Contacts of the helix formed by residues 382 - 400 (chain A) in PDB entry 5T0H
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLY* 4.9 11.3 - - - -
354A ILE* 3.9 19.9 - - - +
381A THR* 1.3 77.4 - - - +
383A ALA* 1.3 66.7 + - - +
384A GLU 3.7 0.7 - - - -
385A ILE* 3.5 8.9 - - - +
386A ARG* 3.1 25.4 + - - +
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Residues in contact with ALA 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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218A PRO* 5.3 6.1 - - + -
219A GLY* 5.6 5.1 - - - +
381A THR* 3.3 4.6 + - - +
382A GLY* 1.3 80.5 - - - +
384A GLU* 1.3 63.6 + - - +
386A ARG* 3.2 29.8 + - - +
387A SER* 3.5 6.4 + - - -
343B ARG* 3.2 48.0 - - + +
344B PRO* 5.4 0.7 - - + -
347B ILE* 4.6 4.9 - - - +
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Residues in contact with GLU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ALA* 1.3 77.9 - - - +
385A ILE* 1.3 52.8 + - + +
387A SER* 2.5 15.5 + - - +
388A VAL* 2.4 42.2 + - + +
416A VAL* 2.8 45.7 - - + +
417A ILE* 3.6 13.0 - - - +
420A TYR* 4.6 11.7 - - + +
343B ARG* 2.9 30.7 + - - +
347B ILE* 3.6 21.8 - - + +
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Residues in contact with ILE 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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351A ARG* 4.2 10.5 - - + -
354A ILE* 3.7 23.3 - - + -
355A PHE* 3.3 41.1 - - + -
358A HIS* 4.1 0.2 - - - -
377A CYS* 4.9 5.2 - - + -
380A SER* 3.4 34.8 - - - +
381A THR 3.1 25.6 - - - +
382A GLY 3.5 12.6 - - - +
384A GLU* 1.3 76.0 - - + +
386A ARG* 1.3 62.0 + - - +
388A VAL* 3.4 17.7 - - + -
389A CYS* 3.5 14.6 + - - -
417A ILE* 5.8 4.3 - - + -
343B ARG* 4.4 0.2 - - - +
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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
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354A ILE* 4.9 7.0 - - + -
357A ILE* 4.8 18.4 - - + +
358A HIS* 2.7 34.9 + - + +
382A GLY 3.1 18.1 + - - +
383A ALA* 3.5 19.9 + - - +
384A GLU 3.1 0.2 - - - -
385A ILE* 1.3 78.3 - - - +
387A SER* 1.3 52.9 + - - +
389A CYS 3.6 0.3 + - - -
390A THR* 2.5 28.9 + - - +
217B LYS* 4.9 17.9 - - - +
220B LYS* 3.6 28.8 - - - +
343B ARG 5.2 1.8 + - - -
344B PRO* 5.0 4.2 + - - +
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ALA 3.5 2.9 + - - -
384A GLU* 2.5 30.3 + - - +
386A ARG* 1.3 77.2 - - - +
388A VAL* 1.3 55.9 + - - +
390A THR* 3.4 8.7 - - - -
391A GLU* 2.6 55.6 + - - +
416A VAL* 6.1 0.3 - - - +
220B LYS* 5.1 7.0 - - - -
347B ILE* 3.4 30.2 - - - +
348B ASP* 4.8 3.2 - - - +
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A PHE* 4.6 4.0 - - + -
373A LEU* 4.3 18.6 - - + -
384A GLU* 2.4 39.1 + - + +
385A ILE* 3.4 24.9 - - + +
386A ARG 3.2 0.2 - - - -
387A SER* 1.3 70.5 - - - +
389A CYS* 1.3 64.1 + - - +
391A GLU* 3.5 11.7 + - - +
392A ALA 4.0 5.5 + - - -
409A PHE* 4.0 4.6 - - + +
413A VAL* 3.4 39.2 - - + +
416A VAL* 3.8 26.9 - - + -
417A ILE* 4.7 3.4 - - + -
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Residues in contact with CYS 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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355A PHE* 3.5 42.0 - - - -
358A HIS* 3.6 34.8 - - + +
362A MET* 6.0 1.7 - - - +
373A LEU* 4.8 6.5 - - - -
385A ILE 3.5 6.8 + - - -
387A SER 3.3 0.4 - - - -
388A VAL* 1.3 77.6 - - - +
390A THR* 1.3 60.1 + - - +
392A ALA* 3.7 16.0 - - - +
393A GLY 4.5 0.7 + - - -
409A PHE* 5.0 13.3 - - + -
216B ILE* 4.1 9.8 - - - +
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Residues in contact with THR 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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358A HIS* 3.4 8.3 + - - -
386A ARG* 2.5 24.9 + - - +
387A SER* 2.8 15.1 + - - -
389A CYS* 1.3 75.5 - - - +
391A GLU* 1.3 60.4 + - - +
392A ALA 3.1 5.2 - - - -
393A GLY* 3.0 20.4 + - - -
394A MET* 3.3 6.6 + - - +
216B ILE* 3.5 31.9 + - + +
217B LYS 4.0 2.0 + - - +
218B PRO* 3.4 37.8 - - + +
220B LYS* 6.2 1.1 - - + -
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Residues in contact with GLU 391 (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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387A SER* 2.6 37.8 + - - +
388A VAL* 3.5 8.5 + - - +
389A CYS 3.5 0.6 - - - -
390A THR* 1.3 78.4 - - - +
