Contacts of the strand formed by residues 183 - 191 (chain Y) in PDB entry 3TDD
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 GLY 183 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39Y PRO* 3.1 17.5 - - - -
40Y PHE* 3.8 9.8 - - - -
178Y VAL* 4.7 2.2 - - - -
179Y THR* 2.6 43.1 + - - +
180Y GLU 3.2 2.0 + - - -
181Y ASP* 1.3 80.8 - - - +
184Y TRP* 1.3 63.6 + - - -
185Y ILE* 4.5 1.4 - - - +
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Residues in contact with TRP 184 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y GLU* 3.4 37.9 - - + +
38Y ASN 2.8 23.4 + - - -
39Y PRO* 3.1 34.0 + - + +
40Y PHE* 4.0 2.9 - - - +
41Y LEU 4.1 5.4 - - - -
42Y LEU* 3.6 42.9 - - + +
176Y TYR* 3.6 22.0 - + + -
177Y HIS 3.1 11.0 - - - +
178Y VAL* 3.9 7.6 - - + +
183Y GLY* 1.3 75.7 - - - -
185Y ILE* 1.3 67.7 + - - +
186Y TYR* 3.7 17.3 - - + -
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Residues in contact with ILE 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176Y TYR* 3.6 1.2 - - - -
177Y HIS* 2.6 44.6 + - + +
179Y THR* 3.8 30.1 - - + +
183Y GLY 4.5 2.5 - - - +
184Y TRP* 1.3 82.4 - - - +
186Y TYR* 1.3 74.3 + - - +
187Y HIS* 3.1 21.0 - - + +
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Residues in contact with TYR 186 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y GLU* 5.5 0.4 - - - +
174Y ASN* 2.7 29.5 + - - -
175Y LEU 3.1 21.1 - - - -
176Y TYR* 3.6 37.2 - + + -
184Y TRP* 3.7 15.5 - - + -
185Y ILE* 1.3 82.8 - - - +
187Y HIS* 1.3 61.8 + - - +
188Y GLY* 3.4 28.9 + - - -
189Y ASN* 3.1 15.3 + - + +
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Residues in contact with HIS 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148Y VAL* 5.5 2.0 - - + -
152Y LEU* 3.4 34.0 - - + +
175Y LEU* 2.8 31.6 + - + +
177Y HIS* 3.7 26.8 + - + +
185Y ILE* 3.1 38.5 + - + +
186Y TYR* 1.3 74.4 + - - +
188Y GLY* 1.3 59.6 + - - +
190Y HIS* 2.9 23.0 + - - -
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Residues in contact with GLY 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Y VAL 3.4 0.7 - - - +
175Y LEU 3.2 24.6 + - - -
186Y TYR* 3.1 29.6 + - - -
187Y HIS* 1.3 76.5 - - - +
189Y ASN* 1.3 60.3 + - - -
190Y HIS* 3.2 13.4 + - - -
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Residues in contact with ASN 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18Y SER* 5.4 0.4 - - - -
30Y THR* 6.3 0.8 - - - +
172Y SER* 2.7 33.1 + - - -
173Y VAL 3.2 4.7 - - - -
174Y ASN* 3.1 26.2 + - - +
186Y TYR* 3.1 7.3 + - - +
188Y GLY* 1.3 72.4 - - - -
190Y HIS* 1.3 63.6 + - - +
191Y ASP* 4.0 5.5 + - - +
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Residues in contact with HIS 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Y LYS* 4.2 26.1 + - + -
172Y SER* 3.8 1.1 - - - -
173Y VAL* 2.7 51.5 + - + +
175Y LEU* 3.8 17.0 - - + +
187Y HIS 2.9 27.1 + - - -
188Y GLY* 3.2 17.9 + - - -
189Y ASN* 1.3 74.9 + - - +
191Y ASP* 1.3 67.0 + - - +
192Y VAL* 3.1 1.2 + - - -
195Y LEU* 4.4 16.9 - - + +
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Residues in contact with ASP 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I ARG* 3.4 17.5 + - - -
171Y GLY 3.3 16.4 - - - +
172Y SER* 3.7 7.8 - - - -
189Y ASN* 4.0 6.3 + - - +
190Y HIS* 1.3 69.3 - - - +
192Y VAL* 1.3 58.8 + - - +
193Y GLY* 2.8 7.9 + - - -
194Y GLU* 2.7 54.1 + - - +
195Y LEU* 2.9 28.6 + - - +
14Z LYS* 6.2 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