Contacts of the helix formed by residues 424 - 438 (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 LEU 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLU* 3.2 21.5 - - + +
407A VAL* 4.5 11.7 - - + -
410A VAL* 3.7 30.1 - - + -
411A ILE* 4.2 17.0 - - + -
416A PRO* 4.7 4.0 - - + -
420A ASP* 2.8 20.7 + - + +
421A MET* 4.4 13.2 - - + +
422A LYS 3.5 0.4 - - - -
423A LYS* 1.3 72.1 - - - +
425A LYS* 1.3 58.7 + - - +
427A THR* 3.4 10.9 + - - +
428A THR* 2.8 31.8 + - - -
527A VAL* 3.7 26.5 - - + +
531A ALA* 4.0 16.4 - - + -
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A GLU* 3.0 4.3 + - - +
421A MET 5.6 0.2 - - - -
422A LYS 3.3 22.4 - - - +
423A LYS* 2.8 15.3 + - - +
424A LEU* 1.3 72.3 - - - +
426A TYR* 1.3 62.0 + - - +
428A THR* 3.3 8.7 + - - -
429A ARG* 3.1 26.7 + - - +
492A LEU* 3.8 28.9 - - + +
493A ASP* 3.0 37.1 + - - +
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Residues in contact with TYR 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A VAL* 3.3 51.1 - - + +
402A LYS* 3.6 37.9 - - + +
403A LEU* 3.8 22.0 - - + -
406A GLU* 2.6 27.6 + - + +
425A LYS* 1.3 72.1 - - - +
427A THR* 1.3 64.8 + - - +
429A ARG* 3.1 3.9 + - + +
430A VAL* 2.9 36.9 + - + +
487A PRO* 3.8 13.0 - - + +
488A GLU* 3.6 22.6 + - + +
492A LEU* 3.7 24.1 - - + +
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 3.3 19.0 - - + +
406A GLU* 2.7 24.8 + - - -
407A VAL* 3.9 10.6 - - - +
424A LEU* 3.7 14.7 - - - +
426A TYR* 1.3 74.0 - - - +
428A THR* 1.3 61.4 + - - +
430A VAL* 3.3 4.7 + - - +
431A MET* 3.1 21.8 + - - +
527A VAL* 3.7 33.2 - - + +
530A ILE* 3.9 25.7 - - + +
531A ALA* 4.2 4.5 - - + +
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A MET 4.0 11.6 + - - -
424A LEU 2.8 20.2 + - - -
425A LYS* 3.4 11.1 - - - -
426A TYR 3.2 0.2 - - - -
427A THR* 1.3 76.5 - - - +
429A ARG* 1.3 52.3 + - - +
431A MET* 3.1 12.9 + - + +
432A ASN* 2.7 56.1 + - - +
496A ASN* 4.0 24.9 - - - +
527A VAL* 3.9 20.0 - - + +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LYS 3.1 13.5 + - - +
426A TYR* 3.1 9.4 + - + +
428A THR* 1.3 76.7 - - - +
430A VAL* 1.3 60.6 + - - +
432A ASN* 3.1 23.1 + - - +
433A GLU* 2.8 33.1 + - - +
487A PRO* 3.4 32.8 - - + +
488A GLU* 5.3 0.4 - - - -
490A TRP* 3.3 31.5 + - - +
491A PRO 2.9 14.8 + - - -
492A LEU* 3.6 24.5 + - + +
494A GLY 2.8 28.7 + - - -
495A PRO 3.4 11.2 + - - -
496A ASN* 2.9 29.4 + - - +
497A PRO* 3.7 3.3 - - - +
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Residues in contact with VAL 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.7 25.6 - - + -
393A LEU* 4.4 7.9 - - + -
399A VAL* 3.9 8.5 - - + -
403A LEU* 4.4 14.8 - - + -
426A TYR* 2.9 41.7 + - + +
427A THR* 3.3 9.8 + - - +
429A ARG* 1.3 74.9 - - - +
431A MET* 1.3 57.5 + - - +
433A GLU* 3.4 1.8 + - - +
434A SER* 2.9 28.6 + - - -
485A PHE* 4.2 13.0 - - + -
487A PRO* 3.8 18.6 - - + -
530A ILE* 4.7 4.9 - - + -
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Residues in contact with MET 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 4.7 6.5 - - + -
389A THR* 4.9 0.4 - - - -
427A THR 3.1 12.5 + - - +
428A THR* 3.4 18.8 - - + +
430A VAL* 1.3 76.6 - - - +
432A ASN* 1.3 90.3 + - - +
434A SER* 3.3 6.3 + - - -
435A LEU* 3.0 40.1 + - + +
