Contacts of the helix formed by residues 397 - 419 (chain B) in PDB entry 3EIJ
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 THR 397 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LYS* 4.3 20.9 - - - +
214A SER* 5.4 2.4 - - - +
391B TRP* 4.5 0.9 - - - -
394B SER* 4.9 10.3 - - - +
395B THR 4.1 2.9 + - - +
396B ILE* 1.3 77.8 - - - +
398B VAL* 1.3 70.0 + - - +
399B ASP* 2.2 31.0 + - - -
400B GLN* 3.0 15.2 + - - +
401B MET* 2.7 21.2 + - - +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE 3.8 17.3 - - - +
177A GLU* 3.2 32.5 - - - +
178A HIS* 3.6 22.2 - - - +
179A GLY* 5.0 1.6 - - - -
218A MET* 4.1 11.2 - - + -
391B TRP* 3.7 29.5 - - + -
397B THR* 1.3 71.7 - - - +
399B ASP* 1.3 62.5 + - - +
401B MET* 2.9 5.0 + - + -
402B LYS* 2.6 40.1 + - + +
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Residues in contact with ASP 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER* 3.2 30.8 + - - +
217A GLU* 6.0 4.0 - - + -
218A MET* 4.2 27.0 - - + +
221A LYS* 4.6 9.3 + - - +
358B HIS* 5.4 1.4 + - - -
397B THR* 2.2 33.8 + - - -
398B VAL* 1.3 76.8 - - - +
400B GLN* 1.3 76.3 + - - +
402B LYS* 3.9 4.4 - - - +
403B ARG* 2.7 40.8 + - - +
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Residues in contact with GLN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PRO 3.5 17.0 - - - +
358B HIS* 3.5 27.5 + - - +
360B HIS* 3.3 15.4 + - + -
361B HIS* 2.8 64.1 + - - +
364B VAL* 4.2 0.3 - - - +
396B ILE* 3.9 7.4 - - + -
397B THR* 3.0 19.5 + - - +
399B ASP* 1.3 101.1 + - - +
401B MET* 1.3 64.8 + - - +
403B ARG* 4.2 2.2 - - - +
404B GLY* 3.0 18.2 + - - -
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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
----------------------------------------------------------
364B VAL* 3.9 15.1 - - - +
387B LEU* 4.2 19.1 - - + +
391B TRP* 4.8 12.6 - - + -
396B ILE* 3.6 22.1 - - + +
397B THR 2.7 15.7 + - - +
398B VAL* 2.9 12.3 + - + +
400B GLN* 1.3 73.9 - - - +
402B LYS* 1.3 63.9 + - - +
404B GLY* 3.0 11.1 + - - -
405B TYR* 3.2 41.0 + - + -
438B ILE* 3.5 55.2 - - + +
439B ILE* 4.3 4.7 - - + -
443B LEU* 5.5 0.4 - - + -
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Residues in contact with LYS 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 5.6 2.7 - - - -
179A GLY* 3.9 25.0 + - - +
181A THR* 5.3 3.0 + - - -
221A LYS* 4.2 26.9 - - - +
225A ASP* 5.1 6.7 + - - -
398B VAL* 2.6 21.5 + - + +
399B ASP* 3.9 3.6 - - - +
401B MET* 1.3 74.5 - - - +
403B ARG* 1.3 65.7 + - - +
404B GLY 3.1 0.5 + - - -
405B TYR* 3.1 3.5 + - - +
406B GLU* 3.0 60.2 + - + +
440B SER* 5.6 2.2 - - - +
442B GLN* 3.5 23.5 + - - +
443B LEU* 3.4 30.7 - - + +
446B LEU* 5.7 1.6 - - - +
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Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLU* 6.3 0.6 - - - -
221A LYS* 4.5 16.4 - - - +
326A HIS* 3.1 39.8 + - - +
361B HIS* 3.4 39.2 + - + +
399B ASP 2.7 25.3 + - - +
400B GLN* 3.5 6.7 - - - +
402B LYS* 1.3 75.7 - - - +
