Contacts of the strand formed by residues 231 - 238 (chain A) in PDB entry 1T0P
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLY* 5.7 1.4 - - - -
129A ASN 2.9 15.5 + - - -
130A VAL* 3.4 13.3 - - + +
131A ASP* 2.9 25.1 + - - +
229A ASP 3.8 1.7 + - - -
230A ALA* 1.3 70.9 - - - +
232A LYS* 1.3 64.7 + - - +
233A VAL* 4.3 6.5 - - + -
255A ILE* 3.8 29.8 - - + -
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Residues in contact with LYS 232 (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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131A ASP* 3.5 6.7 - - + +
216A ALA 5.1 4.2 + - - -
220A PHE* 3.8 53.2 + - + +
226A ALA* 6.4 0.4 - - - -
227A ARG 5.9 2.9 - - - +
228A PRO* 5.9 4.0 - - - -
230A ALA 3.5 9.6 + - - +
231A THR* 1.3 76.2 - - - +
233A VAL* 1.3 63.9 + - - +
253A ASP* 4.3 14.6 + - + +
254A ILE* 3.6 24.5 - - + +
255A ILE* 3.0 26.3 + - - +
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Residues in contact with VAL 233 (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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130A VAL* 3.6 22.7 - - + -
131A ASP 2.9 8.4 + - - +
132A LEU* 3.3 28.9 - - + -
133A VAL 2.9 25.2 + - - -
220A PHE* 3.6 5.7 - - - -
231A THR* 4.3 9.0 - - + -
232A LYS* 1.3 79.4 - - - +
234A LEU* 1.3 66.4 + - - +
235A ILE* 4.5 0.9 - - + -
254A ILE* 4.0 2.9 - - - -
255A ILE* 3.4 22.0 - - + +
257A TYR* 3.9 26.2 - - + -
298A LEU* 4.7 9.9 - - + -
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Residues in contact with LEU 234 (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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133A VAL* 3.4 28.7 - - + +
135A LEU* 3.7 26.9 - - + -
212A ILE* 4.1 26.2 - - + +
215A VAL* 3.9 21.8 - - + -
233A VAL* 1.3 74.7 - - - +
235A ILE* 1.3 63.7 + - - +
236A ILE* 3.8 17.3 - - + -
254A ILE* 3.7 20.6 - - + -
255A ILE 2.8 11.4 + - - +
256A ARG* 4.1 15.9 - - + -
257A TYR* 2.9 30.1 + - - +
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Residues in contact with ILE 235 (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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132A LEU* 3.7 31.6 - - + -
133A VAL 2.9 9.2 + - - +
134A PHE* 3.5 33.5 - - + -
135A LEU* 2.9 26.3 + - - +
153A PHE* 4.6 1.3 - - + -
157A VAL* 4.9 2.5 - - + -
233A VAL* 4.5 4.3 - - + -
234A LEU* 1.3 74.6 - - - +
236A ILE* 1.3 59.1 + - - +
237A ILE* 3.7 13.7 + - + +
257A TYR* 3.7 5.2 - - + -
259A ILE* 3.6 29.6 - - + -
295A LEU* 4.0 32.8 - - + -
298A LEU* 4.2 4.7 - - + -
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Residues in contact with ILE 236 (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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135A LEU* 3.3 20.6 - - + +
173A PHE* 4.3 14.1 - - + -
208A THR* 4.6 7.2 - - + -
212A ILE* 3.7 32.1 - - + -
234A LEU* 3.8 22.7 - - + -
235A ILE* 1.3 72.7 - - - +
237A ILE* 1.3 61.0 + - - +
238A THR* 3.8 19.4 + - + -
256A ARG* 4.6 11.2 - - + -
257A TYR 2.8 17.0 + - - +
258A ILE* 3.3 24.1 - - + +
259A ILE 2.8 25.2 + - - +
277A PHE* 4.4 3.8 - - + -
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Residues in contact with ILE 237 (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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134A PHE* 4.2 10.8 - - + -
135A LEU 3.0 6.9 + - - +
136A PHE* 4.3 5.4 - - + -
137A ASP* 2.9 30.1 + - - +
150A ILE* 3.8 27.2 - - + +
153A PHE* 3.8 15.7 - - + -
154A MET* 3.6 35.4 - - + -
173A PHE* 4.4 0.2 - - - -
235A ILE* 4.0 16.2 - - + +
236A ILE* 1.3 70.8 - - - +
238A THR* 1.3 62.6 + - - +
259A ILE* 3.3 19.5 - - + +
261A ILE* 4.3 2.9 - - + -
289A LEU* 3.8 26.9 - - + -
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Residues in contact with THR 238 (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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137A ASP* 2.6 30.3 + - - -
142A LEU* 5.1 0.2 - - - -
173A PHE* 4.1 12.2 - - + -
208A THR* 5.0 3.7 + - + -
236A ILE* 3.9 22.7 - - + +
237A ILE* 1.3 78.2 - - - +
239A ASP* 1.3 64.7 + - - +
240A GLY* 3.2 20.9 + - - +
241A GLU 4.4 5.5 + - - -
258A ILE* 4.4 15.5 - - + -
259A ILE 3.1 4.5 + - - +
260A GLY* 3.3 9.2 - - - -
261A ILE* 3.2 27.1 + - - +
265A PHE* 4.0 1.0 - - - -
277A PHE* 6.1 1.8 - - + -
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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