Contacts of the helix formed by residues 384 - 401 (chain A) in PDB entry 5OQN
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE 5.5 0.4 - - - +
383A PRO* 1.3 78.8 - - - +
385A ALA* 1.3 67.3 + - - +
386A SER* 3.3 11.1 + - - +
387A LYS* 3.2 19.0 + - + +
388A LEU* 3.0 22.5 + - - +
432A TYR* 4.9 0.9 - - - -
436A ASP* 5.6 6.1 - - - +
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Residues in contact with ALA 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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384A GLU* 1.3 74.9 - - - +
386A SER* 1.3 64.4 + - - +
388A LEU* 3.3 5.5 + - - +
389A SER* 3.3 18.5 + - - -
432A TYR* 4.9 11.5 - - + -
433A ASP* 4.3 10.5 + - - +
434A TYR* 3.6 34.5 - - + -
436A ASP* 5.1 9.3 + - + -
439A GLY* 3.8 17.6 - - - +
443A MET* 4.1 7.7 - - - +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLU* 4.4 13.3 + - - +
385A ALA* 1.3 78.6 - - - +
387A LYS* 1.3 60.4 + - - +
389A SER* 2.4 26.9 + - - -
390A GLU* 3.4 9.6 + - - +
436A ASP* 4.8 6.7 + - - -
438A VAL* 4.6 10.8 - - - +
439A GLY* 3.6 22.7 + - - -
442A SER* 4.4 8.5 + - - -
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Residues in contact with LYS 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 3.8 23.2 + - - +
383A PRO* 4.2 9.6 - - + -
384A GLU* 3.2 30.2 + - + +
386A SER* 1.3 77.6 + - - +
388A LEU* 1.3 56.8 + - - +
390A GLU* 2.7 40.3 + - - +
391A HIS* 2.6 51.0 + - + -
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 3.7 33.7 - - + -
362A PHE* 4.1 16.2 - - + -
383A PRO* 4.5 8.2 - - + +
384A GLU 3.0 15.4 + - - +
385A ALA 3.8 4.7 - - - +
386A SER 3.3 0.2 - - - -
387A LYS* 1.3 73.9 - - - +
389A SER* 1.3 56.2 + - - +
390A GLU 3.0 2.2 - - - -
391A HIS* 2.9 5.5 + - + -
392A LEU* 2.7 37.5 + - + +
425A LEU* 4.4 19.5 - - + +
429A ALA* 4.3 19.5 - - + +
432A TYR* 3.4 35.2 - - + -
443A MET* 4.3 5.8 - - + -
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.3 9.6 + - - -
386A SER 2.4 26.0 + - - -
388A LEU* 1.3 77.9 - - - +
390A GLU* 1.3 63.2 + - - +
392A LEU* 4.3 2.7 - - - -
393A ASN* 3.1 27.4 + - - +
442A SER* 2.8 25.6 + - - -
443A MET* 4.0 22.8 - - - -
446A VAL* 3.9 18.7 - - - +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER 3.4 9.0 + - - +
387A LYS* 2.7 48.0 + - - +
388A LEU 3.0 0.4 - - - -
389A SER* 1.3 83.5 + - - +
391A HIS* 1.3 63.5 + - + +
393A ASN* 4.0 2.5 - - - +
394A HIS* 3.0 26.7 + - - +
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Residues in contact with HIS 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER* 4.6 9.0 - - - -
351A TRP* 3.4 70.5 - + + +
383A PRO* 5.4 0.9 - - + -
387A LYS* 2.6 59.4 + - + -
388A LEU* 2.9 8.1 + - + +
390A GLU* 1.3 75.8 - - + +
392A LEU* 1.3 66.4 + - - +
394A HIS* 3.2 18.1 + + - +
395A TYR* 3.0 28.3 - - + -
425A LEU* 4.5 3.4 - - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 2.7 22.4 + - + +
389A SER* 4.1 4.7 - - - +
391A HIS* 1.3 75.5 - - - +
393A ASN* 1.3 63.8 + - - +
395A TYR* 3.2 10.7 + - - +
396A ILE* 3.4 14.7 + - + +
422A ILE* 4.0 23.1 - - + +
425A LEU* 4.2 22.7 - - + +
426A SER* 3.8 27.6 - - - +
429A ALA* 4.7 10.8 - - + -
443A MET* 3.6 26.9 - - + -
446A VAL* 4.4 13.0 - - + -
447A VAL* 5.2 8.7 - - + -
450A MET* 5.4 3.1 - - + -
467A VAL* 6.1 1.3 - - + -
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Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A SER 3.1 17.0 + - - +
390A GLU* 4.2 2.7 - - - +
392A LEU* 1.3 80.0 - - - +
394A HIS* 1.3 57.0 + - - +