404B GLY* 1.3 61.5 + - - +
406B GLU* 3.5 8.0 + - - +
407B ARG* 3.4 29.4 + - - +
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Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B HIS* 3.8 22.0 - - - -
364B VAL* 4.0 11.9 - - - -
365B TYR* 4.2 3.8 - - - -
400B GLN 3.0 14.3 + - - -
401B MET 3.0 4.4 + - - -
403B ARG* 1.3 77.4 - - - +
405B TYR* 1.3 60.0 + - - +
407B ARG* 3.4 14.6 + - - +
408B ILE* 3.3 20.2 - - - +
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Residues in contact with TYR 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 3.7 19.7 - - + -
368B ILE* 4.2 21.8 - - + -
387B LEU* 3.8 12.9 - - + +
401B MET* 3.2 33.5 + - + +
402B LYS 3.1 5.9 + - - +
404B GLY* 1.3 72.4 - - - +
406B GLU* 1.3 67.1 + - - +
408B ILE* 3.3 3.7 + - - +
409B TYR* 3.0 49.3 + + + -
426B LEU* 5.8 0.2 - - + -
429B PHE* 3.8 4.5 - + - -
430B VAL* 4.2 18.2 - - + -
433B CYS* 2.9 34.5 - - - +
439B ILE* 3.8 28.6 - - + +
443B LEU* 4.0 19.3 - - + -
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LYS* 4.0 13.7 + - - +
402B LYS* 3.0 53.7 + - + +
403B ARG* 3.8 10.0 - - - +
404B GLY 3.3 0.2 - - - -
405B TYR* 1.3 75.7 - - - +
407B ARG* 1.3 63.6 + - - +
409B TYR* 3.3 10.9 + - - +
410B ASN* 2.9 26.5 + - - +
443B LEU* 4.1 13.7 - - + -
446B LEU* 3.9 19.7 - - + +
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Residues in contact with ARG 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 6.2 1.0 - - - +
326A HIS* 3.3 27.8 + - + +
361B HIS* 3.2 29.3 + - - -
362B GLU* 2.6 32.0 + - - +
365B TYR* 3.3 61.9 - - + +
366B GLU* 4.9 0.4 + - - -
403B ARG* 3.4 24.3 + - - +
404B GLY* 3.5 4.0 - - - +
405B TYR 3.2 0.4 - - - -
406B GLU* 1.3 77.2 - - - +
408B ILE* 1.3 65.1 + - - +
410B ASN* 2.7 19.6 + - - +
411B GLU* 2.9 24.4 + - - +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TYR* 3.6 30.9 - - + +
368B ILE* 3.0 52.7 - - + -
369B ILE* 5.0 4.7 - - + +
372B LEU* 4.4 11.7 - - + -
404B GLY 3.3 19.6 + - - +
405B TYR 3.3 7.0 + - - +
407B ARG* 1.3 77.0 - - - +
409B TYR* 1.3 59.7 + - + +
411B GLU* 2.9 4.0 + - - -
412B ILE* 2.7 36.5 + - + +
415B ILE* 4.5 4.8 - - + +
426B LEU* 3.9 34.8 - - + -
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Residues in contact with TYR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TYR* 3.0 34.3 + + + -
406B GLU* 3.4 13.7 - - - +
407B ARG 3.2 0.2 - - - -
408B ILE* 1.3 76.8 - - + +
410B ASN* 1.3 60.8 + - - +
412B ILE* 3.3 21.8 - - - +
413B PRO* 4.1 2.6 - - - +
426B LEU* 3.8 25.1 - - + -
430B VAL* 3.4 24.2 - - + +
443B LEU* 2.7 46.4 + - + +
446B LEU* 3.6 24.7 - - + +
447B CYS* 3.7 15.6 - - + +
448B PRO* 3.7 21.4 - - + +
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Residues in contact with ASN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B GLU* 2.9 13.0 + - - +
407B ARG* 2.7 19.1 + - - +
409B TYR* 1.3 74.3 - - - +
411B GLU* 1.3 62.6 + - + +
412B ILE 3.5 0.2 - - - -
413B PRO* 3.7 9.9 - - - +
