Contacts of the helix formed by residues 391 - 407 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET 3.5 8.9 + - - +
382B ASN* 3.4 27.7 - - - +
383B GLN 3.2 15.3 - - - +
384B ARG* 4.2 2.7 - - + +
385B VAL* 3.4 9.1 - - - +
389B ILE 4.0 1.2 + - - +
390B LEU* 1.3 74.1 - - - +
392B ALA* 1.3 62.8 + - - +
393B SER* 2.7 11.2 + - - -
394B VAL* 2.5 48.3 + - - +
395B VAL* 3.2 15.4 + - - +
437B MET 5.4 2.4 + - - -
438B SER* 5.9 2.8 - - - +
441B THR* 4.5 4.9 + - - -
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 3.3 34.5 + - + +
383B GLN* 3.0 26.0 + - + +
385B VAL* 3.8 7.0 - - + +
391B ASN* 1.3 72.9 - - - +
393B SER* 1.3 65.0 + - - +
396B ALA* 2.8 28.4 + - - +
501B MET* 3.3 25.8 - - + +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 4.2 0.5 - - - +
376B ASP 4.6 3.1 - - - -
377B VAL* 3.8 20.8 - - - +
381B MET* 2.9 24.0 + - - +
391B ASN* 2.7 14.0 + - - -
392B ALA* 1.3 77.8 - - - +
394B VAL* 1.3 59.4 + - - -
396B ALA* 3.3 3.2 + - - +
397B ALA* 3.0 22.5 + - - +
437B MET* 3.8 13.5 - - - +
441B THR* 2.6 31.8 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.5 7.0 - - + -
390B LEU* 4.2 17.5 - - + -
391B ASN* 2.5 42.4 + - - +
393B SER* 1.3 72.1 - - - +
395B VAL* 1.3 57.4 + - - +
397B ALA* 3.2 4.5 + - - +
398B ALA* 2.9 27.1 + - + +
430B LEU* 6.3 0.2 - - + -
433B VAL* 5.0 2.5 - - + +
434B VAL* 3.7 46.9 - - + +
437B MET* 4.3 21.5 - - + -
438B SER* 5.7 0.4 - - - +
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Residues in contact with VAL 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.9 3.8 - - + -
322B PHE* 5.5 4.3 - - + -
325B LEU* 4.3 11.2 - - + -
385B VAL* 3.9 18.8 - - + -
390B LEU* 4.5 8.5 - - + -
391B ASN 3.2 13.2 + - - +
392B ALA* 4.5 0.2 - - - -
394B VAL* 1.3 78.7 - - - +
396B ALA* 1.3 63.3 + - - +
398B ALA* 3.1 6.3 + - - +
399B MET* 2.9 24.2 + - + +
501B MET* 3.0 27.8 - - + -
522B PHE* 2.9 47.1 - - + +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 4.0 13.0 - - + -
381B MET* 4.4 2.7 - - + -
392B ALA 2.8 21.8 + - - +
393B SER 3.5 4.5 - - - +
395B VAL* 1.3 74.0 - - - +
397B ALA* 1.3 58.2 + - - +
399B MET* 3.3 3.5 + - - +
400B CYS* 2.9 27.9 + - - +
467B PHE* 3.5 36.3 - - + +
501B MET* 3.5 16.8 - - + +
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Residues in contact with ALA 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 3.4 24.3 - - + +
393B SER 3.0 13.0 + - - +
394B VAL 3.4 8.1 - - - +
396B ALA* 1.3 77.1 - - - +
398B ALA* 1.3 51.4 + - - +
400B CYS* 2.9 4.5 - - - +
401B MET* 2.8 38.4 + - - +
424B ILE* 3.9 11.2 - - + +
433B VAL* 4.2 6.3 - - + -
437B MET* 3.8 23.8 - - + -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B LEU* 4.5 6.5 - - + -
357B PHE* 3.5 35.0 - - + -
394B VAL* 2.9 12.9 + - + +
395B VAL* 3.1 12.1 + - - +
397B ALA* 1.3 73.7 - - - +
399B MET* 1.3 66.0 + - - +
401B MET* 3.1 10.3 + - - +
402B LEU* 3.0 21.8 + - - +
430B LEU* 4.4 14.6 - - + -
433B VAL* 4.9 3.3 - - + +
522B PHE* 4.9 1.8 - - + -
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Residues in contact with MET 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B PHE* 3.6 31.4 - - + -
395B VAL* 2.9 18.5 + - + +
396B ALA* 3.6 4.0 - - - +
398B ALA* 1.3 77.1 - - - +
400B CYS* 1.3 61.3 + - - +
402B LEU* 3.3 13.1 + - + +
403B VAL* 3.1 27.9 + - + +
467B PHE* 3.3 29.6 - - + -
499B CYS* 4.5 7.4 - - - -
501B MET* 5.6 0.7 - - - -
521B GLY* 4.5 5.8 - - - -
522B PHE* 3.6 42.0 - - + +
526B ALA* 3.6 29.6 - - + -
527B LEU* 6.0 1.1 - - + -