392A ALA* 1.3 64.4 + - - +
394A MET* 3.2 39.0 - - + +
395A PHE* 3.4 12.0 + - - +
409A PHE* 4.6 4.1 - - + +
412A ALA* 5.3 11.6 - - + +
413A VAL* 6.2 0.7 - - + -
416A VAL* 5.2 12.6 - - + -
218B PRO* 4.8 6.2 - - - +
220B LYS* 5.7 1.6 - - - +
346B ARG* 4.6 2.0 + - - -
348B ASP* 2.9 49.2 - - + +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MET* 5.7 2.9 - - - -
389A CYS 3.7 12.9 + - - +
390A THR 3.1 0.2 - - - -
391A GLU* 1.3 76.9 - - - +
393A GLY* 1.3 51.6 + - - +
394A MET 3.1 0.7 + - - -
395A PHE 3.2 0.9 + - - -
396A ALA* 2.6 35.4 + - - +
401A ARG* 2.8 13.5 + - - +
404A ALA* 3.7 19.5 - - + -
409A PHE* 3.4 42.9 - - + +
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Residues in contact with GLY 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A MET* 6.0 1.0 - - - -
389A CYS 4.5 0.8 + - - -
390A THR 3.0 10.5 + - - -
392A ALA* 1.3 74.6 - - - +
394A MET* 1.3 66.1 + - - +
396A ALA* 3.6 11.2 - - - -
397A ILE* 3.2 31.1 + - - +
404A ALA* 5.1 0.4 - - - +
214B MET* 4.6 20.2 - - - -
216B ILE* 5.3 6.7 - - - +
218B PRO* 5.9 4.5 - - - -
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Residues in contact with MET 394 (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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390A THR 3.3 5.8 + - - +
391A GLU* 3.2 38.6 - - + +
392A ALA 3.1 0.4 - - - -
393A GLY* 1.3 81.8 - - - +
395A PHE* 1.3 71.7 + - + +
397A ILE* 4.1 1.9 - - - +
398A ARG* 3.1 42.1 + - - +
196B GLU* 3.3 47.6 - - + +
199B GLU* 4.1 19.4 - - + +
200B SER* 4.8 5.8 - - - +
218B PRO* 5.8 8.8 - - + +
346B ARG* 4.8 6.3 - - - +
348B ASP* 4.6 6.5 - - - +
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Residues in contact with PHE 395 (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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391A GLU 3.4 5.3 + - - +
392A ALA 3.2 2.2 + - - +
394A MET* 1.3 87.0 - - + +
396A ALA* 1.3 55.9 + - - +
398A ARG* 3.2 38.1 - - + +
399A ALA* 2.6 39.5 + - + +
401A ARG* 3.3 18.6 - - - +
408A ASP 5.5 3.6 - - - -
412A ALA* 4.0 29.2 - - + -
415A LYS* 4.7 13.0 - - + -
196B GLU* 5.9 4.3 - - + -
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Residues in contact with ALA 396 (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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392A ALA 2.6 24.0 + - - +
393A GLY* 3.6 13.0 - - - -
394A MET 3.2 0.2 - - - -
395A PHE* 1.3 71.1 - - - +
397A ILE* 1.3 53.8 + - + +
400A ARG* 2.6 32.7 + - - -
401A ARG* 2.7 40.6 + - + +
404A ALA* 4.9 0.2 - - + -
214B MET* 3.7 24.2 - - + -
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Residues in contact with ILE 397 (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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393A GLY 3.2 19.3 + - - +
394A MET 4.1 1.3 - - - +
396A ALA* 1.3 76.5 - - + +
398A ARG* 1.3 61.8 + - - +
400A ARG* 3.2 24.8 + - - +
401A ARG 5.2 0.9 - - - -
199B GLU* 3.4 36.3 - - + +
203B LEU* 4.4 6.1 - - + -
207B HIS* 4.2 10.1 - - + -
210B TYR* 3.4 61.2 - - + +
211B TYR* 3.9 4.9 - - - +
214B MET* 4.9 8.3 - - + -
218B PRO* 6.1 2.2 - - + -
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Residues in contact with ARG 398 (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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394A MET* 3.1 35.0 + - - +
395A PHE* 3.2 38.0 - - + +
396A ALA 3.1 0.8 - - - -
397A ILE* 1.3 78.6 - - - +
399A ALA* 1.3 57.1 + - - +
400A ARG* 3.0 18.7 + - - +
192B ASN* 5.1 0.6 + - - -
195B GLN* 2.2 50.5 + - - +
196B GLU* 3.0 32.3 + - - +
199B GLU* 4.1 18.9 - - + +
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 2.6 24.3 + - + +
398A ARG* 1.3 71.4 - - - +
400A ARG* 1.3 65.3 + - - +
401A ARG* 3.1 26.8 + - + +
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Residues in contact with ARG 400 (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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396A ALA 2.6 12.6 + - - -
397A ILE* 3.2 17.4 + - - +
398A ARG* 3.0 30.7 + - - +
399A ALA* 1.3 74.1 - - - +
401A ARG* 1.3 63.4 + - - -
402A LYS* 3.1 32.2 + - - +
210B TYR* 6.1 5.4 - - - -
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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
------------------------------------------------------------
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