Contacts of the helix formed by residues 394 - 407 (chain A) in PDB entry 5J3V
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 LEU 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A LEU* 4.1 19.5 - - + -
301A ILE* 3.7 26.7 - - + -
383A LEU* 4.2 14.4 - - + -
386A LEU* 4.2 4.5 - - + +
387A ALA* 3.7 35.2 - - + +
390A TYR* 3.9 22.5 + - + +
391A ARG 3.9 9.8 + - - +
392A ASP 3.1 0.6 - - - -
393A GLU* 1.3 78.6 - - - +
395A LEU* 1.3 63.0 + - - +
396A PRO* 3.4 1.6 - - - -
397A HIS* 3.0 17.7 + - + +
398A ILE* 3.1 28.2 + - + +
424A ILE* 4.7 1.6 - - + -
428A CYS* 4.3 6.7 - - - -
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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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392A ASP* 3.5 25.4 - - + +
394A LEU* 1.3 77.8 - - - +
396A PRO* 1.4 65.3 - - + +
397A HIS 3.0 0.2 + - - -
398A ILE* 4.3 3.6 - - + +
399A LEU* 2.8 56.9 + - + +
424A ILE* 4.9 4.9 - - + -
428A CYS* 3.8 25.1 - - + +
431A GLY* 3.6 35.0 - - - +
432A MET* 3.9 22.9 - - + -
435A TYR* 5.4 0.9 - - + -
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Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASP 3.7 4.7 - - - +
393A GLU* 3.5 21.5 - - - +
394A LEU 3.5 0.4 - - - -
395A LEU* 1.4 92.7 - - + +
397A HIS* 1.3 65.5 + - + +
399A LEU* 5.3 1.8 - - + -
400A PRO* 3.3 23.7 - - + +
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Residues in contact with HIS 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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294A VAL* 5.2 2.0 + - + -
297A LEU* 4.1 22.8 - - + +
298A PRO* 3.4 49.0 - - + +
301A ILE* 3.5 27.9 - - + +
393A GLU 3.8 17.8 + - - -
394A LEU* 3.0 9.6 + - + +
396A PRO* 1.3 84.8 - - + +
398A ILE* 1.3 61.2 + - - +
400A PRO* 4.2 3.1 - - - +
401A LEU* 3.3 24.8 - - - +
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Residues in contact with ILE 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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301A ILE* 3.6 23.3 - - + -
305A VAL* 4.4 5.8 - - + -
383A LEU* 3.8 22.0 - - + -
394A LEU* 3.1 31.4 + - + +
395A LEU* 3.0 5.9 + - + +
397A HIS* 1.3 79.1 - - - +
399A LEU* 1.3 59.2 + - + +
400A PRO 3.1 3.1 - - - -
401A LEU* 3.2 8.4 + - + +
402A LEU* 2.7 51.1 + - + +
420A VAL* 4.2 16.8 - - + -
424A ILE* 3.7 29.4 - - + -
428A CYS* 6.1 0.4 - - - -
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU* 2.8 47.8 + - + +
396A PRO* 5.3 0.7 - - + -
398A ILE* 1.3 74.6 - - + +
400A PRO* 1.4 65.8 - - + +
402A LEU* 4.0 15.7 - - + -
403A LYS* 3.0 32.7 + - - +
432A MET* 3.7 30.1 - - + -
435A TYR* 3.4 45.1 - - + +
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Residues in contact with PRO 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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395A LEU 3.7 1.3 - - - +
396A PRO* 3.3 28.0 - - + +
397A HIS 4.2 2.2 - - - +
398A ILE 3.4 4.7 - - - +
399A LEU* 1.4 96.9 - - + +
401A LEU* 1.3 62.6 + - + +
403A LYS* 3.3 11.3 + - + +
404A GLU* 3.5 17.9 + - - +
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Residues in contact with LEU 401 (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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301A ILE* 4.1 11.0 - - + -
302A PRO* 4.4 22.2 - - + -
