Contacts of the strand formed by residues 144 - 150 (chain B) in PDB entry 1PT6
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 ASP 144 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B LEU* 1.3 70.6 - - - +
145B ILE* 1.3 60.5 + - - +
180B GLN* 3.1 17.0 - - - +
196B LEU* 3.8 14.6 - - + -
234B PHE* 3.5 18.6 - - + -
240B ALA* 3.3 8.5 - - - +
241B ARG* 2.9 58.3 + - - +
244B VAL* 3.5 16.4 - - + +
245B LYS 3.0 6.8 + - - +
246B LYS* 3.5 2.7 - - + +
247B VAL 2.9 25.8 + - - -
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Residues in contact with ILE 145 (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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143B LEU* 4.0 18.2 - - + -
144B ASP* 1.3 77.2 - - - +
146B VAL* 1.3 62.7 + - - +
147B ILE* 4.1 13.7 - - + -
168B LEU* 6.2 0.7 - - + -
169B LEU* 6.1 0.2 - - + -
172B MET* 3.7 25.4 - - + -
179B THR* 3.7 17.7 - - + -
180B GLN 2.9 13.1 + - - +
181B VAL* 3.1 10.7 - - + +
182B GLY 2.9 25.1 + - - +
196B LEU* 3.4 1.4 - - - +
247B VAL* 3.2 15.3 - - + +
249B VAL* 4.2 22.2 - - + -
331B ILE* 3.6 27.8 - - + -
332B PHE* 4.2 0.9 - - + -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 1.3 76.2 - - - +
147B ILE* 1.3 70.6 + - - +
148B VAL* 4.1 1.1 - - + -
182B GLY* 3.2 10.8 - - - +
184B VAL* 4.1 8.7 - - + -
196B LEU* 4.1 15.5 - - + -
229B ALA* 3.9 24.9 - - + -
233B ALA* 3.9 23.3 - - + -
234B PHE* 3.4 35.4 - - + -
247B VAL 2.9 7.3 + - - -
248B MET* 3.2 7.7 - - + +
249B VAL 3.0 22.3 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 4.4 12.6 - - + -
146B VAL* 1.3 74.3 - - - +
148B VAL* 1.3 63.1 + - - +
149B LEU* 3.4 30.5 - - + -
164B PHE* 5.2 1.1 - - + -
165B LEU* 3.9 23.3 - - + -
168B LEU* 4.3 14.4 - - + -
169B LEU* 4.0 25.4 - - + -
181B VAL* 4.4 8.5 - - + -
182B GLY 2.9 10.1 + - - +
183B ILE* 3.3 11.3 - - + +
184B VAL* 2.9 28.6 + - - +
249B VAL* 3.4 25.4 - - + +
251B VAL* 4.7 4.7 - - + -
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Residues in contact with VAL 148 (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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146B VAL* 4.1 3.6 - - + -
147B ILE* 1.3 74.7 - - - +
149B LEU* 1.3 61.0 + - - +
150B ASP 4.0 0.2 + - - -
184B VAL* 3.4 9.2 - - + +
186B TYR* 3.6 26.4 - - + -
225B GLY* 3.7 22.0 - - - +
226B THR* 4.1 2.9 - - - +
229B ALA* 3.6 29.6 - - + -
248B MET* 3.6 24.0 - - + -
249B VAL 2.8 11.2 + - - +
250B ILE* 3.4 12.9 - - + +
251B VAL* 2.9 27.0 + - - +
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Residues in contact with LEU 149 (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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147B ILE* 3.4 28.3 - - + -
148B VAL* 1.3 72.4 - - - +
150B ASP* 1.3 65.7 + - - +
151B GLY 3.4 0.5 + - - -
158B TRP* 4.3 15.9 - - + -
161B VAL* 4.2 19.5 - - + -
164B PHE* 5.1 1.1 - - + -
165B LEU* 4.0 31.2 - - + -
183B ILE* 4.0 18.8 - - + -
184B VAL 2.9 11.1 + - - +
185B GLN* 3.3 8.9 - - + -
186B TYR* 2.8 31.4 + - - -
212B ILE* 4.7 7.9 - - + -
251B VAL* 3.9 21.1 - - + -
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Residues in contact with ASP 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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149B LEU* 1.3 71.0 - - - +
151B GLY* 1.3 56.7 + - - +
152B SER* 2.9 31.2 + - - -
155B ILE* 2.9 26.2 - - + +
158B TRP* 3.7 9.5 - - - -
186B TYR* 3.4 22.3 - - - +
187B GLY* 5.2 1.4 - - - -
220B THR* 3.5 16.5 + - - +
251B VAL* 2.9 23.7 + - - +
252B THR* 2.9 25.7 + - - -
253B ASP* 3.2 14.7 + - - +
254B GLY 4.1 0.3 + - - -
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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