Contacts of the strand formed by residues 190 - 197 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA* 5.9 0.2 - - + -
28C ARG* 3.5 43.7 - - + +
30C VAL* 3.8 20.2 - - + -
186C SER* 3.2 6.6 + - - -
187C PHE 3.0 33.2 + - - +
188C LYS 3.1 10.4 - - - +
189C ASP* 1.3 81.0 - - - +
191C ASN* 1.3 63.2 + - - +
192C PHE* 3.6 24.2 + - + -
336C THR* 4.7 3.4 - - - +
339C ILE* 4.3 10.5 - - + -
340C ILE* 3.8 28.7 - - + -
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Residues in contact with ASN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA 2.6 36.1 + - - +
28C ARG 2.8 11.7 + - - +
29C THR* 3.3 17.6 + - + +
30C VAL* 2.7 30.8 + - - +
185C PHE 3.8 3.5 + - - -
186C SER* 4.0 21.8 + - - -
190C LEU* 1.3 70.0 - - - +
192C PHE* 1.3 59.1 + - - +
193C ARG* 5.2 1.8 - - + +
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Residues in contact with PHE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.5 8.5 - - + -
32C LEU* 3.6 34.1 - - + -
184C GLN* 3.2 25.5 - - - +
185C PHE* 2.7 50.9 + + + +
187C PHE* 3.6 32.3 - - + -
190C LEU* 3.7 28.5 - - + -
191C ASN* 1.3 73.5 - - - +
193C ARG* 1.3 63.0 - - - +
194C MET* 3.8 3.1 - - + +
332C PHE* 3.8 17.7 - + - -
336C THR* 3.4 24.7 - - + -
339C ILE* 3.9 10.5 - - + -
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Residues in contact with ARG 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C THR* 3.7 35.7 + - + +
30C VAL 2.8 12.3 + - - +
31C LYS* 3.5 7.3 - - + +
32C LEU* 2.9 25.3 + - - +
182C GLU* 3.8 19.3 + - - +
183C THR 3.7 3.4 - - - -
184C GLN* 4.3 15.9 - - - +
191C ASN* 4.8 2.1 - - + +
192C PHE* 1.3 76.9 - - - +
194C MET* 1.3 59.9 + - - +
195C PHE* 3.5 24.0 - - + -
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Residues in contact with MET 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.3 26.0 - - + +
34C LEU* 3.8 36.6 - - + -
45C ILE* 4.9 3.1 - - + -
46C VAL* 4.5 8.1 - - + -
49C MET* 3.8 29.8 - - + -
181C ILE 3.5 1.0 - - - +
182C GLU* 3.3 2.8 - - - -
183C THR* 2.6 53.9 + - - +
185C PHE* 4.1 10.3 - - + -
192C PHE* 5.3 1.6 - - + -
193C ARG* 1.3 73.0 - - - +
195C PHE* 1.3 62.7 - - - +
196C ASP 4.3 0.4 + - - +
218C ILE* 4.9 2.5 - - + -
332C PHE* 3.6 33.7 - - + -
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Residues in contact with PHE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 4.0 29.2 - - + -
32C LEU 2.8 14.3 + - - +
33C LEU* 3.5 14.0 - - + +
34C LEU* 2.9 26.3 + - - +
35C LEU* 5.9 0.2 - - - +
180C ILE* 4.1 15.0 - - + -
181C ILE 3.3 4.0 - - - +
182C GLU* 3.5 48.9 - - + -
193C ARG* 3.5 32.8 - - + -
194C MET* 1.3 74.4 - - - +
196C ASP* 1.3 61.2 + - - +
210C CYS* 5.8 1.8 - - + -
354C CAC 4.2 13.4 - - + +
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Residues in contact with ASP 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.0 19.1 - - + +
42C LYS* 4.7 5.7 - - + +
43C SER* 3.8 17.9 + - - -
46C VAL* 3.5 34.2 - - + +
177C THR* 4.4 3.3 + - - -
179C GLY 3.7 1.0 - - - +
180C ILE* 3.4 4.9 - - - -
181C ILE* 2.9 71.3 + - - +
183C THR* 4.7 0.9 + - - -
194C MET* 4.3 0.7 - - - +
195C PHE* 1.3 74.4 - - - +
197C VAL* 1.3 66.8 + - - +
354C CAC 3.7 3.7 - - - +
355C ALF 5.6 0.2 - - - -
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU 4.1 4.7 + - - +
35C LEU* 4.1 9.9 - - + -
42C LYS* 3.1 25.7 - - + -
177C THR* 4.8 1.6 - - - -
178C THR 3.6 1.8 - - - +
179C GLY 3.4 8.3 - - - +
196C ASP* 1.3 80.1 - - - +
198C GLY* 1.3 67.6 + - - +
206C LYS* 3.2 30.5 - - - +
207C TRP* 3.2 36.8 - - + +
354C CAC 3.2 37.2 - - + +
355C ALF 3.5 4.5 - - - -
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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