Contacts of the strand formed by residues 106 - 111 (chain E) in PDB entry 6A5T
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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25E ARG* 4.7 8.5 - - - +
27E TYR* 4.3 8.9 + - + +
74E LEU* 5.2 5.2 - - + +
75E GLY 5.2 1.7 + - - -
76E THR 3.3 5.5 + - - -
77E LEU* 3.4 25.0 - - + +
78E TRP* 3.3 23.0 + - - +
99E ILE* 6.1 0.8 - - - +
104E PHE* 4.2 4.7 - - - +
105E SER* 1.3 90.3 + - - +
107E GLY* 1.3 66.0 + - - +
130E ILE* 3.5 15.0 - - + +
132E GLU* 4.2 20.9 - - + +
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Residues in contact with GLY 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E TRP* 3.7 6.1 - - - -
95E PHE* 4.6 8.7 - - - -
99E ILE* 5.0 6.6 - - - +
106E THR* 1.3 72.9 - - - +
108E ILE* 1.3 70.3 + - - +
109E PHE 4.3 0.2 - - - -
130E ILE 3.0 11.7 + - - -
131E ILE* 3.8 18.1 - - - +
132E GLU* 3.2 27.4 + - - +
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Residues in contact with ILE 108 (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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18E VAL* 5.5 2.5 - - + -
21E MET* 4.6 12.3 - - - -
25E ARG* 3.6 23.6 - - - +
77E LEU* 3.6 26.9 - - + -
78E TRP 3.3 9.6 + - - +
79E VAL* 3.6 15.8 - - + -
80E GLU* 3.0 28.4 + - - +
95E PHE* 4.5 4.6 - - - -
106E THR* 5.0 0.4 - - + -
107E GLY* 1.3 80.4 - - - +
109E PHE* 1.3 60.5 + - - +
110E ILE* 3.3 24.2 - - + -
132E GLU* 3.7 17.0 - - + +
133E THR 5.5 0.2 - - - -
134E PHE* 4.1 16.6 - - + -
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Residues in contact with PHE 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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80E GLU* 3.6 9.9 - - + -
81E PHE 4.2 7.0 - - - -
82E CYS* 3.8 32.1 - - + -
87E VAL* 4.2 28.0 - - + -
91E THR* 4.8 8.7 - - + -
92E MET* 4.5 21.3 - - + -
95E PHE* 4.0 45.1 - + + -
108E ILE* 1.3 76.3 - - - +
110E ILE* 1.3 59.7 + - - +
111E TYR* 3.4 21.8 + - + -
115E ILE* 5.0 9.0 - - + -
131E ILE* 5.8 0.4 - - + -
132E GLU 3.7 14.4 + - - +
133E THR* 4.0 16.8 - - + +
134E PHE 3.9 7.4 - - - +
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Residues in contact with ILE 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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14E SER* 6.4 0.7 - - - -
18E VAL* 4.8 10.3 - - + -
54E ARG* 5.8 1.0 + - - -
79E VAL* 4.2 7.2 - - + -
80E GLU 3.1 10.7 + - - +
81E PHE* 3.5 55.0 - - + +
82E CYS 3.9 3.6 + - - +
108E ILE* 3.3 30.7 - - + +
109E PHE* 1.3 73.1 - - - +
111E TYR* 1.3 71.6 + - - +
134E PHE* 3.7 21.1 - - + +
136E GLU* 3.7 29.8 - - + +
139E LEU* 4.6 8.5 - - + -
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Residues in contact with TYR 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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54E ARG* 5.8 0.2 - - - -
82E CYS* 5.2 7.6 - - - -
84E GLU 5.6 0.2 - - - -
85E PRO 5.7 0.7 - - - +
87E VAL* 4.7 9.9 - - + -
109E PHE* 3.4 26.3 + - + -
110E ILE* 1.3 77.8 - - - +
112E GLN* 1.3 65.2 + - - +
113E ASN 3.1 45.0 + - - -
114E ASN* 3.2 20.7 - - - +
115E ILE* 4.3 22.4 - - + -
133E THR* 4.5 6.5 - - - -
134E PHE 3.2 23.1 - - - -
135E GLN* 3.0 37.3 + - + +
136E GLU* 3.3 24.4 + - - +
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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