Contacts of the helix formed by residues 151 - 159 (chain E) in PDB entry 1TYE
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 LEU 151 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115E VAL* 4.4 10.3 - - + +
117E GLU* 3.7 49.6 - - + +
120E GLU* 3.6 32.3 - - + +
121E GLU* 3.9 24.5 - - - +
122E ALA 4.4 0.2 - - - +
149E ASN 3.7 5.8 + - - +
150E THR* 1.3 81.5 - - - +
152E SER* 1.3 67.9 + - - +
153E ARG* 3.3 12.8 - - + +
154E ILE* 3.0 29.0 + - + +
155E TYR* 3.9 1.9 + - - -
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Residues in contact with SER 152 (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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120E GLU* 6.2 0.9 - - - -
121E GLU* 2.9 25.0 + - - -
122E ALA* 3.9 15.1 - - - +
123E GLU* 4.5 7.7 + - - +
150E THR 3.9 1.4 + - - -
151E LEU* 1.3 71.4 - - - +
153E ARG* 1.3 64.4 + - - +
155E TYR* 3.0 18.9 + - - +
156E VAL* 3.4 15.6 + - - +
165E ARG* 3.8 15.5 + - - +
179F ASP* 3.9 17.7 + - - -
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Residues in contact with ARG 153 (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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120E GLU* 3.1 37.8 + - - +
151E LEU* 3.2 12.6 + - + +
152E SER* 1.3 78.1 + - - +
154E ILE* 1.3 87.2 + - - +
156E VAL* 3.2 19.8 + - + +
157E GLU* 3.2 42.3 + - + +
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Residues in contact with ILE 154 (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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150E THR* 3.5 21.5 - - + -
151E LEU* 3.0 20.3 + - + +
153E ARG* 1.3 106.7 - - - +
155E TYR* 1.3 58.6 + - + +
157E GLU* 3.2 12.0 + - - +
158E ASN* 2.9 55.0 + - - +
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Residues in contact with TYR 155 (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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122E ALA* 4.7 0.9 - - + -
148E GLY* 5.4 5.9 - - - -
150E THR* 3.5 45.1 + - + -
151E LEU 3.9 9.2 - - - -
152E SER* 3.0 7.4 + - - +
154E ILE* 1.3 77.5 - - - +
156E VAL* 1.3 57.0 + - - +
158E ASN* 4.0 7.0 - - - -
159E ASP 3.0 6.6 + - - -
160E PHE* 2.6 41.3 + - + -
161E SER 3.9 23.1 - - - -
162E TRP* 4.0 14.6 + - + -
163E ASP* 4.0 12.8 - - + -
164E LYS 5.0 1.9 + - - -
165E ARG* 3.2 57.9 - - + +
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Residues in contact with VAL 156 (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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152E SER* 3.7 18.8 - - - +
153E ARG* 3.2 12.9 + - + +
155E TYR* 1.3 77.4 - - - +
157E GLU* 1.3 64.0 + - + +
159E ASP* 3.4 12.6 + - - +
160E PHE* 4.4 25.6 - - + -
165E ARG* 6.2 0.7 - - - +
179F ASP* 5.3 9.9 - - - +
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Residues in contact with GLU 157 (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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153E ARG* 3.2 48.4 + - + +
154E ILE* 3.2 13.1 + - - +
156E VAL* 1.3 74.8 - - + +
158E ASN* 1.3 64.1 + - - +
159E ASP* 3.1 7.2 + - - +
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Residues in contact with ASN 158 (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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154E ILE* 2.9 44.8 + - - +
155E TYR* 3.6 10.2 - - - +
157E GLU* 1.3 78.8 - - - +
159E ASP* 1.3 64.5 + - - +
161E SER* 2.9 50.8 + - - +
162E TRP* 5.0 8.0 - - - -
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Residues in contact with ASP 159 (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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155E TYR 3.0 3.5 + - - -
156E VAL 3.4 9.0 + - - +
157E GLU 3.1 5.4 - - - +
158E ASN* 1.3 82.5 - - - +
160E PHE* 1.3 79.1 + - - +
161E SER* 3.6 2.0 + - - +
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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