Contacts of the strand formed by residues 196 - 202 (chain E) in PDB entry 3TNP
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 THR 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E GLY* 1.3 72.8 - - - -
197E PHE* 1.3 70.8 + - - +
212E ASN* 5.9 2.7 - - - +
213E TYR 3.3 7.0 - - - +
214E ASP* 3.1 28.9 - - - +
215E ASN* 4.4 3.8 - - - +
236E ALA* 3.7 1.7 - - - +
237E THR* 2.6 48.2 + - - -
238E SER* 3.1 20.8 + - - +
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Residues in contact with PHE 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E VAL* 4.0 17.5 - - + -
179E VAL* 3.8 28.3 - - + -
192E ILE* 3.7 33.0 - - + -
194E ARG 3.8 12.8 - - - -
195E GLY* 3.5 25.4 - - - -
196E THR* 1.3 79.1 - - - +
198E ASP* 1.3 62.9 + - - +
212E ASN* 2.9 24.6 - - - +
213E TYR* 3.0 24.2 + - + -
234E ILE* 3.9 17.9 - - + -
235E THR 3.1 8.5 - - - +
236E ALA* 3.7 14.6 - - + -
237E THR* 4.1 3.6 - - - -
238E SER 6.0 0.2 - - - -
240E GLY* 4.7 1.3 - - - -
242E LEU* 4.2 23.6 - - + -
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Residues in contact with ASP 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ARG* 4.4 4.8 + - - -
197E PHE* 1.3 72.0 - - - +
199E ILE* 1.3 62.8 + - - +
200E TYR* 4.1 3.4 + - + +
209E CYS* 3.9 18.6 - - - -
211E GLY 3.8 3.0 - - - +
212E ASN* 3.4 19.1 - - - +
233E THR 3.8 0.7 - - - +
234E ILE* 3.4 6.2 - - - +
235E THR* 2.7 41.0 + - - +
237E THR* 3.4 23.2 + - + +
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E ASP* 1.3 74.5 - - - +
200E TYR* 1.3 59.0 + - - +
201E VAL* 5.1 1.3 - - + -
209E CYS* 3.3 6.0 - - - -
210E VAL* 2.7 42.3 + - + -
211E GLY* 2.8 21.7 + - - +
212E ASN* 3.9 17.9 - - - +
213E TYR* 3.4 48.2 - - + +
232E ALA* 3.8 23.6 - - + -
233E THR 3.8 2.2 - - - -
234E ILE* 4.3 9.4 - - + -
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Residues in contact with TYR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329C ASP* 2.4 35.1 + - - +
182E GLN* 4.2 1.1 - - - +
198E ASP* 5.0 4.0 - - + +
199E ILE* 1.3 77.7 - - - +
201E VAL* 1.3 72.0 + - - +
202E LYS* 4.7 9.2 - - + +
207E GLY* 3.3 35.4 - - - -
208E ARG* 3.3 15.3 - - - -
209E CYS* 3.9 8.3 - - + -
210E VAL 4.4 0.2 - - - +
233E THR* 2.8 57.5 + - + +
235E THR* 5.5 3.6 - - - +
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Residues in contact with VAL 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E GLN* 3.5 9.2 - - - +
199E ILE* 5.1 1.3 - - + -
200E TYR* 1.3 82.2 - - - +
202E LYS* 1.3 74.9 + - - +
203E CYS* 4.6 9.2 - - + +
207E GLY* 3.5 0.5 - - - -
208E ARG* 2.9 40.6 + - - +
210E VAL* 4.2 21.4 - - + +
231E ALA 3.2 24.0 - - - +
232E ALA* 3.6 10.8 - - + -
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Residues in contact with LYS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331C GLU* 4.8 9.7 + - - +
182E GLN* 2.9 35.8 + - - +
200E TYR* 4.7 10.0 - - + +
201E VAL* 1.3 75.1 - - - +
203E CYS* 1.3 63.5 + - - +
204E ASP 4.7 3.7 + - - +
205E GLY 4.1 25.8 + - - +
206E VAL 3.2 11.4 - - - +
207E GLY* 4.0 9.6 - - - +
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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