Contacts of the helix formed by residues 78 - 89 (chain I) in PDB entry 4M7A
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 78 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6I PHE* 5.6 0.8 - - - -
9I THR* 6.2 0.2 - - - +
77I VAL* 1.3 78.8 - - - +
79I THR* 1.3 62.8 + - - +
80I ASN* 3.0 15.9 + - - +
81I LEU* 2.5 59.0 + - + +
82I LEU* 3.4 18.4 + - - +
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Residues in contact with THR 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LYS* 5.2 11.4 - - + +
77I VAL* 3.8 20.1 + - + +
78I ASP* 1.3 72.0 + - - +
80I ASN* 1.3 68.6 + - - +
81I LEU 3.3 0.2 - - - -
82I LEU* 4.0 1.9 - - - +
83I GLN* 3.0 38.9 + - - +
31J GLN* 3.2 40.1 - - + +
65J MET* 4.6 7.6 - - + -
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Residues in contact with ASN 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I ASP* 3.0 12.6 + - - +
79I THR* 1.3 80.8 + - - +
81I LEU* 1.3 60.1 + - - +
83I GLN* 4.1 14.1 + - - +
84I ASP* 3.0 38.4 + - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I THR* 5.8 3.8 - - - +
78I ASP* 2.5 42.1 + - + +
80I ASN* 1.3 71.3 - - - +
82I LEU* 1.3 67.5 + - + +
84I ASP* 4.3 1.2 - - - +
85I ALA* 2.9 27.8 + - - +
88I ARG* 5.4 0.5 + - - -
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Residues in contact with LEU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I LEU* 5.0 8.3 - - + -
6I PHE* 3.6 61.7 - - + -
77I VAL* 3.7 16.8 - - + -
78I ASP 3.4 12.1 + - - +
79I THR* 4.0 4.5 - - - +
81I LEU* 1.3 79.7 - - + +
83I GLN* 1.3 57.5 + - - +
85I ALA* 3.5 6.6 - - + +
86I THR* 2.8 34.8 + - - -
31J GLN* 3.9 17.0 - - + +
32J ALA* 4.2 14.3 - - + +
40J VAL* 4.6 12.8 - - + -
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Residues in contact with GLN 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I THR* 3.0 32.9 + - - +
80I ASN* 3.8 14.8 + - - +
81I LEU 3.2 0.4 - - - -
82I LEU* 1.3 78.6 - - - +
84I ASP* 1.3 59.2 + - - +
86I THR* 3.4 3.5 + - - -
87I ARG* 2.9 46.5 + - - +
12J LEU* 3.9 15.4 - - + +
13J ASP* 3.0 45.1 + - - +
31J GLN* 2.7 43.2 + - - +
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Residues in contact with ASP 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I ASN* 3.0 21.0 + - - +
81I LEU* 4.3 1.1 - - - +
83I GLN* 1.3 73.6 - - - +
85I ALA* 1.3 60.3 + - - +
87I ARG* 2.7 45.4 + - + +
88I ARG* 2.8 47.0 + - - +
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I LEU* 3.8 18.4 - - + +
81I LEU* 2.9 20.7 + - + +
82I LEU* 3.5 9.0 - - + +
84I ASP* 1.3 74.2 - - - +
86I THR* 1.3 56.8 + - - +
88I ARG* 2.8 28.4 + - - +
89I GLU* 2.8 27.2 + - - +
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Residues in contact with THR 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I LEU* 3.9 14.5 - - - +
82I LEU 2.8 22.0 + - - -
83I GLN 3.4 4.7 - - - -
85I ALA* 1.3 75.0 - - - +
87I ARG* 1.3 63.9 + - - +
88I ARG 3.1 0.9 + - - -
89I GLU* 3.3 13.0 + - - +
91I MET* 4.6 0.2 - - - +
9J LYS* 3.8 10.9 - - - -
12J LEU* 3.8 14.4 - - + -
32J ALA* 3.4 20.8 - - - +
33J PHE* 3.5 53.0 + - + +
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Residues in contact with ARG 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I GLN* 2.9 37.5 + - - +
84I ASP* 2.7 45.1 + - + +
86I THR* 1.3 76.2 - - - +
88I ARG* 1.3 59.4 + - + +
89I GLU 4.5 0.3 - - - +
9J LYS* 4.2 24.8 + - + +
12J LEU* 4.1 31.6 + - + +
13J ASP* 5.9 0.4 - - - +
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Residues in contact with ARG 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I LEU 5.4 0.8 + - - -
84I ASP* 2.8 19.8 + - - +
85I ALA* 2.8 34.9 + - - +
87I ARG* 1.3 80.1 - - + +
89I GLU* 1.3 70.0 + - - +
90I VAL* 3.3 10.0 + - - +
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Residues in contact with GLU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1I MET* 4.7 8.0 + - - +
2I LEU* 2.2 65.2 + - + +
85I ALA 2.8 6.6 + - - -
86I THR 3.3 6.4 + - - +
88I ARG* 1.3 80.5 - - - +
90I VAL* 1.3 72.2 + - - +
91I MET* 3.2 30.1 - - + -
9J LYS* 3.1 24.8 + - - -
34J ASP* 4.4 10.2 - - - +
35J SER 5.5 0.2 - - - +
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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