Contacts of the strand formed by residues 243 - 250 (chain B) 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 SER 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B PRO 3.0 9.9 + - - -
112B VAL* 3.6 5.8 - - - +
113B ASP 2.8 28.6 + - - +
242B ALA* 1.3 73.9 - - - +
244B HIS* 1.3 64.0 + - - +
245B LEU* 3.9 8.5 + - - +
305B ASN* 4.5 10.8 + - - +
347B ALA* 5.2 1.7 + - - +
351B ILE* 3.5 39.8 - - - +
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Residues in contact with HIS 244 (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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113B ASP* 3.7 11.4 - - + -
238B TRP* 3.7 40.2 - + + +
239B ARG 3.1 26.6 + - - -
240B ASN* 4.1 15.7 - - - -
242B ALA 2.9 25.6 + - - -
243B SER* 1.3 76.1 + - - +
245B LEU* 1.3 59.1 + - - +
302B LYS 3.6 11.8 + - - -
303B ASN* 3.3 27.5 + - + +
304B ILE* 3.5 9.0 - - + +
305B ASN* 2.8 38.6 + - - +
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Residues in contact with LEU 245 (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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112B VAL* 4.3 14.6 - - + -
113B ASP 2.7 17.9 + - - +
114B ILE* 3.2 16.3 - - + -
115B TYR 3.0 24.1 + - - -
142B MET* 5.3 0.9 - - + -
238B TRP* 3.7 4.8 - - - -
243B SER* 4.8 6.5 - - - +
244B HIS* 1.3 75.0 - - - +
246B LEU* 1.3 59.2 + - - +
247B VAL* 4.0 1.3 + - + -
305B ASN* 3.7 25.6 - - + +
307B ILE* 3.8 14.8 - - + -
344B ILE* 3.8 37.2 - - + +
347B ALA* 3.6 32.8 - - + -
348B TYR* 5.5 0.9 - - - +
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Residues in contact with LEU 246 (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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115B TYR* 3.5 23.1 - - + +
117B LEU* 4.2 19.3 - - + -
226B ILE* 4.1 16.6 - - + +
229B ALA* 4.7 5.8 - - + -
230B THR* 3.8 22.4 - - - +
238B TRP* 4.4 12.6 - - + -
245B LEU* 1.3 73.4 - - - +
247B VAL* 1.3 69.4 + - - +
248B PHE* 5.1 0.2 - - + -
299B LEU* 4.6 0.9 - - + -
304B ILE* 3.6 23.1 - - + -
305B ASN 2.9 10.5 + - - +
306B LEU* 3.5 24.5 - - + +
307B ILE* 2.9 24.9 + - - +
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Residues in contact with VAL 247 (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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114B ILE* 4.2 15.9 - - + -
115B TYR 3.1 10.4 + - - +
116B TYR* 3.6 24.5 - - + -
117B LEU* 2.9 28.1 + - - +
134B LEU* 4.9 0.7 - - + -
138B LEU* 4.2 9.6 - - + -
245B LEU 4.0 0.9 - - - -
246B LEU* 1.3 74.6 - - - +
248B PHE* 1.3 61.1 + - - +
307B ILE* 3.5 16.6 - - + +
309B ALA* 4.1 24.0 - - + +
340B VAL* 4.6 10.3 - - + -
344B ILE* 3.8 29.2 - - + -
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Residues in contact with PHE 248 (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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117B LEU* 3.8 15.9 - - + -
156B PHE* 3.5 30.7 - + - -
222B GLY* 3.5 27.8 - - - -
223B PHE* 4.6 4.7 - + - -
226B ILE* 3.5 25.8 - - + -
246B LEU* 5.1 0.2 - - + -
247B VAL* 1.3 74.6 - - - +
249B THR* 1.3 61.5 + - - +
250B THR* 3.6 28.3 - - + -
254B THR* 5.5 2.2 - - - -
306B LEU* 4.3 7.0 - - + -
307B ILE 2.9 12.7 + - - +
308B PHE* 3.5 25.8 - + + -
309B ALA* 2.7 34.1 + - - +
310B VAL* 4.9 1.1 - - + -
318B TYR* 4.0 17.0 - + - -
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Residues in contact with THR 249 (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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116B TYR* 3.6 32.7 + - + +
117B LEU 2.8 23.1 + - - -
118B MET* 3.6 4.3 - - - +
119B ASP* 3.2 23.2 + - - +
124B MET* 4.7 0.4 - - - -
131B ILE* 4.3 9.5 - - + +
134B LEU* 4.1 2.9 - - + -
156B PHE* 3.4 10.9 - - - -
248B PHE* 1.3 77.4 - - - +
250B THR* 1.3 69.4 + - - +
309B ALA* 3.1 26.9 - - + +
333B LEU* 4.2 13.2 - - + -
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Residues in contact with THR 250 (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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119B ASP* 3.0 23.3 + - - -
124B MET* 4.3 4.5 - - - +
156B PHE* 4.6 1.7 - - - -
220B GLU* 5.0 2.6 - - - +
248B PHE* 3.6 26.2 - - + -
249B THR* 1.3 79.7 - - - +
251B ASP* 1.3 66.6 + - - +
252B ALA* 3.1 17.8 + - - +
253B LYS 4.3 2.9 + - - -
309B ALA 3.5 2.2 + - - +
310B VAL* 3.3 19.7 - - + +
311B THR* 3.2 23.2 + - - +
318B TYR* 3.6 18.2 - - + +
333B LEU* 4.1 3.0 - - - +
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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