509A PHE* 6.1 0.7 - - + -
523A SER* 3.3 51.4 - - - +
526A ASN* 4.0 20.6 - - + -
527A VAL* 4.1 6.3 - - + -
530A ILE* 4.2 14.8 - - + +
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Residues in contact with ASN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A THR* 2.7 30.2 + - - +
429A ARG* 3.1 33.8 + - - +
431A MET* 1.3 89.9 - - - +
433A GLU* 1.3 56.3 + - - +
435A LEU* 3.3 1.9 + - - +
436A ARG 3.0 17.7 + - - -
490A TRP* 3.5 19.7 - - + -
496A ASN* 4.8 2.5 - - - +
497A PRO* 3.5 19.5 + - + +
506A TYR* 2.7 31.5 + - - +
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Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG 2.8 20.6 + - - +
430A VAL 3.9 3.1 - - - +
432A ASN* 1.3 70.4 - - - +
434A SER* 1.3 65.4 + - - +
436A ARG* 2.7 32.0 + - - +
437A LEU* 3.0 23.6 + - + +
484A LYS 3.0 8.8 - - - +
485A PHE* 3.4 26.5 - - + -
486A ASN 2.7 31.7 + - - +
487A PRO* 3.9 9.9 - - + -
489A ARG* 2.8 27.7 + - - -
490A TRP* 3.5 7.9 - - + -
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.6 9.8 + - - +
388A TRP* 3.8 7.3 - - - +
389A THR* 2.8 45.9 + - - -
392A LEU* 3.8 14.3 - - - +
430A VAL 2.9 16.9 + - - -
431A MET* 3.7 4.9 - - - -
433A GLU* 1.3 77.4 - - - +
435A LEU* 1.3 58.3 + - - +
437A LEU* 3.2 1.6 + - - +
438A TYR* 2.8 32.1 + - - +
485A PHE* 4.5 1.3 - - - -
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 3.7 34.1 - - + -
431A MET* 3.0 34.9 + - + +
432A ASN* 3.8 4.5 - - - +
434A SER* 1.3 74.4 - - - +
436A ARG* 1.3 65.3 + - - +
438A TYR 4.1 9.9 - - - +
439A PRO* 3.3 17.1 - - + +
440A GLN 4.3 8.5 - - - +
473A HIS* 3.2 14.8 + - - -
506A TYR* 3.9 4.0 - - - +
508A PRO* 3.9 26.5 - - + -
509A PHE* 4.1 22.0 - - + -
526A ASN* 5.8 0.7 - - - +
601A HEM 4.0 21.5 - - + -
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Residues in contact with ARG 436 (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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432A ASN 3.0 9.6 + - - +
433A GLU* 2.7 47.1 + - - +
434A SER 3.2 0.4 - - - -
435A LEU* 1.3 77.6 - - - +
437A LEU* 1.3 76.3 + - - +
439A PRO* 3.6 2.6 - - - +
473A HIS* 2.9 70.6 + - + +
474A ARG* 4.4 2.6 - - - +
479A TRP* 3.9 31.6 - - + -
482A ALA* 2.8 36.8 + - - +
484A LYS 3.1 12.3 + - - -
489A ARG* 3.1 15.4 - - - +
490A TRP* 4.2 2.9 - - + -
506A TYR* 3.6 19.0 - - + -
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.9 22.0 - - + -
433A GLU* 3.0 19.9 + - + +
434A SER 4.0 0.9 - - - +
436A ARG* 1.3 104.1 - - - +
438A TYR* 1.3 73.7 + - + +
439A PRO* 3.6 0.8 - - - +
470A TRP* 3.2 7.8 - - - -
474A ARG* 2.8 54.3 + - - +
482A ALA 3.7 11.0 - - - +
483A GLU 4.1 11.4 - - - +
485A PHE* 3.9 31.2 - - + +
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Residues in contact with TYR 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 5.3 2.1 - - - +
388A TRP* 3.7 62.8 - + + -
391A TYR* 3.8 17.7 - + - -
392A LEU* 3.8 33.7 - - + +
434A SER* 2.8 13.5 + - - +
435A LEU* 3.6 7.8 - - - +
437A LEU* 1.3 90.4 - - + +
439A PRO* 1.3 63.7 - - - +
440A GLN* 2.9 24.0 + - - +
470A TRP* 4.0 9.0 - + - -
474A ARG* 3.8 15.9 + - - -
550A MET* 3.8 20.6 - - + -
556A ILE* 4.2 4.7 - - + -
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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