Contacts of the helix formed by residues 396 - 411 (chain A) in PDB entry 6J95
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 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A LEU 3.5 0.8 + - - +
393A LEU 3.3 12.9 + - - +
394A THR 3.4 0.2 - - - -
395A THR* 1.3 93.0 + - - +
397A PRO* 1.3 70.5 - - - +
398A SER* 3.2 8.0 + - - +
399A VAL* 3.1 29.4 + - + +
400A VAL 3.3 8.0 + - - -
484A LYS* 3.1 31.7 + - - +
485A PHE* 3.7 36.5 + - + +
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Residues in contact with PRO 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 LEU 4.8 0.7 - - - +
394A THR 4.7 5.6 - - - +
395A THR 3.8 7.4 - - - +
396A GLU* 1.3 90.4 - - - +
398A SER* 1.3 57.8 + - - +
400A VAL* 3.2 10.2 + - + +
401A ALA* 2.9 28.5 + - - +
540A GLN* 6.3 1.3 - - - +
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.2 9.5 + - - -
397A PRO* 1.3 79.1 - - - +
399A VAL* 1.3 69.8 + - - +
401A ALA* 3.6 7.4 + - - +
402A LYS* 3.2 23.2 + - - +
426A TYR* 5.0 0.2 - - - -
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.0 6.5 - - + -
396A GLU* 3.1 28.1 + - + +
398A SER* 1.3 80.5 + - - +
400A VAL* 1.3 60.0 + - - +
402A LYS 3.3 0.9 + - - -
403A LEU* 2.8 28.1 + - - +
426A TYR* 3.3 30.6 - - + +
430A VAL* 3.9 8.3 - - + -
485A PHE* 3.8 20.4 - - + +
487A PRO* 3.7 32.1 - - + -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 3.3 51.6 - - + +
394A THR* 5.5 0.2 - - - -
396A GLU 3.3 1.9 + - - +
397A PRO* 3.2 12.2 + - + +
399A VAL* 1.3 77.6 - - - +
401A ALA* 1.3 57.0 + - - +
403A LEU* 3.2 6.7 + - - +
404A GLN* 2.8 55.3 + - + +
534A ILE* 5.3 9.2 - - + -
538A ASN* 6.4 0.4 - - - -
539A PHE 6.1 1.1 - - - +
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Residues in contact with ALA 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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397A PRO 2.9 15.8 + - - +
398A SER* 3.8 8.5 - - - +
399A VAL 3.3 0.2 - - - -
400A VAL* 1.3 78.7 - - - +
402A LYS* 1.3 57.5 + - - +
404A GLN* 3.4 13.4 + - - +
405A GLU* 3.0 29.8 + - - +
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A SER 3.2 16.1 + - - +
399A VAL 3.8 3.1 - - - +
401A ALA* 1.3 79.4 - - - +
403A LEU* 1.3 60.5 - - - +
405A GLU* 3.4 11.0 + - + +
406A GLU* 3.2 21.3 + - - +
426A TYR* 3.6 36.7 - - + +
488A GLU* 2.6 35.5 + - - +
492A LEU* 4.9 9.5 - - - +
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Residues in contact with LEU 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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393A LEU* 4.0 24.0 - - + -
399A VAL 2.8 17.3 + - - +
400A VAL* 3.2 4.7 + - - +
402A LYS* 1.3 74.7 - - - +
404A GLN* 1.3 65.1 + - - +
406A GLU* 3.2 4.2 + - - +
407A VAL* 3.1 32.2 + - + +
426A TYR* 3.8 13.6 - - + -
427A THR* 3.3 46.2 - - + +
430A VAL* 4.4 7.2 - - + -
530A ILE* 3.9 13.5 - - + -
534A ILE* 3.7 33.7 - - + -
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Residues in contact with GLN 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 VAL* 2.8 42.1 + - + +
401A ALA* 3.7 12.3 - - - +
403A LEU* 1.3 72.3 - - - +
405A GLU* 1.3 61.4 + - - +
407A VAL* 3.3 8.2 - - - +
408A ASP* 3.0 32.6 + - - -
534A ILE* 3.7 17.6 - - + +
