Contacts of the helix formed by residues 391 - 407 (chain A) in PDB entry 2I91
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 ASN 391 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A MET 3.5 9.3 + - - +
382A ASN* 3.4 36.4 + - - +
383A GLN 3.2 6.1 - - - +
384A ARG* 4.7 2.2 - - + +
385A VAL* 3.4 9.6 - - - +
389A ILE 4.0 1.6 + - - +
390A LEU* 1.3 73.9 - - - +
392A ALA* 1.3 62.2 + - - +
393A SER* 2.7 10.8 + - - -
394A VAL* 2.6 47.5 + - - +
395A VAL* 3.2 15.6 + - - +
437A MET 5.4 2.6 + - - -
438A SER* 5.9 2.8 - - - +
441A THR* 4.6 5.7 + - - -
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A MET* 3.3 34.7 + - + +
383A GLN* 3.0 26.1 + - + +
385A VAL* 3.8 6.8 - - + +
391A ASN* 1.3 73.3 - - - +
393A SER* 1.3 64.8 + - - +
396A ALA* 2.8 27.9 + - - +
501A MET* 3.3 25.7 - - + +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 4.2 0.7 - - - +
376A ASP 4.6 3.1 - - - -
377A VAL* 3.7 21.8 - - - +
381A MET* 2.9 23.5 + - - +
391A ASN* 2.7 19.0 + - - -
392A ALA* 1.3 73.0 - - - +
394A VAL* 1.3 59.3 + - - -
396A ALA* 3.6 2.9 - - - +
397A ALA* 3.0 23.0 + - - +
437A MET* 3.8 13.6 - - - +
441A THR* 2.7 31.4 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.4 7.2 - - + -
390A LEU* 4.2 18.4 - - + -
391A ASN* 2.6 42.2 + - - +
393A SER* 1.3 71.8 - - - +
395A VAL* 1.3 58.4 + - - +
397A ALA* 3.1 4.2 + - - +
398A ALA* 2.9 27.0 + - + +
430A LEU* 6.3 0.2 - - + -
433A VAL* 5.0 3.1 - - + +
434A VAL* 3.7 46.9 - - + +
437A MET* 4.3 21.3 - - + -
438A SER* 6.2 0.4 - - - -
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Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.9 3.8 - - + -
322A PHE* 5.6 4.3 - - + -
325A LEU* 4.3 11.4 - - + -
385A VAL* 3.8 19.3 - - + -
390A LEU* 4.5 8.1 - - + -
391A ASN 3.2 13.9 + - - +
394A VAL* 1.3 79.0 - - - +
396A ALA* 1.3 63.2 + - - +
398A ALA* 3.1 6.0 + - - +
399A MET* 2.9 24.4 + - + +
501A MET* 3.0 28.7 - - + -
522A PHE* 2.9 47.1 - - + +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 4.0 13.2 - - + -
381A MET* 4.4 2.7 - - + -
392A ALA 2.8 22.8 + - - +
393A SER 3.6 3.8 - - - +
395A VAL* 1.3 73.2 - - - +
397A ALA* 1.3 57.2 + - - +
399A MET* 3.3 3.7 + - - +
400A CYS* 2.9 27.9 + - - +
467A PHE* 3.4 37.8 - - + +
501A MET* 3.8 16.2 - - + -
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.4 23.9 - - + +
393A SER 3.0 13.2 + - - +
394A VAL 3.1 8.9 + - - +
396A ALA* 1.3 77.2 - - - +
398A ALA* 1.3 51.0 + - - +
400A CYS* 2.9 4.3 - - - +
401A MET* 2.8 38.7 + - - +
424A ILE* 3.9 10.9 - - + +
433A VAL* 4.2 6.3 - - + -
437A MET* 3.8 23.1 - - + -
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Residues in contact with ALA 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.4 6.1 - - + -
357A PHE* 3.4 35.5 - - + -
394A VAL* 2.9 12.9 + - + +
395A VAL* 3.1 11.6 + - - +
397A ALA* 1.3 74.0 - - - +
399A MET* 1.3 66.2 + - - +
401A MET* 3.1 10.9 + - - +
402A LEU* 3.0 21.5 + - - +
430A LEU* 4.4 14.4 - - + -
433A VAL* 4.9 3.7 - - + +
522A PHE* 4.8 2.2 - - + -
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Residues in contact with MET 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A PHE* 3.5 32.1 - - + -
395A VAL* 2.9 18.4 + - + +
396A ALA* 3.6 4.9 - - - +
398A ALA* 1.3 75.4 - - - +
400A CYS* 1.3 62.7 + - - +
402A LEU* 3.3 13.7 + - + +
403A VAL* 3.1 28.1 + - + +
467A PHE* 3.3 28.9 - - + -
499A CYS* 4.5 7.0 - - - -
501A MET* 5.6 0.4 - - - -
521A GLY* 4.5 6.7 - - - -
522A PHE* 3.6 39.5 - - + +
526A ALA* 3.6 28.7 - - + -
527A LEU* 6.0 0.9 - - + -
530A ILE* 5.7 4.0 - - + -
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Residues in contact with CYS 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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373A LEU* 3.7 31.0 - - - +
375A ILE* 3.7 28.7 - - + -
