Contacts of the helix formed by residues 74 - 84 (chain F) in PDB entry 3AOI
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 ASP 74 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66F SER 4.2 9.6 - - - +
67F THR* 5.2 9.4 - - - +
72F LYS 4.6 3.5 - - - +
73F GLU* 1.3 77.2 - - - +
75F VAL* 1.3 62.1 + - - +
76F VAL* 4.1 6.7 - - + +
77F GLU* 2.6 25.5 + - - +
78F ILE* 2.8 30.6 + - - +
608H GLY 5.4 3.8 - - - +
627H ARG 5.3 0.7 - - - +
628H PHE* 4.0 26.7 - - + -
638H ASP* 4.5 9.7 - - - +
639H GLN 5.3 2.9 - - - +
640H ARG* 3.2 23.2 + - - +
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Residues in contact with VAL 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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58F ILE* 5.2 8.5 - - + -
61F VAL* 3.9 30.1 - - + -
63F HIS 4.3 1.8 - - - +
64F GLU* 3.2 31.6 - - - +
66F SER 3.1 24.6 + - - +
67F THR* 4.8 0.4 - - - +
68F ILE* 4.4 14.1 - - + +
74F ASP* 1.3 73.3 - - - +
76F VAL* 1.3 56.2 + - - +
78F ILE* 3.4 9.6 - - + +
79F ILE* 2.9 45.4 + - + +
165F ILE* 4.7 8.7 - - + -
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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
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64F GLU* 3.3 25.4 - - + +
65F PHE* 4.2 10.3 - - + -
74F ASP* 3.1 3.6 - - + -
75F VAL* 1.3 73.1 - - - +
77F GLU* 1.3 63.3 + - - +
79F ILE* 3.3 16.1 - - + +
80F LEU* 3.2 24.4 + - - +
572H ILE* 4.1 24.9 - - + -
628H PHE* 4.2 25.8 - - + -
640H ARG* 5.3 5.6 - - - +
703H ILE* 5.8 5.8 - - + -
830H LYS* 5.4 7.9 - - - +
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Residues in contact with GLU 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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72F LYS* 5.8 4.8 + - - -
73F GLU* 3.5 31.7 - - + +
74F ASP* 2.6 46.4 + - - +
76F VAL* 1.3 80.9 - - - +
78F ILE* 1.3 63.0 + - - +
80F LEU* 3.4 17.9 - - + +
81F ASN* 3.2 25.6 + - - +
640H ARG* 3.2 23.6 + - - +
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Residues in contact with ILE 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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58F ILE* 5.6 4.7 - - + -
68F ILE* 6.0 4.9 - - + -
71F VAL* 4.9 4.9 - - + -
73F GLU* 3.0 49.6 - - + +
74F ASP 2.8 26.2 + - - +
75F VAL* 3.4 9.4 - - + +
77F GLU* 1.3 73.3 - - - +
79F ILE* 1.3 61.2 + - + +
80F LEU 3.0 1.1 - - - -
81F ASN* 2.6 28.1 + - - +
82F LEU* 2.9 20.6 + - + +
129F ILE* 3.4 27.8 - - + +
130F ALA* 4.1 10.5 - - + -
138F LEU* 6.1 2.7 - - + -
140F MET* 4.7 11.0 - - - -
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Residues in contact with ILE 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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56F VAL* 3.9 27.8 - - + -
64F GLU* 2.9 43.1 - - + +
75F VAL* 2.9 22.1 + - + +
76F VAL* 3.3 12.6 - - + +
78F ILE* 1.3 77.8 - - + +
80F LEU* 1.3 69.9 + - - +
82F LEU* 3.0 21.3 + - + +
83F LYS* 3.2 16.3 + - - +
165F ILE* 4.0 19.1 - - + -
166F PRO 5.6 0.2 - - - +
167F VAL* 4.0 20.4 - - + +
830H LYS* 4.9 2.9 - - - +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76F VAL 3.2 15.9 - - - +
77F GLU* 3.4 18.6 - - + +
78F ILE 3.0 0.2 - - - -
79F ILE* 1.3 82.2 - - - +
81F ASN* 1.3 96.2 - - - +
83F LYS* 2.9 32.5 + - - +
84F GLU* 3.7 3.6 + - - +
572H ILE* 5.3 7.0 - - + -
573H ARG* 4.1 36.1 - - + +
697H ARG 5.5 1.3 - - - +
698H ASP* 5.5 12.8 - - + +
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Residues in contact with ASN 81 (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 GLU* 3.5 27.1 + - - -
77F GLU* 3.4 13.1 + - - +
78F ILE* 2.6 17.1 + - - +
80F LEU* 1.3 92.7 - - - +
82F LEU* 1.3 55.4 + - + +
84F GLU* 3.0 29.3 + - - +
127F LEU* 3.4 19.8 - - + +
128F HIS* 3.6 27.7 + - - +
129F ILE* 4.3 6.5 + - + +
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53F VAL* 2.9 31.8 - - + +
56F VAL* 3.5 36.3 - - + -
78F ILE* 2.9 18.2 + - + +
79F ILE* 3.0 20.1 + - + +
81F ASN* 1.3 72.7 - - - +
83F LYS* 1.3 55.1 + - - +
84F GLU 2.9 5.2 - - - -
85F LEU* 2.8 26.4 + - + +
114F PHE* 4.7 10.3 - - + -
127F LEU* 5.0 2.2 - - + -
129F ILE* 3.8 18.6 - - + -
140F MET* 3.5 26.5 - - + -
142F VAL* 3.6 15.7 - - + -
167F VAL* 5.9 0.4 - - + -
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Residues in contact with LYS 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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52F ALA* 5.8 0.3 - - - +
53F VAL* 4.5 10.1 - - + +
79F ILE 3.2 3.0 + - - +
80F LEU* 2.9 18.2 + - - +
82F LEU* 1.3 75.8 - - - +
84F GLU* 1.3 59.4 + - - +
85F LEU 3.2 5.5 + - - +
167F VAL* 3.2 29.2 - - + -
168F ASP* 2.8 41.4 - - + +
170F VAL* 3.6 30.7 - - + +
696H LYS 3.1 17.5 + - - -
697H ARG* 5.8 0.7 - - - +
698H ASP* 2.7 42.0 + - - -
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Residues in contact with GLU 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 3.7 2.6 + - - +
81F ASN* 3.0 23.5 + - - +
82F LEU 2.9 0.6 - - - -
83F LYS* 1.3 78.4 - - - +
85F LEU* 1.3 59.2 + - - +
86F VAL* 3.4 4.5 + - - +
124F ASN* 3.3 16.2 + - - +
127F LEU* 4.5 13.0 - - + -
573H ARG* 5.8 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