530B ILE* 5.7 3.8 - - + -
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Residues in contact with CYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.7 30.5 - - - +
375B ILE* 3.6 29.6 - - + -
396B ALA 2.9 14.7 + - - +
397B ALA 2.9 13.5 - - - +
399B MET* 1.3 75.0 - - - +
401B MET* 1.3 62.5 + - - +
402B LEU 3.3 0.2 + - - -
403B VAL 3.3 2.0 + - - +
404B ALA* 2.9 24.1 + - - +
412B MET* 3.8 24.7 - - - -
424B ILE* 5.4 0.2 - - + -
467B PHE* 3.9 12.7 - - + -
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Residues in contact with MET 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TYR* 3.1 24.5 - - + +
397B ALA 2.8 21.2 + - - +
398B ALA* 3.1 9.4 + - - +
400B CYS* 1.3 72.6 - - - +
402B LEU* 1.3 58.8 + - - +
404B ALA* 3.2 5.3 + - - +
405B ARG* 2.6 56.3 + - - +
412B MET* 4.5 9.6 - - - +
424B ILE* 4.5 14.6 - - + -
425B THR 3.3 30.5 - - - +
426B VAL* 3.6 8.5 - - - +
428B MET* 3.1 32.1 - - + +
430B LEU* 5.9 0.4 - - + -
433B VAL* 4.4 14.4 - - + -
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TYR* 3.8 33.8 - - + +
361B PHE* 3.3 57.2 - - + -
363B LEU* 4.8 2.7 - - + -
398B ALA 3.0 11.6 + - - +
399B MET* 3.3 17.9 - - + +
400B CYS 3.1 0.2 - - - -
401B MET* 1.3 78.9 - - - +
403B VAL* 1.3 62.7 + - - +
405B ARG* 3.3 7.6 + - - +
406B THR* 3.1 22.3 + - - +
527B LEU* 3.4 37.7 - - + +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PHE* 4.7 11.7 - - + -
373B LEU* 3.3 34.8 - - + -
399B MET* 3.1 14.6 + - + +
400B CYS* 3.8 6.3 - - - +
402B LEU* 1.3 78.4 - - - +
404B ALA* 1.3 58.4 + - - +
406B THR* 3.5 3.0 + - - -
407B GLU* 3.2 33.7 + - + +
465B ILE* 4.1 10.1 - - + -
467B PHE* 4.9 5.2 - - + -
527B LEU* 4.1 17.0 - - + -
530B ILE* 4.0 28.5 - - + -
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B LEU* 3.9 8.7 - - + -
400B CYS 2.9 17.3 + - - +
401B MET* 3.6 4.9 - - - +
403B VAL* 1.3 79.6 - - - +
405B ARG* 1.3 57.9 + - - +
406B THR 3.2 1.1 - - - -
407B GLU 3.3 15.7 - - - +
408B LYS* 4.2 6.4 - - - +
410B SER* 3.5 18.5 + - - +
412B MET* 4.1 21.5 - - + -
426B VAL* 3.9 21.4 - - + +
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ASP* 5.3 3.0 + - - -
355B ASN* 6.0 1.8 - - - +
358B TYR* 3.7 37.9 + - + -
401B MET* 2.6 41.1 + - - +
402B LEU* 3.3 4.9 + - - +
404B ALA* 1.3 77.9 - - - +
406B THR* 1.3 60.2 + - - +
408B LYS* 2.9 27.7 + - - +
426B VAL* 3.1 39.5 + - + -
427B ASN* 4.6 2.5 - - - -
428B MET 3.1 22.0 + - - -
429B LEU* 5.3 1.8 - - - +
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Residues in contact with THR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 5.9 1.2 - - - +
364B VAL* 3.8 34.3 - - + +
366B PRO* 3.3 23.9 - - + +
402B LEU* 3.1 18.4 + - - +
403B VAL* 3.9 4.9 - - - -
404B ALA 3.2 0.2 - - - -
405B ARG* 1.3 81.3 - - - +
407B GLU* 1.3 76.6 + - + +
408B LYS* 3.7 9.8 + - - +
527B LEU* 4.5 15.0 - - + +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 5.3 2.8 - - - +
365B GLU 4.4 1.4 - - - +
366B PRO* 3.5 10.8 - - - +
367B THR* 3.2 25.3 + - - +
368B GLY* 3.1 28.4 + - - -
369B LYS 5.0 0.9 - - - +
371B PHE* 3.3 46.1 - - + -
403B VAL* 3.2 17.4 + - + +
404B ALA 3.3 5.1 - - - +
406B THR* 1.3 84.5 - - + +
408B LYS* 1.3 57.9 + - - +
409B ASP 3.2 2.8 + - - +
410B SER* 2.6 30.0 + - - +
531B ARG* 5.6 0.7 - - - +
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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
------------------------------------------------------------
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