Contacts of the helix formed by residues 72 - 82 (chain A) in PDB entry 4TR8
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 ALA 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 4.5 2.1 - - - +
18A ALA* 4.1 14.9 - - + +
21A VAL* 3.9 25.8 - - + -
31A SER 3.0 19.3 + - - +
33A VAL* 3.9 27.1 - - + +
70A VAL 3.0 4.8 + - - -
71A PRO* 1.3 71.4 - - - +
73A ARG* 1.4 57.6 + - - +
75A LEU* 3.3 3.5 + - - +
76A MET* 2.9 29.3 + - - +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.8 4.2 - - + +
21A VAL* 5.5 1.0 - - + +
31A SER 4.6 1.2 + - - -
71A PRO* 3.6 0.8 - - - +
72A ALA* 1.4 75.9 - - - +
74A LYS* 1.3 52.3 + - + +
76A MET* 3.3 18.8 + - - +
77A ASP* 2.8 73.9 + - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 3.8 26.5 + - + +
72A ALA 3.4 0.4 - - - -
73A ARG* 1.3 73.1 - - + +
75A LEU* 1.4 65.6 + - - +
77A ASP* 3.8 1.6 - - - +
78A ILE* 2.9 32.3 + - - +
108A LEU* 3.8 14.4 - - + -
273B ILE* 4.4 18.4 - - + +
274B LEU* 4.1 15.3 - - + -
297B ASN* 3.8 6.8 - - - +
299B GLU* 2.9 25.5 + - - +
301B GLU* 2.7 33.6 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.3 10.1 - - + -
14A LEU* 3.9 20.4 - - + -
33A VAL* 4.3 8.7 - - + -
35A LEU* 4.2 18.2 - - + -
70A VAL* 3.9 20.2 - - + -
71A PRO 3.1 19.7 + - - +
72A ALA* 3.3 4.5 + - - +
74A LYS* 1.4 75.5 - - - +
76A MET* 1.3 62.8 + - - +
78A ILE* 3.4 6.3 + - + +
79A CYS* 3.0 24.6 + - + +
90A ILE* 4.7 10.3 - - + -
97A LEU* 4.4 4.5 - - + -
99A VAL* 4.0 30.7 - - + -
108A LEU* 4.1 15.8 - - + +
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 3.8 - - + +
14A LEU* 3.6 20.3 - - + +
15A GLN* 3.8 48.2 - - + +
18A ALA* 3.9 16.2 - - + -
72A ALA 2.9 17.4 + - - +
73A ARG* 3.6 20.9 - - - +
75A LEU* 1.3 75.5 - - - +
77A ASP* 1.4 58.0 + - - +
79A CYS* 3.2 3.3 + - - +
80A LYS* 2.9 40.7 + - + +
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 2.8 64.6 + - - +
74A LYS* 3.9 2.8 - - - +
76A MET* 1.4 77.5 - - - +
78A ILE* 1.4 61.6 + - - +
80A LYS* 3.8 9.9 - - - +
81A SER* 3.0 26.9 + - - -
273B ILE* 3.6 24.6 - - + +
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS 2.9 22.8 + - - +
75A LEU* 3.7 6.7 - - + +
77A ASP* 1.4 74.9 - - - +
79A CYS* 1.4 63.1 + - - +
81A SER* 2.6 24.3 + - - -
82A LEU* 3.1 15.3 + - + +
99A VAL* 4.2 15.9 - - + -
106A PHE* 3.7 56.1 - - + -
108A LEU* 3.9 35.4 - - + -
273B ILE* 3.8 20.2 - - + -
274B LEU* 4.5 4.3 - - + -
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Residues in contact with CYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.2 48.0 + - - +
10A LEU* 3.9 16.4 - - + -
11A LEU* 3.9 19.7 - - + -
14A LEU* 4.2 10.3 - - + -
75A LEU* 3.0 18.3 + - + +
76A MET 3.5 4.5 - - - +
78A ILE* 1.4 74.8 - - - +
80A LYS* 1.3 62.1 + - - +
82A LEU* 3.2 18.2 + - - +
88A ILE* 3.8 17.9 - - + -
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 2.7 33.7 + - - +
11A LEU* 3.9 16.7 - - + +
15A GLN* 3.9 22.4 - - - +
76A MET* 2.9 25.4 + - + +
77A ASP* 3.8 11.4 - - - +
79A CYS* 1.3 71.3 - - - +
81A SER* 1.3 62.8 + - - +
82A LEU 3.6 0.9 - - - +
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Residues in contact with SER 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP 3.0 14.9 + - - -
78A ILE* 2.6 23.4 + - - -
80A LYS* 1.3 73.4 - - - +
82A LEU* 1.4 62.3 + - - +
83A PRO* 4.8 0.3 - - - +
266B GLU* 5.2 4.2 - - - +
269B SER* 5.8 0.9 - - - -
270B ARG* 2.9 48.9 + - - +
273B ILE* 3.8 8.3 - - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ARG* 3.0 17.2 + - + -
78A ILE* 3.1 29.6 + - + +
79A CYS* 3.2 12.3 + - - +
80A LYS 3.6 1.7 - - - +
81A SER* 1.4 79.4 - - - +
83A PRO* 1.4 76.9 - - + +
84A ASN* 3.6 1.2 + - - +
86A VAL* 3.9 9.6 - - + -
88A ILE* 3.7 31.0 - - + -
99A VAL* 5.0 2.9 - - + -
101A ALA* 3.8 29.2 - - + -
104A SER* 4.1 11.9 - - - +
106A PHE* 4.1 11.7 - - + -
270B ARG* 3.7 21.8 - - - +
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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