Contacts of the helix formed by residues 75 - 84 (chain B) in PDB entry 4TKR
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 MET 75 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 5.5 10.8 - - + -
9A LEU* 5.2 5.6 - - + -
73B ILE* 3.7 5.6 - - - +
74B LEU* 1.3 86.1 - - + +
76B PRO* 1.3 77.4 - - + +
77B SER* 3.8 20.2 - - - +
78B GLN* 3.1 8.9 + - + +
79B ALA* 3.1 23.2 + - - +
138B PHE* 3.7 24.7 - - + -
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Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ILE* 4.6 4.9 - - + -
74B LEU 4.9 0.2 - - - +
75B MET* 1.3 90.1 - - + +
77B SER* 1.3 60.3 + - - +
79B ALA* 3.6 6.9 + - + +
80B ILE* 3.3 29.8 + - + +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.0 9.2 - - - +
56A PHE* 3.6 28.2 - - - -
75B MET* 3.8 14.1 - - - +
76B PRO* 1.3 79.6 - - - +
78B GLN* 1.3 60.1 + - - +
79B ALA 3.4 0.2 - - - -
80B ILE* 3.5 6.3 - - - +
81B ILE* 3.2 31.5 + - - +
138B PHE* 3.4 24.9 - - - -
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR 2.9 18.7 + - - +
73B ILE* 3.2 5.0 - - - -
74B LEU* 2.9 29.1 + - + -
75B MET* 3.1 29.8 + - + +
77B SER* 1.3 77.0 + - - +
79B ALA* 1.3 67.0 + - - +
80B ILE 3.2 1.1 - - - -
81B ILE* 4.3 2.5 - - - +
82B GLU* 2.7 67.7 + - + +
83B TYR* 4.9 0.2 - - - -
138B PHE* 3.4 37.0 - - + -
139B TRP* 3.7 11.1 - - - +
301B TPP 5.1 0.2 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PHE* 3.8 25.8 - - + -
73B ILE* 3.8 24.0 - - + -
75B MET 3.1 14.8 + - - +
76B PRO* 3.9 7.0 - - + +
78B GLN* 1.3 83.4 - - - +
80B ILE* 1.3 58.2 + - + +
83B TYR* 3.0 39.2 + - + +
84B ILE* 4.0 0.7 + - - +
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 4.0 22.9 - - + -
59A LEU* 3.5 26.5 - - + -
60A LEU* 3.8 27.4 - - + -
63A LEU* 4.1 18.4 - - + -
76B PRO* 3.3 17.8 + - + +
77B SER* 3.5 8.3 - - - +
78B GLN 3.2 0.4 - - - -
79B ALA* 1.3 78.9 - - + +
81B ILE* 1.3 63.0 + - - +
84B ILE* 3.2 37.4 + - + +
85B LEU* 3.2 3.6 + - + -
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.9 1.6 - - + -
52A TRP* 4.8 5.8 - - + -
56A PHE* 3.6 29.8 - - + -
77B SER 3.2 17.8 + - - +
78B GLN* 3.9 4.5 - - - +
80B ILE* 1.3 75.0 - - - +
82B GLU* 1.3 59.7 + - + +
85B LEU* 3.2 13.2 - - + +
86B ALA* 3.0 28.1 + - - +
130B TRP* 3.7 42.3 - - + +
133B VAL* 4.9 2.9 - - + -
134B ALA* 4.2 8.3 - - + +
137B LEU* 4.2 15.0 - - + -
138B PHE* 3.9 23.1 - - + -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLN* 2.7 47.3 + - - +
81B ILE* 1.3 76.4 - - + +
83B TYR* 1.3 69.4 + - + +
84B ILE 3.5 0.2 - - - -
86B ALA* 3.4 3.0 - - - +
87B PHE* 3.1 24.4 - - - -
130B TRP 5.4 0.2 - - - -
131B HIS* 3.0 35.7 + - + +
134B ALA* 3.5 21.3 - - + -
139B TRP* 2.9 15.4 + - - -
301B TPP 2.4 47.3 + - + +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.6 0.9 - - - +
62B GLY* 3.3 28.2 - - - +
63B LEU 3.9 0.3 + - - -
65B HIS* 3.5 41.1 - + + -
66B PHE* 3.8 17.4 - + + -
70B LYS 3.8 3.8 + - - -
71B ALA* 3.5 24.7 - - + -
72B TYR* 2.9 35.5 + - - +
73B ILE* 5.3 0.2 - - + -
78B GLN* 4.9 0.7 - - - -
79B ALA* 3.0 24.8 + - + +
82B GLU* 1.3 82.7 - - + +
84B ILE* 1.3 66.4 + - - +
87B PHE* 3.8 18.0 - + - +
301B TPP 3.3 42.7 - - + +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 3.5 17.9 - - + -
63A LEU* 4.8 13.5 - - + -
84A ILE* 3.5 32.5 - - + -
88A SER* 4.9 0.7 - - - +
59B LEU* 3.7 11.0 - - + +
63B LEU* 4.1 21.5 - - + -
66B PHE* 4.3 13.5 - - + -
79B ALA 4.5 0.9 - - - +
80B ILE* 3.2 28.7 + - + +
82B GLU 3.5 0.2 - - - -
83B TYR* 1.3 86.2 - - - +
85B LEU* 1.3 62.0 + - - +
86B ALA 3.4 0.9 - - - -
87B PHE 3.7 1.5 + - - +
88B SER* 2.5 34.3 + - - +
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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