Contacts of the helix formed by residues 381 - 396 (chain A) in PDB entry 5E3H
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 HIS 381 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ASN* 4.0 14.1 + - + +
348A PRO* 4.9 0.4 - - + -
376A ASN* 3.2 48.3 + - + +
378A SER 3.3 10.7 + - - +
380A GLN* 1.3 81.3 - - - +
382A PRO* 1.3 81.1 - - + +
383A TYR* 3.1 36.4 + + - +
384A ASN* 3.0 13.6 + - - +
385A MET* 3.2 8.7 + - - +
1004A MG 3.5 20.4 - - - -
4B C 3.3 21.8 + - - -
5B G 3.8 22.4 + - - -
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Residues in contact with PRO 382 (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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348A PRO* 3.6 28.9 - - + -
349A GLN* 3.5 33.2 - - + +
352A VAL* 3.6 4.7 - - + +
380A GLN 4.1 1.8 - - - +
381A HIS* 1.3 98.6 - - + +
383A TYR* 1.3 61.0 + - - +
385A MET* 3.2 11.4 + - + +
386A ILE* 3.2 27.2 + - - +
4B C 3.5 17.7 - - + +
13C C 5.9 0.2 - - - +
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.3 38.7 + - + -
298A ASN* 3.8 16.6 + - + +
348A PRO* 3.6 29.8 - - + -
371A PHE* 3.5 24.2 - + + -
372A ASP 2.7 31.1 + - - -
373A GLU* 3.5 12.1 - - + -
374A CYS* 4.4 1.3 - - - -
376A ASN* 3.8 21.1 - - + -
377A THR* 3.4 27.6 - - - +
381A HIS* 3.1 15.3 + + - +
382A PRO* 1.3 76.6 - - - +
384A ASN* 1.3 61.9 + - - +
386A ILE* 3.3 8.3 + - - +
387A MET* 3.3 23.2 + - - +
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Residues in contact with ASN 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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377A THR* 3.6 17.2 - - - +
378A SER* 3.0 34.7 - - - +
379A LYS* 2.9 29.2 + - - +
381A HIS 3.0 10.5 + - - +
383A TYR* 1.3 75.9 - - - +
385A MET* 1.3 60.6 + - - +
387A MET* 3.1 4.4 + - - +
388A PHE* 2.8 65.0 + - - -
391A LEU* 6.0 0.3 - - - +
433A SER* 4.1 13.0 + - - -
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Residues in contact with MET 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A VAL* 3.9 24.9 - - + -
355A LEU* 5.4 0.7 - - - +
380A GLN* 3.4 52.3 - - + +
381A HIS 3.2 12.2 + - - +
382A PRO* 3.5 11.7 - - + +
384A ASN* 1.3 77.0 - - - +
386A ILE* 1.3 62.8 + - - +
388A PHE* 3.4 25.2 + - - +
389A ASN* 3.3 19.8 + - - +
4B C 5.4 2.9 - - - +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE* 3.6 25.1 - - + -
348A PRO* 3.6 36.8 - - + +
351A LEU* 3.6 26.9 - - + -
352A VAL* 3.8 12.8 - - + +
355A LEU* 4.8 4.7 - - + -
363A LEU* 3.4 17.3 - - + +
369A MET* 4.4 4.0 - - + -
371A PHE* 4.2 22.4 - - + -
382A PRO 3.2 9.6 + - - +
383A TYR* 3.5 6.3 - - - +
384A ASN 3.2 0.2 - - - -
385A MET* 1.3 76.5 - - - +
387A MET* 1.3 57.0 + - - +
389A ASN* 3.3 10.3 - - - +
390A TYR 3.1 17.7 + - - -
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Residues in contact with MET 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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369A MET* 3.9 13.9 - - - -
371A PHE* 3.8 30.5 - - + -
377A THR* 4.0 10.1 - - + -
383A TYR 3.3 11.6 + - - +
384A ASN* 3.1 13.5 + - - +
386A ILE* 1.3 75.3 - - - +
388A PHE* 1.3 55.3 + - - +
389A ASN 3.1 1.8 - - - -
390A TYR* 2.9 35.8 + - + +
391A LEU* 2.6 45.1 + - + +
405A VAL* 4.5 5.2 - - + -
433A SER 3.3 29.8 - - - +
434A LEU* 3.8 21.8 - - + +
435A ASP* 4.3 1.3 - - + -
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Residues in contact with PHE 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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379A LYS 3.8 11.2 - - - -