414B ASP* 5.3 1.6 - - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 5.4 7.8 - - - +
365B TYR* 2.3 39.3 + - - -
407B ARG* 2.9 21.9 + - - +
408B ILE* 4.8 0.2 - - - -
410B ASN* 1.3 81.3 - - + +
412B ILE* 1.3 66.6 + - - +
413B PRO* 3.3 4.5 - - - -
414B ASP* 2.9 27.8 + - + +
415B ILE* 2.9 28.2 + - + +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.9 22.0 - - + -
408B ILE* 2.7 14.8 + - + +
409B TYR* 3.3 20.0 - - - +
411B GLU* 1.3 77.0 - - - +
413B PRO* 1.3 65.7 - - + +
415B ILE* 4.1 7.4 - - + -
416B ASN* 2.8 32.9 + - - +
422B SER* 3.6 36.6 - - - +
423B TYR* 3.8 29.2 - - + +
426B LEU* 4.4 12.3 - - + -
448B PRO* 3.5 24.0 - - + -
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Residues in contact with PRO 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR 4.1 2.0 - - - +
410B ASN 3.7 12.8 - - - +
411B GLU 3.3 5.4 - - - -
412B ILE* 1.3 98.5 - - + +
414B ASP* 1.3 63.9 + - - +
416B ASN* 3.8 10.1 - - + +
417B LEU* 3.7 16.5 - - - +
423B TYR* 3.6 19.1 - - + +
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Residues in contact with ASP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B ASN 5.3 1.1 - - - +
411B GLU* 2.9 20.5 + - + +
413B PRO* 1.3 78.4 - - - +
415B ILE* 1.3 68.0 + - + +
416B ASN 3.0 1.3 - - - -
417B LEU* 2.9 35.0 + - + +
418B ASP* 4.0 3.1 + - - +
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Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TYR* 4.9 4.7 - - - +
369B ILE* 4.9 16.8 - - + -
372B LEU* 4.4 23.3 - - + -
373B GLU* 6.3 0.7 - - + -
408B ILE* 4.5 11.0 - - + +
411B GLU* 2.9 45.8 + - + +
412B ILE* 3.8 9.9 - - + +
414B ASP* 1.3 74.8 - - + +
416B ASN* 1.3 58.0 + - - +
417B LEU 3.1 0.5 + - - -
418B ASP* 3.4 4.6 + - - +
419B VAL* 2.9 39.3 + - + +
422B SER* 3.3 17.0 - - - +
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Residues in contact with ASN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE 2.8 18.4 + - - +
413B PRO 3.8 8.1 - - - +
414B ASP 3.0 0.6 + - - -
415B ILE* 1.3 76.5 - - - +
417B LEU* 1.3 63.6 + - + +
419B VAL 3.3 20.8 - - - +
420B PRO* 3.5 13.4 - - - +
421B HIS 4.5 0.7 + - - -
422B SER* 3.2 22.2 + - - -
423B TYR* 3.4 33.3 + - + +
450B ARG* 3.6 18.0 - - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PRO 3.7 13.2 - - - +
414B ASP* 2.9 24.0 + - - +
416B ASN* 1.3 83.3 - - + +
418B ASP* 1.3 70.2 + - - +
420B PRO* 4.5 5.7 - - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASP 4.0 2.2 + - - +
415B ILE* 3.4 5.8 + - - +
417B LEU* 1.3 85.6 - - - +
419B VAL* 1.3 68.7 + - + +
420B PRO* 3.6 7.5 - - - +
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Residues in contact with VAL 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B LEU* 3.0 30.5 - - + +
373B GLU* 4.3 23.1 - - + +
415B ILE* 2.9 22.9 + - + +
416B ASN* 3.3 8.8 - - - -
418B ASP* 1.3 90.5 - - + +
420B PRO* 1.3 76.1 - - - +
421B HIS* 4.7 5.2 - - + -
422B SER* 2.9 30.7 + - - +
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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