Contacts of the strand formed by residues 211 - 217 (chain B) in PDB entry 3TJK
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA* 3.8 26.7 - - + -
80B LYS 3.6 31.6 - - - +
81B ILE* 3.4 3.5 - - - +
82B SER 2.8 30.1 + - - -
83B LYS 3.0 11.9 + - - +
85B ALA* 3.9 14.2 - - + +
86B PRO* 5.4 0.4 - - + -
188B TYR* 5.4 0.7 - - + -
203B PHE* 3.8 22.4 - - + -
204B ILE 3.5 17.5 - - - +
205B ILE* 3.9 11.2 - - + +
209B GLY 3.8 2.2 + - - -
210B ILE* 1.3 73.1 - - - +
212B ARG* 1.3 59.7 + - - +
213B GLN 3.6 18.4 - - - +
214B ILE* 3.9 17.5 - - + -
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Residues in contact with ARG 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 3.0 57.9 + - - +
220A PRO* 4.1 13.5 - - - +
81B ILE* 3.7 8.1 - - - -
110B TYR* 3.4 15.2 + - + +
204B ILE* 2.8 12.7 + - + +
206B ASP* 3.2 40.3 + - + +
210B ILE* 3.3 24.9 - - - +
211B LEU* 1.3 75.8 - - - +
213B GLN* 1.3 60.6 + - + +
235B PHE* 3.3 43.2 - - + -
238B THR* 5.2 1.0 + - - -
239B ASP* 3.0 27.7 + - - -
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A THR* 3.6 12.1 - - - +
216A LEU 3.4 5.5 + - - +
217A ASN* 3.1 28.7 + - - +
81B ILE* 3.6 3.5 - - - +
202B LEU* 3.9 12.6 - - - +
203B PHE* 3.4 4.9 - - - -
204B ILE* 3.0 44.5 + - + +
211B LEU* 3.6 3.3 - - - +
212B ARG* 1.3 79.7 - - - +
214B ILE* 1.3 88.9 + - - +
215B THR* 2.6 30.6 + - - -
231B LEU* 3.9 19.9 - - + +
235B PHE* 3.9 15.7 - - + -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A HIS* 6.5 0.4 - - + -
214A ILE* 3.9 0.8 - - + +
215A THR* 3.6 0.9 - - - -
216A LEU* 2.8 60.8 + - + -
79B ALA* 4.2 14.4 - - + +
81B ILE* 3.6 21.1 - - + +
202B LEU 3.5 4.3 - - - +
203B PHE* 3.9 17.9 - - + -
211B LEU* 3.9 24.7 - - + -
213B GLN* 1.3 83.4 + - - +
215B THR* 1.3 64.6 + - - +
216B LEU* 3.6 33.7 - - + -
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 3.5 22.7 - - - +
214A ILE 3.5 3.4 - - - +
215A THR* 4.5 5.0 - - + +
231A LEU* 6.2 0.9 - - + -
200B ARG 3.6 2.1 - - - +
201B GLY* 3.4 1.9 - - - -
202B LEU* 2.7 50.1 + - + +
213B GLN* 2.6 33.2 + - - +
214B ILE* 1.3 72.7 - - - +
216B LEU* 1.3 60.6 - - - +
217B ASN* 3.8 8.7 - - - +
223B ARG* 4.8 11.6 - - + -
231B LEU* 4.8 4.0 - - - +
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.8 12.0 - - + +
213A GLN* 3.3 8.0 + - - -
214A ILE* 2.8 67.2 + - + +
216A LEU* 6.4 0.2 - - + -
75B HIS* 5.5 6.7 - - + +
188B TYR 5.5 0.2 - - - +
189B GLY 5.1 9.0 - - - +
190B VAL* 3.9 17.0 - - + -
199B LEU* 4.3 13.5 - - + -
200B ARG 3.4 2.9 - - - -
201B GLY* 3.7 15.3 - - - -
203B PHE* 4.2 5.4 - - + -
214B ILE* 3.6 25.1 - - + -
215B THR* 1.3 80.2 - - - +
217B ASN* 1.3 62.6 + - - +
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Residues in contact with ASN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.4 4.0 - - - -
212A ARG 4.1 3.1 - - - -
213A GLN* 2.9 31.8 + - - -
231A LEU* 3.7 16.4 - - - +
235A PHE* 4.9 2.0 - - + -
199B LEU* 3.8 6.0 - - - +
200B ARG* 2.9 37.6 + - + -
215B THR* 3.8 8.3 - - - +
216B LEU* 1.3 73.4 - - - +
218B ASP* 1.3 64.9 + - - +
219B LEU 3.8 0.3 + - - -
221B VAL* 3.1 30.4 + - - +
222B GLY 3.5 14.6 + - - -
223B ARG* 3.7 15.3 - - - +
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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