Contacts of the strand formed by residues 190 - 197 (chain B) in PDB entry 1TAD
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.4 45.8 - - + +
30B VAL* 4.0 9.2 - - + -
186B SER* 3.3 4.9 - - - -
187B PHE 2.8 32.6 + - - +
188B LYS 3.9 9.0 - - - +
189B ASP* 1.3 85.6 - - - +
191B ASN* 1.3 60.8 + - - +
192B PHE* 3.5 21.2 + - + -
336B THR* 4.4 5.2 - - + -
339B ILE* 3.9 23.1 - - + -
340B ILE* 3.7 29.8 - - + -
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Residues in contact with ASN 191 (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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27B ALA* 2.7 34.1 + - - -
28B ARG 2.8 13.4 + - - +
29B THR* 3.3 17.4 - - + +
30B VAL* 2.9 25.8 + - - +
185B PHE 3.9 4.0 + - - -
186B SER* 3.0 24.4 + - - +
189B ASP 4.0 0.9 - - - +
190B LEU* 1.3 70.0 - - - +
192B PHE* 1.3 62.4 + - - +
193B ARG* 4.4 2.9 - - + +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.6 15.7 - - + -
32B LEU* 4.1 12.8 - - + -
184B GLN* 3.1 8.3 - - - +
185B PHE* 2.7 66.0 + + + +
187B PHE* 3.7 32.8 - + + -
190B LEU* 3.7 22.4 - - + -
191B ASN* 1.3 72.8 - - - +
193B ARG* 1.3 63.4 + - - +
194B MET* 3.8 2.7 - - + +
332B PHE* 3.6 22.9 - + - -
336B THR* 3.5 26.7 - - + -
339B ILE* 3.8 25.4 - - + -
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Residues in contact with ARG 193 (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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63A LEU* 6.0 4.9 - - - +
29B THR* 3.2 38.7 + - + +
30B VAL 2.8 12.2 + - - +
31B LYS* 3.4 7.3 - - - +
32B LEU* 2.9 25.0 + - - +
182B GLU* 3.8 23.8 - - - +
183B THR 3.8 3.1 - - - -
184B GLN* 4.5 14.3 - - + +
191B ASN* 4.4 3.5 + - + +
192B PHE* 1.3 77.8 - - - +
194B MET* 1.3 59.7 + - - +
195B PHE* 3.5 19.1 - - + -
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Residues in contact with MET 194 (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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32B LEU* 3.3 33.7 - - + -
34B LEU* 4.0 27.6 - - + -
45B ILE* 5.0 2.2 - - + -
46B VAL* 4.7 6.3 - - + -
49B MET* 3.7 32.3 - - + -
181B ILE 3.6 0.9 - - - +
182B GLU* 3.3 3.1 - - - -
183B THR* 2.6 59.0 + - - +
185B PHE* 4.1 8.7 - - + -
192B PHE* 5.4 1.3 - - + -
193B ARG* 1.3 74.5 - - - +
195B PHE* 1.3 63.6 + - - +
196B ASP* 5.4 0.4 - - - +
218B ILE* 4.9 2.9 - - + -
332B PHE* 3.7 33.7 - - + -
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Residues in contact with PHE 195 (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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59A LEU* 3.6 33.0 - - + -
60A GLU* 5.4 0.9 - - - -
63A LEU* 3.9 18.2 - - + -
31B LYS* 3.9 23.6 - - + -
32B LEU 2.8 12.0 + - - -
33B LEU* 3.6 17.2 - - + +
34B LEU* 2.8 27.9 + - - +
180B ILE* 4.1 10.8 - - + -
181B ILE 3.2 4.3 - - - +
182B GLU* 3.5 50.5 - - + -
193B ARG* 3.5 28.3 - - + -
194B MET* 1.3 73.7 - - - +
196B ASP* 1.3 60.9 + - - +
354B CAC 4.1 10.7 - - + +
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Residues in contact with ASP 196 (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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34B LEU* 3.8 30.5 - - + +
42B LYS* 4.8 5.1 - - + +
43B SER* 3.9 16.5 + - - -
46B VAL* 3.3 24.6 - - + +
177B THR* 4.3 4.3 + - - -
179B GLY 3.7 0.3 - - - +
180B ILE* 3.4 1.9 - - - +
181B ILE* 3.0 65.3 + - - +
183B THR* 4.6 1.2 + - - -
194B MET* 5.4 0.5 - - - +
195B PHE* 1.3 75.8 - - - +
197B VAL* 1.3 74.4 + - - +
354B CAC 4.1 0.9 - - - -
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Residues in contact with VAL 197 (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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34B LEU 4.1 2.9 + - - +
35B LEU* 4.3 10.3 - - + -
42B LYS* 3.0 25.3 - - - +
177B THR* 4.6 2.0 - - - -
178B THR 4.3 2.7 - - - +
179B GLY 3.4 14.4 - - - +
180B ILE* 3.4 15.9 - - + -
196B ASP* 1.3 87.2 - - - +
198B GLY* 1.3 62.1 + - - +
206B LYS* 5.2 2.2 - - - +
207B TRP* 3.5 30.1 - - + +
354B CAC 3.1 49.6 - - + +
355B ALF 3.3 4.2 - - - -
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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