Contacts of the helix formed by residues 375 - 391 (chain A) in PDB entry 5UDJ
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 GLU 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE 4.9 3.0 - - - +
192A LYS* 3.9 20.4 + - - -
195A THR* 4.4 11.0 - - + -
373A VAL* 3.2 16.2 - - + +
374A GLU* 1.3 89.6 + - - +
376A THR* 1.3 59.8 + - - +
377A MET 3.0 0.4 - - - -
378A GLN* 2.8 45.0 + - - +
379A ASP* 3.4 6.7 - - - +
408A ILE* 4.7 5.3 - - + +
410A GLN* 3.7 41.4 + - + +
412A SER* 5.6 1.8 - - - -
3B A 5.6 0.2 - - - -
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Residues in contact with THR 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 GLU* 4.5 12.8 - - + +
341A VAL* 4.0 27.4 - - + +
344A LEU* 5.4 2.0 - - + -
371A PRO* 4.2 9.5 - - + +
373A VAL* 3.1 31.4 + - - +
375A GLU* 1.3 78.0 - - - +
377A MET* 1.3 61.6 + - - +
379A ASP* 3.1 13.9 + - + +
380A ILE* 3.0 34.4 + - + +
3B A 4.2 12.7 + - + +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A LEU 3.7 15.3 - - - +
367A LEU* 4.3 11.7 - - - +
369A MET 3.3 26.5 - - - +
371A PRO* 4.0 14.1 - - + +
374A GLU 3.1 13.6 + - - +
375A GLU 3.0 1.0 - - - -
376A THR* 1.3 77.9 - - - +
378A GLN* 1.3 62.9 + - - +
380A ILE* 3.9 29.8 - - + +
381A HIS* 3.0 52.1 + - + +
408A ILE* 3.7 13.5 - - + -
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A GLU* 2.8 23.0 + - - +
377A MET* 1.3 78.5 - - - +
379A ASP* 1.3 59.0 + - - +
381A HIS 3.4 0.2 + - - -
382A PHE* 2.9 30.3 + - - +
405A ALA* 3.6 25.9 - - + +
408A ILE* 2.8 49.6 + - + +
410A GLN* 2.9 20.4 + - - +
412A SER* 2.7 26.5 + - - -
414A THR* 3.6 13.9 - - + +
415A ARG* 3.8 10.6 - - + +
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 6.2 0.2 - - - +
344A LEU* 4.0 8.1 - - + -
375A GLU* 3.4 15.1 - - - +
376A THR* 3.1 6.9 + - + +
378A GLN* 1.3 73.3 - - - +
380A ILE* 1.3 61.3 + - - +
383A HIS* 2.9 45.2 + - + +
414A THR* 2.5 34.5 + - - +
3B A 3.0 46.8 + - + +
4B A 4.9 5.7 + - - +
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Residues in contact with ILE 380 (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 GLU* 5.1 3.6 - - + -
344A LEU* 4.4 16.8 - - + -
363A PHE* 4.5 5.5 - - + +
366A LEU* 3.8 53.6 - - + +
367A LEU* 3.9 23.6 - - + -
369A MET* 5.6 0.4 - - + -
371A PRO* 5.1 4.3 - - + -
376A THR* 3.0 26.7 + - + +
377A MET* 3.7 30.5 - - + +
378A GLN 3.3 0.2 - - - -
379A ASP* 1.3 76.8 - - - +
381A HIS* 1.4 57.7 + - - +
383A HIS* 4.0 0.9 - - - +
384A TYR* 3.0 28.5 + - + +
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Residues in contact with HIS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A LEU* 3.5 23.3 - - + +
377A MET* 3.0 48.7 + - + +
380A ILE* 1.4 72.6 - - - +
382A PHE* 1.3 59.4 + - - +
384A TYR* 4.5 1.6 - - - -
385A GLY* 2.8 26.0 + - - -
401A HIS* 3.0 50.5 + + - +
404A LYS* 3.4 46.3 - - + +
405A ALA* 3.8 8.7 - - + +
408A ILE* 4.3 3.5 - - + +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLN 2.9 18.8 + - - +
379A ASP 3.8 1.3 - - - +
380A ILE 3.3 0.2 - - - -
381A HIS* 1.3 76.1 - - - +
383A HIS* 1.3 86.2 + + - +
385A GLY* 3.1 2.9 + - - -
386A ARG* 2.9 63.1 + - + +
402A TYR* 3.9 10.1 - + - -
405A ALA* 4.2 2.2 - - - +
414A THR* 3.6 15.5 - - + -
417A LYS* 3.8 43.1 - - + -
418A SER* 3.3 28.9 - - - +
421A SER* 3.5 23.6 - - - -
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Residues in contact with HIS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.1 18.6 - - + -
348A ARG* 3.5 46.6 + - + -
351A ILE* 5.4 1.0 - - - +
363A PHE* 3.8 20.3 - - + -
379A ASP* 2.9 39.8 + - + +
382A PHE* 1.3 103.1 - + - +
384A TYR* 1.3 59.0 + - - +
386A ARG* 3.4 15.4 + - - +
387A PHE* 3.0 27.4 + - - +
414A THR* 5.7 0.2 + - - -
417A LYS* 5.4 4.4 + - - -
