Contacts of the strand formed by residues 149 - 156 (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 LEU 149 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B VAL* 3.1 32.8 - - + +
114B ILE* 4.3 12.8 - - + -
139B ALA* 3.9 23.6 - - - +
142B MET* 3.7 37.5 - - + -
143B ARG* 4.1 17.4 - - - +
146B THR* 4.3 10.1 - - + +
147B SER 3.9 2.2 + - - -
148B ASN* 1.3 77.8 + - - +
150B ARG* 1.3 88.5 + - - +
151B ILE* 4.1 10.8 - - + +
197B THR 4.7 0.2 - - - -
198B ASP* 3.7 15.0 - - - +
200B VAL* 5.0 9.3 - - + +
239B ARG* 4.5 0.2 - - - +
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Residues in contact with ARG 150 (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 3.3 5.1 + - - -
113B ASP* 3.4 16.2 - - - +
114B ILE 3.3 14.6 + - - -
148B ASN* 4.3 11.5 + - - -
149B LEU* 1.3 87.1 + - - +
151B ILE* 1.3 60.5 + - - +
196B LEU* 3.3 25.5 - - + +
197B THR* 3.4 9.0 - - - +
198B ASP* 3.5 34.4 + - - +
239B ARG* 3.4 41.3 - - - +
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Residues in contact with ILE 151 (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* 3.3 32.8 - - + +
116B TYR* 5.8 0.4 - - + -
138B LEU* 4.4 6.7 - - + -
139B ALA* 3.8 37.9 - - + +
149B LEU* 4.1 12.4 - - + +
150B ARG* 1.3 73.2 - - - +
152B GLY* 1.3 68.9 + - - +
195B THR 3.8 1.4 - - - +
196B LEU* 3.3 3.8 - - - -
197B THR* 2.8 39.2 + - + +
199B GLN 5.4 0.4 - - - +
200B VAL* 5.0 11.4 - - + -
203B PHE* 3.6 47.2 - - + -
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Residues in contact with GLY 152 (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 3.1 6.8 + - - +
115B TYR* 3.5 7.9 - - - -
116B TYR* 2.9 20.3 + - - +
151B ILE* 1.3 78.8 - - - +
153B PHE* 1.3 63.2 + - - +
194B LEU* 3.4 15.5 - - - -
195B THR 4.3 1.1 - - - -
196B LEU* 3.4 8.5 - - - +
203B PHE* 3.5 15.2 - - - -
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Residues in contact with PHE 153 (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* 3.4 14.8 + - - -
116B TYR* 3.1 24.7 - - + +
118B MET* 3.4 32.5 - - - -
152B GLY* 1.3 76.4 - - - +
154B GLY* 1.3 63.9 + - - +
155B ALA* 5.7 0.4 - - + -
193B VAL* 3.4 33.3 + - + +
194B LEU* 3.0 58.2 + - + +
203B PHE* 3.7 17.3 - + + -
206B GLU* 3.8 21.5 - - + -
207B VAL* 3.9 13.2 - - + -
210B GLN* 3.9 20.9 - - + -
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Residues in contact with GLY 154 (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* 3.3 17.7 + - - -
116B TYR 2.8 9.3 + - - +
117B LEU* 3.4 6.5 - - - -
118B MET* 2.8 27.4 + - - +
153B PHE* 1.3 75.8 - - - +
155B ALA* 1.3 61.5 + - - +
190B TYR* 4.3 1.3 - - - -
191B LYS 3.4 10.5 - - - -
193B VAL* 3.6 8.5 - - - -
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Residues in contact with ALA 155 (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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118B MET* 3.2 11.9 - - + +
120B LEU* 3.4 33.0 - - + -
153B PHE* 5.7 0.2 - - + -
154B GLY* 1.3 75.0 - - - +
156B PHE* 1.3 63.8 + - - +
188B PHE* 3.4 13.2 - - + -
190B TYR* 3.2 7.6 - - - -
191B LYS* 2.8 40.8 + - + +
193B VAL* 4.3 5.3 - - + +
210B GLN* 4.7 4.3 - - - +
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Residues in contact with PHE 156 (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* 4.1 10.8 - - + -
118B MET 2.9 12.0 + - - -
119B ASP* 3.5 32.4 - - + -
120B LEU* 3.0 25.8 + - - +
155B ALA* 1.3 77.2 - - - +
157B VAL* 1.3 71.9 + - - +
188B PHE* 4.0 2.9 - - - -
189B GLY 3.2 15.5 - - - +
190B TYR* 4.3 0.4 - - - -
220B GLU* 4.2 9.9 - - + -
221B GLY 3.9 4.9 - - - +
222B GLY* 3.4 24.5 - - - -
225B ALA* 3.8 26.9 - - + -
248B PHE* 3.5 32.5 - + - -
249B THR 3.4 23.6 - - - -
250B THR* 4.6 1.1 - - - -
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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