - - +
79O GLU* 3.0 25.8 + - - +
98O VAL* 4.0 17.5 - - - +
226O PHE* 4.0 8.5 - - - -
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Residues in contact with VAL 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O LEU* 5.3 0.2 - - + -
71O VAL* 4.3 7.6 - - + -
72O PHE 3.1 16.3 + - - +
73O LEU* 2.9 12.4 + - + +
75O GLY* 1.3 77.7 - - - +
77O ILE* 1.3 63.3 + - - +
79O GLU* 3.7 5.1 - - - +
80O LEU* 3.0 21.9 + - + +
226O PHE* 3.5 40.8 - - + +
229O ALA* 4.0 8.7 - - + -
230O SER* 3.6 37.3 + - - +
233O LEU* 3.9 14.1 - - + -
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Residues in contact with ILE 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73O LEU* 3.0 35.8 + - + +
74O ARG* 3.8 9.2 - - - +
76O VAL* 1.3 76.6 - - - +
78O ALA* 1.3 63.5 + - - +
80O LEU* 3.1 7.1 + - - +
81O LEU* 3.0 32.7 + - + +
233O LEU* 4.0 20.4 - - + -
297O VAL* 4.1 18.8 - - + +
300O PHE* 3.6 59.5 - - + +
302O VAL* 5.2 0.7 - - + -
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Residues in contact with ALA 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ARG* 2.9 20.1 + - + +
75O GLY 3.8 3.6 - - - +
77O ILE* 1.3 77.8 - - - +
79O GLU* 1.3 62.9 + - - +
81O LEU* 3.4 4.0 + - - +
82O TRP* 3.0 23.6 + - - +
93O LEU* 3.7 6.8 - - + +
96O GLN* 3.7 31.4 - - - +
98O VAL* 3.9 17.3 - - + -
297O VAL* 4.7 8.0 - - + +
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Residues in contact with GLU 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O GLY 3.0 17.9 + - - +
76O VAL* 3.7 4.4 - - - +
78O ALA* 1.3 75.8 - - - +
80O LEU* 1.3 57.0 + - - +
82O TRP* 3.1 15.4 - - + +
83O PHE* 2.9 59.5 + - + -
93O LEU* 4.0 6.7 - - + +
100O ILE* 3.5 23.1 - - + +
101O TRP* 2.9 27.0 + - + +
188O HIS* 5.4 1.0 + - - -
226O PHE* 4.2 16.3 - - - +
230O SER* 4.7 8.3 + - - -
650O UMP 5.6 1.7 - - - +
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Residues in contact with LEU 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O VAL 3.0 12.6 + - - +
77O ILE* 3.1 8.9 + - - +
79O GLU* 1.3 73.7 + - - +
81O LEU* 1.3 66.1 + - + +
82O TRP 3.0 1.3 - - - -
83O PHE* 3.0 19.4 + - + +
84O VAL* 3.0 29.3 + - + +
131O TRP* 4.6 7.2 - - + -
230O SER* 3.6 35.7 - - - +
233O LEU* 3.6 20.0 - - + -
234O LEU* 3.7 27.4 - - + +
237O MET* 3.5 30.3 - - - -
300O PHE* 5.0 4.0 - - + -
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77O ILE* 3.0 24.1 + - + +
78O ALA* 4.0 3.8 - - - +
80O LEU* 1.3 76.1 - - + +
82O TRP* 1.3 56.9 + - - +
84O VAL* 3.6 6.8 + - + +
85O SER* 3.1 28.1 + - - -
237O MET* 3.8 19.3 - - + -
292O ILE 5.9 0.2 - - - +
295O PHE* 3.7 30.3 - - + +
296O LYS* 3.7 10.8 - - - -
297O VAL* 3.5 43.7 - - + +
300O PHE* 4.0 9.4 - - + -
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Residues in contact with TRP 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O ALA 3.0 13.9 + - - +
79O GLU* 3.1 14.8 - - + +
81O LEU* 1.3 76.4 - - - +
83O PHE* 1.3 98.3 + + - +
85O SER* 2.6 22.6 + - - -
86O GLY 3.4 3.1 + - - -
87O CYS* 3.4 43.2 + - + +
88O THR* 3.7 24.2 - - - -
89O ASP 3.1 24.5 + - - -
90O ALA* 4.0 5.8 - - - -
92O MET* 4.1 12.5 - - + +
93O LEU* 3.7 24.9 - - + +
96O GLN* 5.9 0.2 - - - +
101O TRP* 3.7 22.4 - + - -
123O LEU* 3.5 24.7 - - + -
126O VAL* 4.7 6.3 - - + -
127O TYR* 5.3 0.4 - + - -
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Residues in contact with PHE 83 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79O GLU* 2.9 49.2 + - + -
80O LEU* 3.0 16.4 + - + +
82O TRP* 1.3 101.9 - + - +
84O VAL* 1.3 58.7 + - - +
86O GLY* 2.8 18.5 + - - -
87O CYS 5.7 0.4 - - - -
101O TRP* 4.7 0.2 - - - -
127O TYR* 3.4 45.1 - + + -
128O GLY* 3.1 22.1 - - - +
131O TRP* 3.6 34.8 - + + -
132O ARG* 4.5 0.9 - - - +
188O HIS* 3.8 21.3 - + - -
230O SER* 4.5 9.9 - - - -
231O TYR* 6.1 0.2 - + - -
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Residues in contact with VAL 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O LEU* 3.0 27.3 + - + +
81O LEU* 3.7 8.3 - - + +
83O PHE* 1.3 80.8 - - - +
85O SER* 1.3 59.7 + - - +
86O GLY 3.1 1.0 + - - -
131O TRP* 4.6 4.5 - - + -
132O ARG* 2.7 32.8 + - - +
153O LEU* 3.8 27.4 - - + -
234O LEU* 4.6 8.1 - - + -
237O MET* 4.3 20.0 - - + -
292O ILE* 3.4 26.0 - - + +
293O ASP* 3.7 12.8 - - - +
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Residues in contact with SER 85 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O LEU 3.1 13.8 + - - -
82O TRP* 2.6 24.1 + - - -
84O VAL* 1.3 76.5 - - - +
86O GLY* 1.3 58.9 + - - +
87O CYS* 3.1 18.8 + - - +
132O ARG* 4.7 2.9 - - - +
133O HIS* 5.2 3.6 + - - -
293O ASP* 4.7 5.8 - - - -
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Residues in contact with GLY 86 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83O PHE 2.8 10.6 + - - -
84O VAL 3.0 1.2 - - - -
85O SER* 1.3 78.4 - - - +
87O CYS* 1.3 62.4 + - - +
88O THR* 3.8 4.0 + - - +
128O GLY 3.2 26.2 - - - -
129O PHE* 3.6 18.6 + - - +
132O ARG* 4.1 9.4 - - - -
133O HIS* 4.8 8.9 - - - -
145O TYR* 5.9 1.4 - - - -
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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