Contacts of the strand formed by residues 184 - 192 (chain V) 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 ALA 184 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21O GLY* 3.0 37.8 + - - +
39V PRO 3.5 23.6 - - - +
40V LYS* 4.2 8.5 - - + +
42V TRP* 3.9 10.5 - - + +
176V CYS* 4.7 1.8 - - - -
177V VAL 3.3 6.3 - - - -
178V MET* 3.7 29.6 - - + +
182V LYS 3.9 1.0 + - - -
183V ASP* 1.3 72.1 - - - +
185V GLU* 1.3 59.7 + - - +
186V TYR 4.0 0.4 - - - -
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Residues in contact with GLU 185 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O THR* 3.6 16.9 - - - -
148V LYS* 2.8 36.1 + - - +
152V ILE* 5.4 0.5 - - - +
176V CYS* 3.3 4.3 - - - -
177V VAL* 2.7 55.7 + - + +
182V LYS* 6.3 0.2 - - - -
183V ASP 4.7 6.1 - - - +
184V ALA* 1.3 72.6 - - - +
186V TYR* 1.3 60.7 + - - +
187V LEU* 3.7 26.7 + - + +
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Residues in contact with TYR 186 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O THR* 2.7 78.1 + - + +
32V ALA* 4.0 18.2 - - - +
34V LEU* 4.0 31.9 + - + +
42V TRP* 3.7 34.5 - + + -
174V ASP* 4.6 2.5 + - + -
175V VAL 3.8 7.6 - - - -
176V CYS* 4.1 8.7 - - + -
184V ALA 4.0 0.8 + - - -
185V GLU* 1.3 69.8 - - - +
187V LEU* 1.3 66.9 + - - +
189V ARG* 3.6 43.5 + - + -
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Residues in contact with LEU 187 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V ILE* 4.9 5.4 - - + -
175V VAL* 2.6 50.3 + - + +
177V VAL* 4.3 14.1 - - + -
185V GLU* 3.8 28.7 - - + +
186V TYR* 1.3 78.7 - - - +
189V ARG* 1.3 65.0 + - - +
190V ASN 3.3 1.9 + - - -
191V TYR* 3.4 43.3 + - + -
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Residues in contact with ARG 189 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O GLY 4.9 6.3 - - - +
30V ASN* 2.7 52.4 + - - +
31V CYS 3.5 13.3 + - - -
32V ALA* 3.7 15.0 - - - +
174V ASP* 2.7 41.8 + - - -
186V TYR* 3.6 38.0 + - + +
187V LEU* 1.3 69.1 - - - +
190V ASN* 1.3 78.2 + - + +
191V TYR* 3.5 0.5 + - - -
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Residues in contact with ASN 190 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V ASN* 3.1 39.8 + - - +
172V ASN* 3.7 13.9 + - - +
173V VAL 3.5 4.3 - - - -
174V ASP* 2.6 24.2 + - - +
187V LEU 3.3 0.6 + - - -
189V ARG* 1.3 85.5 - - + +
191V TYR* 1.3 62.4 + - - +
192V LEU* 2.9 13.5 + - - +
193V THR* 3.8 18.5 - - + +
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Residues in contact with TYR 191 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152V ILE* 3.4 30.5 - - + +
153V LYS* 5.5 1.2 + - - -
156V SER* 3.6 22.0 - - - -
173V VAL* 2.8 11.0 + - + +
175V VAL* 3.9 18.4 - - + -
187V LEU* 3.4 41.5 + - + +
189V ARG 3.3 2.6 - - - -
190V ASN* 1.3 76.7 - - - +
192V LEU* 1.3 81.5 + - + +
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Residues in contact with LEU 192 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156V SER* 3.0 25.1 - - - +
160V GLN* 3.6 26.9 - - - +
172V ASN* 3.1 8.3 - - - +
173V VAL* 3.0 45.8 + - + +
190V ASN 3.8 0.4 - - - -
191V TYR* 1.3 100.9 - - + +
193V THR* 1.3 65.6 + - - +
194V PRO* 3.4 10.1 - - + -
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Residues in contact with THR 193 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172V ASN* 3.2 25.1 - - - +
190V ASN* 3.8 27.4 - - + +
192V LEU* 1.3 82.6 - - - +
194V PRO* 1.3 58.7 - - - +
195V ASN 3.2 9.5 + - - -
196V VAL* 3.6 22.0 - - - +
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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