Contacts of the strand formed by residues 349 - 356 (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 SER 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A SER* 3.8 19.5 + - - -
225A GLY 3.6 19.5 - - - -
227A ALA 4.0 9.0 - - - -
228A ALA* 4.8 1.6 - - - +
348A GLU* 1.3 83.0 - - - +
350A MET* 1.3 67.5 + - - +
351A THR* 4.0 1.2 + - - -
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Residues in contact with MET 350 (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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224A SER* 3.4 2.8 - - - -
225A GLY* 2.5 36.2 + - - +
227A ALA 4.4 5.0 + - - +
228A ALA 5.0 1.8 - - - +
229A LYS* 3.4 59.5 - - + +
348A GLU* 4.6 7.0 - - + +
349A SER* 1.3 81.9 - - - +
351A THR* 1.3 60.9 + - - +
352A LEU* 3.9 1.3 - - + +
725A MET* 3.5 41.1 - - + +
726A ASP* 5.7 2.7 - - - +
729A ASP* 4.0 28.0 - - + +
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Residues in contact with THR 351 (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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222A ILE* 3.5 26.6 - - + +
223A ILE 3.9 3.4 - - - -
224A SER* 4.3 5.3 + - - +
349A SER 4.0 1.3 + - - -
350A MET* 1.3 73.7 - - - +
352A LEU* 1.3 59.5 + - - +
353A ALA 3.3 31.2 - - - +
354A THR* 4.0 10.3 - - - -
725A MET* 3.5 24.6 - - - +
728A ILE* 4.2 22.3 - - + +
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Residues in contact with LEU 352 (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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189A MET* 3.4 31.0 - - + +
223A ILE* 2.7 12.1 + - + +
224A SER 4.0 4.5 - - - +
225A GLY* 3.6 35.7 - - - +
226A GLN* 4.2 18.4 - - - +
350A MET* 3.9 3.1 - - + +
351A THR* 1.3 74.6 - - - +
353A ALA* 1.3 62.5 + - - +
721A ASP 5.2 2.4 - - - +
724A TRP* 3.8 19.2 - - - -
725A MET* 3.6 38.1 + - + +
728A ILE* 4.1 3.0 - - - +
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Residues in contact with ALA 353 (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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185A LEU* 4.1 17.5 - - + -
189A MET* 4.0 24.7 - - + -
222A ILE* 3.6 0.5 - - - -
223A ILE* 3.0 29.2 + - + -
351A THR* 3.3 7.6 - - - +
352A LEU* 1.3 79.9 - - - +
354A THR* 1.3 65.2 + - - +
611A TYR* 3.6 20.9 - - - +
728A ILE* 4.3 5.2 - - - -
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Residues in contact with THR 354 (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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185A LEU* 3.8 4.7 - - - +
220A PRO* 5.2 3.1 - - - +
221A LEU 3.3 9.1 + - - -
222A ILE* 3.7 17.0 - - - +
351A THR* 4.0 9.4 - - - -
353A ALA* 1.3 78.6 - - - +
355A ILE* 1.3 72.1 + - - +
603A LEU* 4.2 22.2 - - + -
607A ARG* 3.2 21.8 + - - +
611A TYR* 4.6 1.0 + - - -
724A TRP* 5.3 2.3 - - + +
728A ILE* 4.0 27.0 - - + +
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Residues in contact with ILE 355 (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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181A GLY 4.7 3.8 - - - +
184A TYR* 4.0 20.0 - - + -
185A LEU* 3.7 27.4 - - + -
220A PRO* 3.7 1.2 - - - +
221A LEU* 2.8 38.7 + - + +
354A THR* 1.3 80.9 + - - +
356A THR* 1.3 80.5 + - - +
359A ASN* 3.7 6.5 - - + +
360A TYR* 3.4 37.0 - - + +
363A MET* 4.9 2.5 - - + -
607A ARG* 3.4 33.7 - - - +
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Residues in contact with THR 356 (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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217A ALA 3.4 12.7 + - - -
218A ARG* 3.6 27.1 - - + +
219A THR 3.2 8.3 - - - +
220A PRO* 4.5 4.3 - - + -
221A LEU* 5.2 1.8 - - - -
355A ILE* 1.3 81.3 - - - +
357A PHE* 1.3 69.1 + - - +
358A GLN* 3.1 4.7 + - - +
359A ASN* 3.2 30.4 + - - +
360A TYR* 2.9 25.4 + - - +
600A ASP* 5.0 10.1 + - - +
607A ARG* 5.0 0.4 - - - +
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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