Contacts of the helix formed by residues 358 - 376 (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 GLY 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A PRO* 1.3 76.1 - - - +
359A PRO* 1.3 77.2 - - - +
360A LEU* 3.3 2.9 - - - -
361A GLN* 3.1 7.8 + - - +
362A ASP* 3.0 30.5 + - - +
365A ARG* 5.8 0.2 - - - +
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Residues in contact with PRO 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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358A GLY* 1.3 83.6 - - - +
360A LEU* 1.3 57.5 + - - +
362A ASP* 3.4 12.0 + - + +
363A ILE* 3.0 37.7 + - + +
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Residues in contact with LEU 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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156A HIS* 3.7 53.6 - - + +
157A ASP* 5.6 4.9 - - + +
355A LYS* 6.5 1.3 - - + -
356A ALA 6.1 0.4 - - - +
358A GLY 3.3 1.2 - - - -
359A PRO* 1.3 76.9 - - - +
361A GLN* 1.3 61.0 + - - +
363A ILE* 3.3 15.8 + - + +
364A GLU* 3.0 43.8 + - - +
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Residues in contact with GLN 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 3.4 28.5 - - + +
353A GLU* 3.8 14.6 - - - +
355A LYS* 2.8 35.8 - - + +
356A ALA 3.1 22.0 + - - +
357A PRO* 3.6 10.9 - - - +
358A GLY 3.1 10.5 + - - +
360A LEU* 1.3 78.8 - - - +
362A ASP* 1.3 61.1 + - - +
364A GLU* 3.4 7.6 + - + +
365A ARG* 2.8 61.8 + - - +
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Residues in contact with ASP 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 GLY* 3.0 23.7 + - - +
359A PRO* 3.6 11.8 - - + +
360A LEU 3.3 0.2 - - - -
361A GLN* 1.3 73.7 - - - +
363A ILE* 1.3 61.9 + - + +
365A ARG* 2.6 41.5 + - - +
366A HIS* 3.0 41.7 + - + +
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Residues in contact with ILE 363 (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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187A THR* 3.7 33.4 - - + -
359A PRO* 3.0 25.1 + - + +
360A LEU* 3.6 17.0 - - + +
361A GLN 3.2 0.2 - - - -
362A ASP* 1.3 74.9 - - - +
364A GLU* 1.3 69.1 + - + +
366A HIS* 3.0 10.6 + - + +
367A LYS* 2.9 36.9 + - + +
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Residues in contact with GLU 364 (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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157A ASP* 5.1 8.8 - - - +
315A ARG* 4.1 23.2 + - - +
316A ASN* 6.0 3.8 - - - +
352A LEU* 3.5 23.4 - - + +
355A LYS* 4.4 16.7 + - - +
360A LEU* 3.0 38.3 + - - +
361A GLN* 3.8 7.0 - - - +
363A ILE* 1.3 78.5 - - + +
365A ARG* 1.3 55.7 + - - +
367A LYS* 3.2 9.6 + - + +
368A LEU* 2.9 30.1 + - - +
25B G 5.6 0.9 + - - -
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Residues in contact with ARG 365 (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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352A LEU* 3.6 16.3 - - + +
353A GLU* 4.4 17.6 + - - +
358A GLY 5.8 0.6 - - - +
361A GLN* 2.8 46.3 + - - +
362A ASP* 2.6 38.1 + - - +
364A GLU* 1.3 69.8 - - - +
366A HIS* 1.3 72.0 + - + +
368A LEU* 3.5 3.3 + - - +
369A ASN* 2.9 49.1 + - - +
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Residues in contact with HIS 366 (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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362A ASP* 3.0 30.5 + - + +
363A ILE* 3.0 8.3 + - + +
365A ARG* 1.3 86.5 - - + +
367A LYS* 1.3 58.1 - - + +
369A ASN* 3.3 9.4 + - - +
370A ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 367 (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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152A SER* 5.4 2.4 + - - -
185A ASP* 3.2 19.0 + - - +
187A THR* 4.0 12.5 - - - +
188A THR* 3.0 19.6 + - - -
316A ASN* 3.8 29.5 - - + +
317A ILE 4.3 1.7 + - - -
318A GLU* 2.7 27.9 + - - +
363A ILE* 2.9 38.3 + - + +
364A GLU* 3.2 9.4 + - + +
366A HIS* 1.3 74.5 - - + +
368A LEU* 1.3 65.7 + - - +
370A ALA* 3.4 8.3 + - - +
371A MET* 3.1 19.9 + - - +
388A TYR* 3.5 14.5 + - + +