305A VAL* 4.2 20.0 - - + -
397A HIS 3.3 18.4 - - - +
398A ILE* 3.3 27.1 - - + +
400A PRO* 1.3 77.9 - - + +
402A LEU* 1.3 72.9 + - + +
404A GLU* 3.2 20.6 + - - +
405A LEU* 3.2 34.5 + - + +
420A VAL* 5.4 1.3 - - + -
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Residues in contact with LEU 402 (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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398A ILE* 2.7 41.2 + - + +
399A LEU* 3.9 18.4 - - + +
401A LEU* 1.3 75.3 - - + +
403A LYS* 1.3 63.8 + - - +
405A LEU* 3.1 14.0 + - + +
406A LEU* 3.2 34.0 + - + +
417A GLY* 3.4 29.4 - - - +
420A VAL* 4.0 15.5 - - + -
421A LEU* 4.2 20.0 - - + +
424A ILE* 4.2 13.0 - - + -
432A MET* 4.8 2.9 - - + -
439A LEU* 5.4 1.1 - - + -
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Residues in contact with LYS 403 (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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399A LEU* 3.0 23.0 + - - +
400A PRO* 3.5 7.4 - - + +
401A LEU 3.2 0.2 - - - -
402A LEU* 1.3 77.3 - - - +
404A GLU* 1.3 60.7 + - + +
405A LEU 3.2 1.8 + - - -
406A LEU* 4.3 3.1 + - + -
407A PHE* 3.5 42.3 + - + +
435A TYR* 3.6 35.0 - - - +
438A GLU* 4.6 17.0 + - - +
439A LEU* 5.8 6.5 - - + +
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Residues in contact with GLU 404 (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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400A PRO 3.5 13.6 + - - +
401A LEU* 3.2 15.8 + - - +
402A LEU 3.1 0.4 - - - -
403A LYS* 1.3 81.5 - - + +
405A LEU* 1.3 60.3 + - - +
407A PHE 5.0 2.0 - - - -
408A HIS* 3.6 24.4 - - - -
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Residues in contact with LEU 405 (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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305A VAL* 3.7 28.3 - - + -
309A LYS* 5.1 8.1 - - - +
401A LEU* 3.2 33.0 - - + +
402A LEU* 3.1 11.6 + - + +
404A GLU* 1.3 81.2 - - - +
406A LEU* 1.3 65.8 + - - +
407A PHE 3.3 1.9 + - - -
408A HIS* 3.4 9.4 + - - +
413A VAL* 3.4 38.1 - - + +
414A LYS* 3.4 24.8 - - - -
416A SER* 4.3 6.1 - - - +
417A GLY* 3.8 19.7 - - - -
420A VAL* 4.9 1.3 - - + -
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Residues in contact with LEU 406 (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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402A LEU* 3.2 32.2 + - + +
403A LYS* 4.3 2.7 + - + +
405A LEU* 1.3 76.7 - - - +
407A PHE* 1.3 75.4 + - + +
408A HIS 3.4 0.4 - - - -
414A LYS* 3.4 29.1 - - - +
417A GLY 3.3 32.3 - - - +
418A ILE* 3.7 16.1 - - + +
421A LEU* 4.3 13.9 - - + -
439A LEU* 3.7 36.8 - - + -
442A HIS* 3.5 13.1 - - + +
443A LEU* 5.2 3.8 - - + -
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Residues in contact with PHE 407 (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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403A LYS* 3.5 37.2 - - + +
404A GLU* 5.6 1.1 - - - -
405A LEU 3.3 1.6 - - - +
406A LEU* 1.3 84.3 - - + +
408A HIS* 1.3 64.4 + - - +
409A HIS 3.9 0.3 + - - -
414A LYS* 5.2 1.3 - - - +
438A GLU* 3.8 26.0 - - + -
439A LEU* 4.1 18.2 - - + -
442A HIS* 3.4 47.3 - + + -
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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