Contacts of the helix formed by residues 357 - 362 (chain A) in PDB entry 1TF5
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 PHE 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ASN* 3.9 23.3 - - + -
178A ASN* 3.7 34.5 - - - -
212A ILE* 3.7 36.3 - - + +
213A LEU* 4.9 0.7 - - + -
216A GLU* 3.2 44.6 - - + +
217A ALA 3.6 0.6 + - - +
219A THR* 3.4 31.3 + - + -
221A LEU* 4.0 21.3 - - + -
356A THR* 1.3 73.1 - - - +
358A GLN* 1.3 63.5 + - - +
360A TYR* 3.2 5.0 + + - +
361A PHE* 3.0 37.0 + + + -
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Residues in contact with GLN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.7 2.7 + - - -
217A ALA* 3.1 27.2 + - - +
218A ARG* 5.1 4.9 - - - +
356A THR* 3.8 3.7 + - - +
357A PHE* 1.3 82.2 - - - +
359A ASN* 1.3 68.2 + - - +
361A PHE 4.1 0.2 - - - -
362A ARG* 3.2 46.8 + - - +
384A ILE* 3.6 26.7 - - - +
385A TYR* 3.2 37.6 + - + +
597A LEU* 3.9 19.0 - - - +
600A ASP* 4.4 13.2 - - - +
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Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE* 3.7 5.7 - - + +
356A THR* 3.2 20.8 + - - +
358A GLN* 1.3 80.1 + - - +
360A TYR* 1.3 64.9 + - - +
362A ARG* 2.9 40.7 + - - +
363A MET* 3.3 22.0 + - - +
600A ASP* 4.5 17.0 + - - +
601A ASP* 5.3 0.2 + - - -
604A ARG* 2.9 32.9 - - - +
607A ARG* 3.4 23.0 + - - +
608A GLU* 4.9 0.9 - - - +
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Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASN 4.8 2.0 - - - -
180A LEU* 3.5 26.4 - - + +
181A GLY* 4.0 13.9 - - - -
184A TYR* 3.4 44.0 - + + -
198A GLN* 3.1 19.6 + - - -
201A LEU* 3.9 14.2 - - + +
221A LEU* 5.6 1.3 - - + -
355A ILE* 3.4 17.6 - - + +
356A THR 2.9 17.3 + - - +
357A PHE* 3.6 5.2 - + - +
359A ASN* 1.3 78.6 - - - +
361A PHE* 1.3 80.6 + + - +
363A MET* 2.9 27.9 + - + +
364A TYR* 2.6 41.7 + + - -
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 4.1 22.0 - - + -
177A ASN* 3.2 40.2 - - + -
180A LEU* 4.4 2.5 - - + -
204A ALA* 4.2 5.2 - - + -
206A ILE* 3.8 21.1 - - + -
212A ILE* 4.0 9.0 - - + -
213A LEU* 3.9 24.5 - - + -
357A PHE* 3.0 30.0 + + + +
358A GLN 4.2 3.4 - - - +
360A TYR* 1.3 96.1 - + - +
362A ARG* 1.3 55.5 + - - +
363A MET 3.0 9.0 + - - -
364A TYR* 3.2 35.9 + + - +
367A LEU* 3.3 26.1 - - + +
385A TYR* 5.2 0.7 - - + -
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Residues in contact with ARG 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A GLN* 3.2 21.0 + - - +
359A ASN* 2.9 33.1 + - - +
360A TYR 3.2 1.0 - - - -
361A PHE* 1.3 75.5 - - - +
363A MET* 1.3 65.6 + - - +
364A TYR 3.3 5.6 + - - +
367A LEU* 4.8 3.6 - - + -
383A ASN 5.4 0.6 + - - -
384A ILE* 3.4 40.4 + - - +
385A TYR* 3.8 18.4 - - + +
597A LEU* 3.6 16.6 - - - +
600A ASP* 6.3 0.2 - - - +
601A ASP* 3.2 25.7 + - - -
604A ARG* 3.6 28.1 - - - +
608A GLU* 5.4 1.0 - - - +
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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