396A ALA 2.9 14.0 + - - +
397A ALA 2.9 15.3 - - - +
399A MET* 1.3 76.1 - - - +
401A MET* 1.3 62.6 + - - +
402A LEU 3.3 0.2 + - - -
403A VAL 3.3 1.7 + - - -
404A ALA* 2.9 24.8 + - - +
412A MET* 3.8 23.8 - - - -
424A ILE* 5.4 0.2 - - + -
467A PHE* 4.0 12.3 - - + -
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Residues in contact with MET 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 3.1 24.5 - - + +
397A ALA 2.8 21.2 + - - +
398A ALA* 3.1 9.6 + - - +
400A CYS* 1.3 73.5 - - - +
402A LEU* 1.3 57.3 + - - +
404A ALA* 3.2 4.4 + - - +
405A ARG* 2.6 68.2 + - - +
412A MET* 4.5 10.1 - - - +
424A ILE* 4.5 14.8 - - + -
425A THR 3.3 30.7 - - - +
426A VAL* 3.6 8.1 - - - +
428A MET 3.2 17.0 - - - +
430A LEU* 5.9 0.4 - - + -
433A VAL* 4.3 18.2 - - + -
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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
----------------------------------------------------------
358A TYR* 3.8 34.9 - - + +
361A PHE* 3.3 56.1 - - + -
363A LEU* 4.7 2.2 - - + -
398A ALA 3.0 11.6 + - - +
399A MET* 3.3 17.9 - - + +
400A CYS 3.2 0.4 - - - -
401A MET* 1.3 78.9 - - - +
403A VAL* 1.3 62.8 + - - +
405A ARG* 3.3 7.8 + - - +
406A THR* 3.1 22.0 + - - +
527A LEU* 3.4 37.5 - - + +
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Residues in contact with VAL 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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371A PHE* 4.7 11.4 - - + -
373A LEU* 3.3 33.7 - - + -
399A MET* 3.1 15.0 + - + +
400A CYS* 3.9 6.3 - - - +
402A LEU* 1.3 79.9 - - + +
404A ALA* 1.3 58.1 + - - +
406A THR* 3.5 3.6 + - - -
407A GLU* 3.2 33.7 + - + +
410A SER* 5.5 0.2 - - - -
465A ILE* 4.2 9.9 - - + -
467A PHE* 4.9 5.4 - - + -
527A LEU* 4.1 16.6 - - + -
530A ILE* 4.0 29.4 - - + -
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Residues in contact with ALA 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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373A LEU* 3.9 9.4 - - + -
400A CYS 2.9 17.6 + - - +
401A MET* 3.6 5.4 - - - +
403A VAL* 1.3 79.3 - - - +
405A ARG* 1.3 58.8 + - - +
406A THR 3.2 0.9 - - - -
407A GLU 3.3 15.0 - - - +
408A LYS* 4.2 6.4 - - - +
410A SER* 3.5 18.2 + - - +
412A MET* 4.0 21.5 - - + -
426A VAL* 3.9 20.5 - - + +
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Residues in contact with ARG 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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354A ASP* 5.3 2.4 + - - -
355A ASN* 6.0 1.4 - - - +
358A TYR* 3.6 38.2 + - + -
401A MET* 2.6 42.6 + - - +
402A LEU* 3.3 5.3 + - - +
404A ALA* 1.3 77.7 - - - +
406A THR* 1.3 60.6 + - - +
408A LYS* 2.9 27.1 + - - +
426A VAL* 3.1 38.8 + - + -
427A ASN* 4.6 2.5 + - - -
428A MET 3.2 22.8 + - - +
429A LEU* 5.4 2.0 - - - +
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Residues in contact with THR 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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363A LEU* 6.0 1.2 - - - +
364A VAL* 3.8 34.1 - - + +
366A PRO* 3.4 22.3 - - + +
402A LEU* 3.1 18.5 + - - +
403A VAL* 3.9 5.4 - - - -
404A ALA 3.2 0.4 - - - -
405A ARG* 1.3 79.9 - - - +
407A GLU* 1.3 77.4 + - + +
408A LYS* 3.7 10.7 + - - +
527A LEU* 4.5 14.6 - - + +
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL* 5.3 2.9 - - - +
365A GLU 4.4 1.0 - - - +
366A PRO* 3.6 11.2 - - - +
367A THR* 3.1 38.4 + - - +
368A GLY* 3.1 14.9 + - - -
369A LYS 5.0 0.9 - - - +
371A PHE* 3.3 46.9 - - + -
403A VAL* 3.2 17.6 + - + +
404A ALA 3.3 4.6 - - - +
406A THR* 1.3 83.8 - - + +
408A LYS* 1.3 58.3 + - - +
409A ASP 3.2 2.9 + - - +
410A SER* 2.6 29.8 + - - +
531A ARG* 5.6 0.9 - - - +
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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