Contacts of the strand formed by residues 106 - 112 (chain E) in PDB entry 3TKR
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 THR 106 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E TYR* 3.4 30.2 - - + +
74E LEU 4.6 0.2 - - - -
75E VAL* 4.0 19.3 - - + +
101E PHE* 3.0 43.8 + - + +
102E ARG* 3.4 12.3 + - - +
104E ILE* 2.9 16.4 + - - +
105E ASN* 1.3 75.6 - - - +
107E GLU* 1.3 77.4 + - - +
195E VAL* 3.4 17.7 - - + +
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E TYR* 3.6 38.7 - - + -
72E LYS* 3.2 37.3 + - + +
73E TYR 3.0 9.6 + - - +
74E LEU* 3.5 3.7 - - + -
75E VAL 2.9 25.1 + - - -
98E LEU* 5.4 1.3 - - - +
102E ARG* 3.2 42.9 + - - +
105E ASN 5.6 0.3 - - - -
106E THR* 1.3 80.9 + - - +
108E VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E TYR* 5.1 0.2 + - - -
75E VAL* 3.3 20.9 - - + +
77E PHE* 3.8 28.0 - - + -
94E PHE* 4.3 10.1 - - + -
98E LEU* 3.7 27.3 - - + +
101E PHE* 4.0 24.9 - - + -
107E GLU* 1.3 84.4 + - - +
109E VAL* 1.3 67.1 + - - +
137E ILE* 3.5 20.5 - - + +
138E PRO* 3.3 22.3 - - - +
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Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E TRP* 4.3 10.3 - - + -
64E LEU* 4.1 9.0 - - + -
69E TYR* 3.2 41.7 - - + +
74E LEU* 3.8 8.4 - - + +
75E VAL 3.0 6.6 + - - +
76E PHE* 3.5 28.2 - - + -
77E PHE* 2.9 27.4 + - - +
108E VAL* 1.3 81.7 - - - +
110E ALA* 1.3 72.0 + - - +
137E ILE* 4.2 1.1 - - - -
138E PRO* 4.0 14.1 - - + +
140E LEU* 4.3 6.1 - - + -
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Residues in contact with ALA 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PHE* 3.1 32.5 - - + +
79E TYR* 3.8 18.6 - - + -
91E ILE* 4.5 2.5 - - + -
109E VAL* 1.3 75.4 - - - +
111E CYS* 1.3 55.0 + - - +
137E ILE* 3.8 5.0 - - + +
138E PRO 3.1 8.5 + - - +
139E LEU* 3.9 17.0 - - + -
140E LEU* 2.7 35.7 + - - +
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Residues in contact with CYS 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E PHE* 4.0 15.5 - - + -
77E PHE 2.8 9.1 + - - +
78E PHE* 3.1 35.0 - - + +
79E TYR* 2.9 29.9 + - - +
110E ALA* 1.3 76.8 - - - +
112E SER* 1.3 63.5 + - - +
140E LEU* 3.4 34.5 - - + -
142E ASP* 3.8 23.1 - - - -
147E ILE* 4.7 2.7 - - - -
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Residues in contact with SER 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 5.3 2.0 - - - -
79E TYR* 3.2 40.9 + - - -
80E PRO 4.1 1.6 - - - -
111E CYS* 1.3 73.2 - - - +
113E VAL* 1.3 60.5 + - - +
114E ASP* 2.7 31.5 + - - -
119E HIS* 3.2 15.1 - - - -
140E LEU 3.2 7.5 + - - +
141E SER* 3.7 0.7 - - - -
142E ASP* 2.9 28.2 + - - +
148E SER* 5.3 0.9 - - - -
161E THR* 5.3 2.2 - - - -
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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