Contacts of the helix formed by residues 380 - 389 (chain A) in PDB entry 4TMU
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 CYS 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A THR* 1.3 78.5 + - - +
381A ARG* 1.3 66.1 + - - +
382A ARG 3.6 1.3 - - - -
383A LEU* 3.0 50.3 + - + +
384A VAL* 3.2 11.6 + - - +
396A PRO* 4.0 6.3 - - + -
397A CYS* 3.3 25.6 - - - -
400A CYS* 3.9 4.3 - - - -
402A ILE* 3.8 6.2 - - - +
403A CYS* 3.8 7.9 - - - -
601A ZN 2.3 35.4 - - - -
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Residues in contact with ARG 381 (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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215A TYR* 4.2 13.5 - - + +
216A MET 5.3 0.4 - - - -
217A LEU* 3.5 30.5 - - - +
374A PHE* 2.9 62.1 + - + -
375A ALA 3.3 13.7 + - - -
377A ALA* 3.5 18.3 + - - +
379A THR 3.2 2.6 + - - -
380A CYS* 1.3 72.0 - - - +
382A ARG* 1.3 58.4 + - - +
384A VAL* 3.2 5.4 + - - +
385A LEU* 3.0 24.2 + - - +
400A CYS* 3.4 22.8 - - + -
401A ASP* 2.8 43.0 + - - +
402A ILE* 3.8 18.5 - - + +
514A ARG* 4.0 3.8 - - - +
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Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 3.6 17.6 + - - +
210A ARG 2.9 33.9 + - - +
211A PRO* 3.8 5.1 - - - +
213A ILE 2.8 22.4 + - - -
215A TYR* 3.6 24.5 - - + -
380A CYS* 3.2 12.5 - - - -
381A ARG* 1.3 78.0 - - - +
383A LEU* 1.3 62.3 + - + +
385A LEU* 3.8 8.9 - - + +
386A LEU* 2.9 54.1 + - + +
393A ARG* 4.5 5.6 - - - +
397A CYS* 3.1 26.4 - - + +
399A ASN* 2.8 36.2 + - - +
400A CYS* 4.8 0.4 - - - -
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Residues in contact with LEU 383 (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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379A THR* 4.4 13.9 - - + +
380A CYS* 3.0 32.0 + - + +
382A ARG* 1.3 80.8 - - + +
384A VAL* 1.3 63.0 + - + +
386A LEU* 4.8 0.7 - - - -
387A ASN* 2.9 34.3 + - - +
393A ARG* 3.6 38.4 - - + +
394A GLN* 3.3 23.3 - - - +
395A ALA 3.3 20.0 - - - +
396A PRO* 4.0 9.0 - - + -
397A CYS* 6.3 0.2 - - + -
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Residues in contact with VAL 384 (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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317A ILE* 5.0 7.9 - - + -
370A ALA 5.3 0.7 - - - +
373A ALA* 5.1 2.9 - - + -
374A PHE* 4.0 32.3 - - + +
377A ALA* 4.0 17.7 - - + -
379A THR* 3.8 21.1 - - + -
380A CYS 3.2 14.1 + - - +
381A ARG* 3.5 7.9 - - - +
382A ARG 3.2 0.2 - - - -
383A LEU* 1.3 77.8 - - - +
385A LEU* 1.3 57.2 + - - +
387A ASN* 4.0 1.1 - - - +
388A TYR* 2.9 32.5 + - + +
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Residues in contact with LEU 385 (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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215A TYR* 3.7 46.7 - - + +
317A ILE* 3.8 25.8 - - + +
320A TYR* 4.0 16.4 - - + -
321A TYR* 4.7 11.7 - - + -
374A PHE* 3.7 20.4 - - + -
381A ARG 3.0 19.1 + - - +
382A ARG* 3.8 7.2 - - + +
384A VAL* 1.3 76.6 - - - +
386A LEU* 1.3 70.5 + - + +
388A TYR* 3.2 5.9 + - - +
389A PHE* 3.1 37.3 + - + -
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Residues in contact with LEU 386 (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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208A PHE* 4.0 35.4 - - + +
209A ASP* 4.1 7.9 - - - +
321A TYR* 5.6 1.8 - - + -
382A ARG* 2.9 34.3 + - + +
383A LEU* 4.3 2.7 - - - +
385A LEU* 1.3 85.6 - - + +
387A ASN* 1.3 63.2 + - - +
389A PHE* 3.2 11.1 + - + +
391A GLU* 3.0 49.6 + - + +
393A ARG* 3.7 45.1 - - + +
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Residues in contact with ASN 387 (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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383A LEU* 2.9 33.7 + - - +
384A VAL* 4.2 1.8 - - - +
386A LEU* 1.3 75.8 - - - +
388A TYR* 1.3 66.3 + - - +
390A GLY* 2.9 14.4 + - - +
391A GLU 3.9 6.0 + - - +
392A GLY* 3.5 9.7 - - - -
393A ARG* 2.9 42.0 + - - +
394A GLN* 5.3 0.9 + - - -
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Residues in contact with TYR 388 (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 ASP* 2.7 43.6 + - + +
186A ASP 5.6 0.5 + - - -
316A ASN* 5.7 0.2 - - - +
317A ILE* 3.5 46.0 + - + +
318A GLU* 4.6 3.1 + - - +
367A LYS* 3.5 23.5 - - + +
370A ALA* 3.7 24.0 - - + -
384A VAL* 2.9 20.5 + - + +
385A LEU* 3.3 7.4 - - - +
387A ASN* 1.3 77.3 - - - +
389A PHE* 1.3 70.6 + + - +
390A GLY 3.3 3.8 + - - -
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Residues in contact with PHE 389 (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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183A THR* 4.2 7.6 - - + -
184A ALA 4.2 0.2 - - - -
185A ASP* 4.1 20.9 - - + -
186A ASP 6.0 0.4 - - - -
189A ARG* 3.4 21.9 + - - +
205A ILE* 5.7 0.7 - - - +
208A PHE* 3.5 55.1 - + + -
317A ILE* 3.9 25.8 - - + -
318A GLU* 3.9 23.1 - - + -
321A TYR* 3.8 39.5 - + + -
385A LEU* 3.1 27.2 + - + -
386A LEU 3.2 5.8 + - - +
387A ASN 3.1 0.8 - - - -
388A TYR* 1.3 79.4 - + - +
390A GLY* 1.3 61.2 + - - +
391A GLU 3.3 1.2 + - - -
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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