396A ILE* 2.7 35.6 + - - +
397A LEU* 3.2 42.0 + - - +
446A VAL* 3.3 30.7 - - + +
449A ASN* 5.8 2.6 - - - +
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Residues in contact with HIS 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 5.2 5.8 - - + -
352A LYS* 5.3 10.8 + - - -
390A GLU 3.0 21.3 + - - +
391A HIS* 3.2 17.9 + + - +
393A ASN* 1.3 75.4 - - - +
395A TYR* 1.3 78.1 + + - +
397A LEU* 4.2 8.9 + - - +
398A LEU* 3.4 37.0 + - + +
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Residues in contact with TYR 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A TRP* 2.9 27.8 + - + -
352A LYS 4.2 4.7 + - - -
354A PHE* 2.9 26.0 + + + +
391A HIS* 3.0 30.1 - - + -
392A LEU 3.2 3.9 + - - +
393A ASN 3.0 0.6 - - - -
394A HIS* 1.3 93.1 - + - +
396A ILE* 1.3 64.6 + - - +
398A LEU* 3.8 14.3 - - + +
399A ARG* 3.2 24.8 + - - +
418A LEU* 3.8 24.8 - - + +
421A ILE* 4.0 33.4 - - + -
422A ILE* 3.4 24.7 - - + +
425A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 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 LEU* 3.4 20.2 - - + +
393A ASN* 2.7 22.0 + - - +
395A TYR* 1.3 69.5 - - - +
397A LEU* 1.3 65.2 + - + +
399A ARG* 3.1 2.0 + - - +
400A TYR* 2.8 34.8 + - + +
401A HIS* 5.1 2.5 - - + +
422A ILE* 4.0 16.8 - - + -
446A VAL* 3.8 29.6 - - + +
449A ASN 5.4 1.1 - - - +
450A MET* 3.8 37.5 - - + +
453A LEU* 3.7 28.0 - - + -
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Residues in contact with LEU 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 ASN* 3.2 55.4 + - - +
394A HIS* 4.4 7.2 - - - +
396A ILE* 1.3 79.1 - - + +
398A LEU* 1.3 63.9 + - - +
399A ARG 3.0 1.7 + - - -
401A HIS* 3.2 61.2 + - + +
402A HIS* 3.6 13.0 + - - +
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Residues in contact with LEU 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 HIS* 3.4 36.6 + - + +
395A TYR* 3.9 18.2 - - + +
396A ILE 3.3 0.6 - - - -
397A LEU* 1.3 77.1 - - - +
399A ARG* 1.3 57.9 + - - +
402A HIS* 4.3 8.2 - - - +
403A ASN 4.9 3.6 - - - +
418A LEU* 3.6 29.5 - - + +
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Residues in contact with ARG 399 (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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395A TYR 3.2 16.7 + - - +
396A ILE 3.1 3.0 + - - +
397A LEU 3.0 0.4 - - - -
398A LEU* 1.3 80.7 - - - +
400A TYR* 1.3 115.3 + - + +
401A HIS 3.8 0.2 - - - -
402A HIS 4.1 7.2 - - - +
403A ASN 5.2 0.5 - - - +
415A TYR* 3.1 65.3 + - - +
418A LEU* 3.7 17.7 - - + -
419A GLU* 2.6 35.1 + - + +
422A ILE* 4.2 5.4 - - + -
455A THR* 4.3 9.7 + - - +
457A SER* 5.5 1.4 - - - -
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Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 2.8 24.4 + - + +
399A ARG* 1.3 121.8 - - + +
401A HIS* 1.3 66.0 + - - +
402A HIS 4.7 0.2 - - - -
419A GLU* 3.9 6.1 + - - +
422A ILE* 4.7 5.4 - - + -
450A MET* 5.5 0.2 - - + -
453A LEU* 3.6 36.4 - - + +
455A THR* 3.0 44.0 - - + +
456A LEU* 3.5 22.4 - - + -
457A SER* 3.3 16.3 + - - -
460A LEU* 3.0 27.5 - - + +
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Residues in contact with HIS 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ILE* 4.3 4.4 + - + -
397A LEU* 3.2 47.6 + - + +
400A TYR* 1.3 83.7 - - - +
402A HIS* 1.3 81.2 + + + +
403A ASN* 4.3 2.4 + - - +
449A ASN* 5.2 6.5 - - + -
453A LEU* 4.3 24.4 - - + +
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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