380A GLN* 4.6 8.7 - - - -
384A ASN* 2.8 54.3 + - - -
385A MET* 3.5 32.3 - - - +
387A MET* 1.3 75.3 - - - +
389A ASN* 1.3 60.7 + - - +
391A LEU* 3.9 5.3 - - + -
392A ASP* 3.0 36.4 + - - +
433A SER* 6.0 0.4 - - - -
791A ARG* 3.5 55.6 - - - +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.6 39.8 + - + +
361A PRO 5.8 1.0 + - - -
362A SER* 5.1 2.3 + - - -
363A LEU* 3.6 20.3 + - + +
385A MET 3.3 8.7 + - - +
386A ILE 3.3 11.0 - - - +
387A MET 3.1 0.4 - - - -
388A PHE* 1.3 80.5 - - - +
390A TYR* 1.3 59.9 + - - +
392A ASP* 3.7 7.0 + - - +
393A GLN* 3.5 23.7 + - - +
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Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASN* 3.6 5.9 + - - -
363A LEU* 3.6 16.8 - - + +
369A MET* 4.2 8.3 - - + -
386A ILE 3.1 8.4 + - - +
387A MET* 2.9 31.9 + - + +
389A ASN* 1.3 77.6 - - - +
391A LEU* 1.3 68.3 + - + +
393A GLN* 3.5 4.6 + - - +
394A LYS* 3.2 21.8 + - + +
402A LEU* 3.8 29.7 - - + +
403A PRO* 3.4 53.9 + - + -
405A VAL* 3.9 8.5 - - + -
435A ASP* 2.7 39.9 + - + -
1005A GOL 4.6 3.1 + - - -
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 2.6 25.8 + - + +
388A PHE* 3.9 8.5 - - + +
390A TYR* 1.3 85.9 - - + +
392A ASP* 1.3 62.1 + - - +
394A LYS* 3.2 5.1 + - + +
395A LEU* 2.9 41.3 + - + +
432A ALA 3.9 12.8 - - - +
433A SER* 4.3 15.0 - - - +
435A ASP* 4.7 1.8 - - + -
784A GLN* 3.5 48.0 - - + +
787A GLU* 6.1 1.6 - - + -
791A ARG* 3.9 27.8 - - - +
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Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PHE* 3.0 24.5 + - - +
389A ASN* 4.1 7.1 - - - +
391A LEU* 1.3 76.9 - - - +
393A GLN* 1.3 57.5 + - - +
396A GLY* 2.8 30.3 + - - -
398A SER* 5.5 0.3 - - - -
788A LYS* 3.0 32.3 + - - +
791A ARG* 3.7 19.3 + - - -
792A ASP* 4.9 5.1 - - - +
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Residues in contact with GLN 393 (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 SER* 2.7 33.7 + - - -
363A LEU* 4.1 5.9 - - - +
364A SER* 3.2 19.4 + - - +
389A ASN* 3.5 16.3 + - - +
390A TYR* 3.5 5.8 + - - +
391A LEU 3.3 0.2 - - - -
392A ASP* 1.3 78.2 - - - +
394A LYS* 1.3 61.6 + - - +
396A GLY 4.0 1.5 - - - +
398A SER* 3.0 47.2 - - - +
399A SER 5.0 2.3 - - - +
400A GLY* 4.5 9.9 + - - +
402A LEU* 3.1 29.3 - - + +
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Residues in contact with LYS 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 TYR* 3.2 16.7 + - + +
391A LEU* 3.5 13.9 - - + +
392A ASP 3.2 0.6 - - - -
393A GLN* 1.3 79.1 - - - +
395A LEU* 1.3 70.5 + - + +
396A GLY 3.3 8.8 - - - +
398A SER 4.9 0.2 - - - +
402A LEU* 3.6 23.8 - - + +
435A ASP* 5.8 1.6 - - - +
784A GLN* 5.7 2.0 - - - +
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Residues in contact with LEU 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 LEU* 2.9 23.6 + - + +
394A LYS* 1.3 76.1 - - + +
396A GLY* 1.3 63.8 + - - +
781A LEU* 3.4 33.2 - - + -
784A GLN* 3.6 44.2 - - + +
785A THR* 3.7 14.8 - - + +
788A LYS* 3.7 29.7 - - + -
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Residues in contact with GLY 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 ASP 2.8 22.7 + - - -
393A GLN 4.6 0.2 - - - -
394A LYS 3.2 10.5 - - - +
395A LEU* 1.3 83.7 - - - +
397A GLY* 1.3 61.2 + - - -
398A SER* 3.1 14.4 + - - +
788A LYS* 4.9 5.6 - - - +
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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