3B A 4.7 4.2 - - - -
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Residues in contact with TYR 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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360A GLU* 2.7 38.6 + - - -
363A PHE* 3.4 41.6 - + + -
364A GLN* 3.2 12.1 + - - -
367A LEU* 3.9 18.8 - - + -
380A ILE* 3.0 19.9 + - + +
381A HIS* 3.8 4.0 - - - +
383A HIS* 1.3 78.0 - - - +
385A GLY* 1.3 56.0 + - - +
387A PHE* 3.2 11.5 + + - +
388A GLN* 2.9 56.3 + - + +
397A ASN* 6.1 0.2 - - + -
401A HIS* 3.5 42.4 - + - -
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Residues in contact with GLY 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A HIS 2.8 19.1 + - - -
382A PHE 3.5 3.4 - - - -
384A TYR* 1.3 74.7 - - - +
386A ARG* 1.3 56.0 + - - +
388A GLN* 3.2 2.1 + - - +
389A GLU* 2.9 24.9 + - - +
398A ALA* 3.4 19.4 - - - +
401A HIS* 3.9 14.5 - - - +
402A TYR* 3.7 15.9 - - - -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 6.0 2.0 - - - +
382A PHE* 2.9 55.2 + - + +
383A HIS* 3.7 17.5 + - - +
384A TYR 3.3 0.2 - - - -
385A GLY* 1.3 71.9 - - - +
387A PHE* 1.3 61.1 + - - +
389A GLU 3.2 0.3 + - - -
390A PHE* 2.8 63.3 + - + +
391A GLN* 4.4 1.6 - - - -
402A TYR* 3.5 17.0 - - - +
421A SER* 4.8 4.2 + - - +
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Residues in contact with PHE 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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351A ILE* 3.6 25.5 - - + +
356A HIS* 3.5 31.9 - + + -
359A ALA* 4.0 14.4 - - + -
360A GLU* 3.7 28.9 - - + -
363A PHE* 3.9 13.2 - + + -
383A HIS 3.0 14.0 + - - +
384A TYR* 3.2 26.7 + + - +
386A ARG* 1.3 75.8 - - - +
388A GLN* 1.3 60.2 + - - +
391A GLN* 2.9 56.8 + - + +
392A LYS* 3.0 34.2 + - + -
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Residues in contact with GLN 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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360A GLU* 3.9 6.1 + - - -
384A TYR* 2.9 57.4 + - + +
385A GLY 3.2 7.8 + - - +
387A PHE* 1.3 77.0 - - - +
389A GLU* 1.3 59.9 + - - +
392A LYS* 3.5 21.5 - - - +
393A LYS 3.0 6.9 + - - -
394A SER* 2.8 38.3 + - - +
397A ASN* 3.4 38.9 + - + +
398A ALA* 3.6 17.3 - - - +
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Residues in contact with GLU 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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385A GLY 2.9 15.8 + - - +
386A ARG 3.8 3.1 - - - +
388A GLN* 1.3 79.9 - - - +
390A PHE* 1.3 89.5 + - + +
393A LYS* 3.4 22.2 - - - +
394A SER 4.3 4.5 - - - +
395A ASP* 4.0 14.3 - - - +
398A ALA* 3.7 11.2 - - + +
402A TYR* 2.7 32.7 + - - -
421A SER* 4.5 3.6 - - - +
424A LYS* 5.9 1.0 - - - +
425A LEU* 3.9 19.8 + - + +
428A ARG* 3.1 22.4 + - - +
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Residues in contact with PHE 390 (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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386A ARG* 2.8 58.5 + - + +
389A GLU* 1.3 111.4 - - + +
391A GLN* 1.3 75.3 + - - +
393A LYS* 3.2 23.6 - - - +
402A TYR* 4.3 5.6 - - - -
421A SER* 6.1 0.7 - - - -
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Residues in contact with GLN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ILE* 3.6 28.7 - - + +
356A HIS* 3.5 39.9 + - + +
386A ARG 4.0 2.8 - - - +
387A PHE* 2.9 47.6 + - + +
390A PHE* 1.3 91.0 + - - +
392A LYS* 1.3 64.0 + - - +
393A LYS* 3.4 7.2 + - - +
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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
------------------------------------------------------------
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