Contacts of the strand formed by residues 211 - 217 (chain C) in PDB entry 3TJF
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 211 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ALA* 3.7 31.2 - - + -
80C LYS 3.7 19.1 - - - +
81C ILE* 3.3 3.9 - - - -
82C SER* 2.6 33.8 + - - -
83C LYS 3.0 17.1 + - - +
85C ALA* 3.9 12.5 - - + +
86C PRO* 5.1 3.8 - - + -
188C TYR* 5.4 0.7 - - + -
203C PHE* 3.8 22.9 - - + -
204C ILE 3.6 11.2 - - - +
205C ILE* 4.1 10.5 - - + +
210C ILE* 1.3 71.1 - - - +
212C ARG* 1.3 58.8 + - - +
213C GLN 3.6 23.3 - - - +
214C ILE* 3.7 20.9 - - + -
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Residues in contact with ARG 212 (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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81C ILE* 3.7 6.2 - - - +
110C TYR* 3.3 20.8 + - + +
204C ILE* 2.8 15.1 + - + +
206C ASP* 3.3 33.9 + - + +
210C ILE* 3.5 20.5 - - - +
211C LEU* 1.3 76.5 - - - +
213C GLN* 1.3 61.9 + - + +
235C PHE* 3.3 39.3 - - + -
238C THR* 4.8 1.2 + - - -
239C ASP* 2.8 28.1 + - - -
218D ASP* 2.9 60.5 + - - +
220D PRO* 4.0 16.6 - - - +
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Residues in contact with GLN 213 (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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81C ILE* 3.6 3.1 - - - +
202C LEU* 4.2 5.4 - - - +
203C PHE* 3.4 5.9 - - - -
204C ILE* 2.9 43.3 + - + +
211C LEU* 3.6 5.1 - - - +
212C ARG* 1.3 80.5 - - - +
214C ILE* 1.3 80.4 + - - +
215C THR* 2.8 30.1 + - - -
231C LEU* 3.8 25.4 - - + +
235C PHE* 3.7 18.8 - - + -
215D THR* 3.5 11.1 - - - +
216D LEU 3.4 6.7 + - - +
217D ASN* 3.0 29.4 + - - +
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Residues in contact with ILE 214 (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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79C ALA* 4.3 13.9 - - + +
80C LYS* 5.2 0.2 - - - -
81C ILE* 3.5 25.1 - - + +
202C LEU 3.5 3.4 - - - -
203C PHE* 3.8 24.7 - - + -
211C LEU* 3.7 20.4 - - + -
213C GLN* 1.3 79.1 + - - +
215C THR* 1.3 64.8 + - - +
216C LEU* 3.8 34.5 - - + -
214D ILE* 3.9 1.1 - - + +
215D THR* 3.5 1.6 - - - -
216D LEU* 2.8 58.2 + - + -
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Residues in contact with THR 215 (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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200C ARG 3.6 1.6 - - - +
201C GLY* 3.4 2.1 - - - -
202C LEU* 2.7 51.9 + - + +
213C GLN* 2.8 31.7 + - - -
214C ILE* 1.3 72.0 - - - +
216C LEU* 1.3 60.3 + - - +
217C ASN* 3.7 10.1 - - - +
223C ARG* 4.6 14.4 - - + -
231C LEU* 4.8 3.6 - - - +
213D GLN* 3.6 20.9 - - - +
214D ILE 3.6 3.4 - - - -
215D THR* 4.4 4.8 - - + +
227D GLU* 6.0 1.6 - - - +
231D LEU* 6.0 1.6 - - + -
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Residues in contact with LEU 216 (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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75C HIS* 5.3 9.6 - - + +
188C TYR 6.0 0.2 - - - +
189C GLY 4.7 11.7 - - - +
190C VAL* 3.7 18.2 - - + -
199C LEU* 4.1 10.3 - - + -
200C ARG 3.5 2.0 - - - -
201C GLY* 3.7 17.0 - - - -
203C PHE* 4.1 4.7 - - + -
214C ILE* 3.8 24.7 - - + -
215C THR* 1.3 82.6 - - - +
217C ASN* 1.3 61.2 + - - +
81D ILE* 3.9 14.6 - - + +
213D GLN* 3.4 8.3 + - - -
214D ILE* 2.8 61.4 + - + +
216D LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 217 (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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199C LEU* 3.7 6.5 - - - +
200C ARG* 2.8 39.9 + - + +
215C THR* 3.7 7.6 - - - +
216C LEU* 1.3 73.3 - - - +
218C ASP* 1.3 64.5 + - - +
221C VAL* 3.0 29.9 + - - +
222C GLY 3.3 20.0 + - - -
223C ARG* 3.6 15.0 - - - +
81D ILE* 4.6 3.1 - - - -
212D ARG 4.2 2.2 - - - -
213D GLN* 3.1 25.2 + - - +
231D LEU* 3.6 20.2 - - - +
235D PHE* 4.8 2.2 - - + -
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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