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Residues in contact with LEU 368 (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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314A PRO 4.5 2.2 - - - +
315A ARG* 3.4 24.5 + - - +
345A MET* 3.7 24.3 - - + +
348A LEU* 3.8 26.5 - - + -
349A ARG* 3.5 48.5 - - + +
352A LEU* 4.2 16.6 - - + -
364A GLU 2.9 17.1 + - - +
365A ARG* 3.7 4.7 - - - +
367A LYS* 1.3 75.6 - - - +
369A ASN* 1.3 60.0 + - - +
371A MET* 2.9 21.0 + - + +
372A GLY 3.0 10.2 + - - -
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Residues in contact with ASN 369 (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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345A MET* 4.7 2.2 - - - -
349A ARG* 3.2 36.1 + - - +
365A ARG* 2.9 40.9 + - - +
366A HIS* 3.6 11.4 + - - +
367A LYS 3.2 0.2 - - - -
368A LEU* 1.3 76.8 - - - +
370A ALA* 1.3 57.5 + - - +
372A GLY* 3.2 3.2 + - - +
373A ALA* 3.0 27.1 + - - +
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Residues in contact with ALA 370 (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* 3.6 14.6 - - + +
366A HIS 3.0 13.6 + - - +
367A LYS 3.5 9.2 - - - +
369A ASN* 1.3 73.5 - - - +
371A MET* 1.3 65.0 + - - +
373A ALA* 3.2 8.3 + - - +
374A PHE 2.9 19.8 + - - -
384A VAL* 5.3 0.9 - - - +
388A TYR* 3.7 31.0 - - + -
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Residues in contact with MET 371 (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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313A ILE* 3.7 23.3 - - + -
314A PRO* 3.4 28.0 - - - +
316A ASN* 3.7 30.7 - - - +
317A ILE* 3.8 10.4 - - + +
320A TYR* 3.9 22.9 - - + -
338A LEU* 4.2 6.5 - - + -
345A MET* 5.2 0.9 - - - -
367A LYS 3.1 11.8 + - - +
368A LEU* 2.9 13.9 + - + +
370A ALA* 1.3 74.1 - - - +
372A GLY* 1.3 56.9 + - - +
374A PHE* 3.3 42.5 + - + +
375A ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 372 (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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313A ILE* 4.8 0.2 - - - -
340A TYR* 5.0 1.8 - - - -
345A MET* 3.8 27.8 - - - +
349A ARG* 5.5 1.8 - - - -
368A LEU 3.0 10.3 + - - -
369A ASN 3.2 4.2 + - - -
370A ALA 3.2 0.2 - - - -
371A MET* 1.3 76.6 - - - +
373A ALA* 1.3 56.4 + - - +
375A ALA* 3.3 7.6 + - - +
376A GLU* 2.9 37.2 + - - +
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Residues in contact with ALA 373 (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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369A ASN 3.0 13.7 + - - +
370A ALA* 3.2 11.4 + - - +
372A GLY* 1.3 74.6 - - - +
374A PHE* 1.3 60.5 + - - +
376A GLU* 3.6 5.4 - - - -
377A ALA* 2.9 30.8 + - - +
384A VAL* 5.1 3.6 - - + -
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Residues in contact with PHE 374 (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* 4.9 1.6 - - + -
216A MET 6.2 0.4 - - - -
217A LEU* 5.3 2.5 - - + -
317A ILE* 4.3 7.0 - - + -
320A TYR* 3.5 40.2 - + - -
338A LEU* 4.3 9.4 - - + -
370A ALA 2.9 14.1 + - - +
371A MET* 3.3 31.4 + - + +
373A ALA* 1.3 75.5 - - - +
375A ALA* 1.3 60.2 + - - +
377A ALA* 3.4 7.9 + - - +
381A ARG* 2.9 74.0 + - + -
384A VAL* 4.0 25.4 - - + +
385A LEU* 3.7 22.0 - - + -
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Residues in contact with ALA 375 (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 LEU* 3.3 28.1 - - + +
313A ILE* 3.8 9.0 - - + -
338A LEU* 4.6 2.0 - - + -
340A TYR* 3.7 39.1 - - + -
371A MET 3.0 13.5 + - - +
372A GLY 3.5 8.3 - - - +
373A ALA 3.2 0.2 - - - -
374A PHE* 1.3 79.8 - - - +
376A GLU* 1.3 57.2 - - - +
377A ALA 3.3 0.4 - - - -
381A ARG* 3.3 14.9 + - - -
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Residues in contact with GLU 376 (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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340A TYR* 2.4 36.2 + - - +
342A PRO* 4.4 6.8 - - - +
372A GLY 2.9 22.5 + - - +
373A ALA* 3.4 5.8 + - - +
375A ALA* 1.3 73.3 - - - +
377A ALA* 1.3 66.9 + - - +
378A GLN* 3.2 22.1 + - - +
478A HIS* 3.7 47.7 + - + +
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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