537A PHE 4.5 4.0 + - - -
538A ASN* 3.1 28.9 + - - +
569A ARG* 3.3 36.7 + - - +
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Residues in contact with GLU 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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401A ALA 3.0 18.4 + - - +
402A LYS* 3.5 12.4 - - + +
403A LEU 3.2 0.4 - - - -
404A GLN* 1.3 77.1 - - - +
406A GLU* 1.3 62.1 + - - +
408A ASP* 4.0 4.3 - - - +
409A SER* 3.2 25.4 + - - -
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Residues in contact with GLU 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 LYS 3.2 9.6 + - - +
403A LEU 3.2 8.3 + - - +
405A GLU* 1.3 78.1 - - - +
407A VAL* 1.3 60.7 + - - +
409A SER* 3.1 4.2 + - - -
410A VAL* 2.7 45.2 + - + +
423A LYS 3.7 3.0 - - - +
424A LEU* 3.2 13.1 - - + +
425A LYS* 3.0 14.9 + - - +
426A TYR* 2.6 34.0 + - + +
427A THR* 2.7 37.1 + - - -
492A LEU* 5.7 1.2 - - - +
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Residues in contact with VAL 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 LEU* 3.1 20.3 + - + +
404A GLN* 3.3 18.4 - - - +
406A GLU* 1.3 76.4 - - - +
408A ASP* 1.3 64.9 + - - +
411A ILE* 3.1 17.8 + - + +
412A GLY* 2.8 26.1 + - - +
424A LEU* 4.5 3.8 - - + -
427A THR* 3.9 14.4 - - - +
531A ALA* 3.8 38.1 - - + +
534A ILE* 4.2 3.8 - - + -
535A ARG* 3.9 28.3 - - + +
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Residues in contact with ASP 408 (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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404A GLN 3.0 20.5 + - - +
405A GLU* 4.0 4.7 - - - +
407A VAL* 1.3 77.7 - - - +
409A SER* 1.3 61.5 + - - +
412A GLY* 3.7 11.8 + - - -
535A ARG* 2.8 34.9 + - - +
569A ARG* 2.7 40.5 + - - -
579A PRO* 4.4 4.5 - - - +
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Residues in contact with SER 409 (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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405A GLU* 3.2 17.4 + - - -
406A GLU* 3.1 5.5 + - - -
408A ASP* 1.3 81.2 - - - +
410A VAL* 1.3 66.6 + - - +
579A PRO* 3.6 16.1 - - - +
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Residues in contact with VAL 410 (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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406A GLU* 2.7 37.6 + - + +
409A SER* 1.3 80.6 - - - +
411A ILE* 1.3 64.3 + - + +
414A ARG* 2.8 18.5 + - - -
420A ASP* 4.2 2.7 - - - +
423A LYS* 3.9 47.8 + - + +
424A LEU* 3.7 23.3 - - + -
579A PRO* 3.5 10.3 - - - +
580A ILE* 5.8 0.2 - - - -
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Residues in contact with ILE 411 (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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407A VAL* 3.1 19.0 + - + +
410A VAL* 1.3 86.0 - - + +
412A GLY* 1.3 75.2 + - - +
413A ASP 3.1 0.3 + - - -
414A ARG* 2.9 45.8 + - - +
416A PRO* 4.3 13.2 - - + -
420A ASP* 3.8 33.0 - - + +
424A LEU* 4.2 10.3 - - + -
531A ALA* 3.7 38.8 - - + +
532A MET* 4.4 4.3 - - + +
535A ARG* 5.0 0.7 - - + -
536A ARG* 5.7 0.2 - - - +
579A PRO* 3.2 13.3 - - - +
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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