Contacts of the helix formed by residues 394 - 413 (chain O) in PDB entry 5A31
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 394 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I ASP* 5.9 7.2 - - + +
393O LYS* 1.3 74.6 - - - +
395O ALA* 1.3 65.7 + - - +
396O ASN* 3.6 15.3 + - - +
397O LYS* 2.8 65.7 + - + +
398O LEU* 3.0 12.2 + - - +
615O ARG* 3.2 27.9 - - - +
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Residues in contact with ALA 395 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I TYR* 4.6 10.1 - - + +
393O LYS 3.2 6.1 + - - -
394O THR* 1.3 70.5 - - - +
396O ASN* 1.3 61.0 + - - +
398O LEU* 3.4 5.9 + - - +
399O MET* 3.0 37.6 + - + +
429O TRP* 3.8 33.7 - - + -
432O TYR* 4.3 20.2 - - + -
434O ARG* 5.8 1.3 - - - +
615O ARG* 4.6 0.8 - - - +
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Residues in contact with ASN 396 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I ASP* 5.6 3.4 - - - +
134I GLU* 3.1 47.2 + - - +
361I TYR* 4.4 3.1 - - - -
394O THR* 3.8 13.8 + - - +
395O ALA* 1.3 80.0 + - - +
397O LYS* 1.3 59.3 + - + +
399O MET* 3.3 6.4 + - - +
400O ASP* 2.9 31.8 + - - +
403O LYS* 5.4 1.9 + - - -
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Residues in contact with LYS 397 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388O ARG* 5.3 2.1 + - - -
393O LYS* 5.0 14.8 - - + -
394O THR* 2.8 51.3 + - + +
396O ASN* 1.3 70.9 - - + +
398O LEU* 1.3 66.4 + - - +
400O ASP* 3.4 13.2 + - - +
401O ALA* 3.3 20.6 + - - +
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Residues in contact with LEU 398 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385O VAL* 4.0 23.9 - - + +
388O ARG* 3.6 38.1 - - + +
389O ALA* 3.7 14.8 - - + +
393O LYS* 4.1 12.8 - - + +
394O THR 3.0 12.6 + - - +
395O ALA* 3.6 7.6 - - - +
397O LYS* 1.3 76.6 - - - +
399O MET* 1.3 69.5 + - + +
401O ALA* 3.3 4.6 + - - +
402O LEU* 3.0 29.3 + - - +
428O ILE* 4.3 7.4 - - + -
432O TYR* 3.3 38.4 - - + +
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Residues in contact with MET 399 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357I GLU* 5.1 9.2 - - - +
395O ALA* 3.0 24.3 + - + +
396O ASN* 3.9 4.5 - - - +
398O LEU* 1.3 81.5 - - + +
400O ASP* 1.3 54.7 + - - +
402O LEU* 3.6 10.6 - - + +
403O LYS* 2.8 53.5 + - + +
425O LYS* 4.0 29.5 + - + +
428O ILE* 4.0 26.5 - - + -
429O TRP* 3.3 53.4 - - + +
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Residues in contact with ASP 400 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396O ASN* 2.9 17.5 + - - +
397O LYS* 3.5 17.9 - - - +
398O LEU 3.3 0.4 - - - -
399O MET* 1.3 74.4 - - - +
401O ALA* 1.3 61.8 + - - +
403O LYS* 3.2 20.4 + - - +
404O ASP* 3.0 22.0 + - - +
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Residues in contact with ALA 401 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381O ILE* 3.9 11.1 - - + +
384O LEU* 5.7 0.2 - - + -
385O VAL* 3.6 23.3 - - + -
388O ARG* 3.7 21.5 - - - +
397O LYS 3.3 9.1 + - - +
398O LEU* 3.3 2.7 + - - +
400O ASP* 1.3 77.6 - - - +
402O LEU* 1.3 57.8 + - - +
404O ASP* 3.4 11.3 + - - +
405O SER* 3.0 26.0 + - - -
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Residues in contact with LEU 402 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382O GLN* 3.5 38.1 - - - +
385O VAL* 3.7 37.9 - - + -
398O LEU 3.0 12.1 + - - +
399O MET* 3.9 14.4 - - - +
401O ALA* 1.3 73.6 - - - +
403O LYS* 1.3 53.6 + - - +
405O SER* 3.2 3.9 + - - -
406O ASP* 2.6 40.8 + - - +
421O SER* 4.7 7.6 - - - +
424O GLN* 4.4 2.5 - - + +
425O LYS* 3.7 44.2 - - + +
428O ILE* 4.6 6.3 - - + -
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Residues in contact with LYS 403 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I LEU* 6.0 1.4 - - - +
143I PRO* 6.2 1.8 - - + +
349I ILE* 4.8 14.2 - - + +
350I SER* 4.9 15.4 + - - +
353I GLN* 6.4 0.2 - - - -
354I SER* 3.6 34.6 + - - +
357I GLU* 4.2 15.9 + - - -
396O ASN 5.4 1.4 + - - -
399O MET* 2.8 36.3 + - - +
400O ASP* 3.5 20.5 + - - +
402O LEU* 1.3 70.3 - - - +
404O ASP* 1.3 66.1 + - - +
406O ASP* 3.8 6.6 - - + +
407O LEU* 2.9 27.5 + - - +
425O LYS* 5.1 7.9 - - - +
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Residues in contact with ASP 404 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381O ILE* 4.2 20.0 - - - +
400O ASP 3.0 12.3 + - - +
401O ALA* 3.4 15.0 - - - +
403O LYS* 1.3 78.2 - - - +
405O SER* 1.3 65.1 + - - +
407O LEU* 3.5 11.5 + - - +
408O LEU* 3.6 14.9 + - - +
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Residues in contact with SER 405 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378O SER* 3.8 6.6 + - - -
381O ILE* 3.9 27.4 - - - -
382O GLN* 2.3 30.5 + - - -
401O ALA 3.0 13.7 + - - -
402O LEU* 3.4 9.4 - - - -
404O ASP* 1.3 75.5 - - - +
406O ASP* 1.3 58.7 + - - +
408O LEU* 3.2 9.6 + - - +
409O HIS* 2.6 45.6 + - - -
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Residues in contact with ASP 406 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ILE* 4.7 8.1 - - + -
402O LEU* 2.6 22.2 + - - +
403O LYS* 3.3 6.7 + - + +
405O SER* 1.3 72.0 - - - +
407O LEU* 1.3 63.9 + - - +
409O HIS* 3.2 24.5 + - - +
410O TRP* 3.4 26.4 + - + -
418O ILE* 5.3 2.2 - - - +
421O SER* 2.8 27.8 + - - -
422O ILE* 5.6 3.6 - - - +
425O LYS* 2.9 30.7 + - - -
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Residues in contact with LEU 407 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I GLN* 6.3 0.9 - - + -
346I LYS* 4.5 20.2 - - + +
349I ILE* 3.2 28.4 - - + +
350I SER* 4.1 17.9 - - - +
403O LYS 2.9 17.9 + - - +
404O ASP* 3.6 8.5 - - - +
405O SER 3.2 0.2 - - - -
406O ASP* 1.3 79.6 - - - +
408O LEU* 1.3 62.5 + - - +
410O TRP* 3.4 3.9 + - + +
411O LYS* 3.3 21.3 + - + +
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Residues in contact with LEU 408 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369O VAL* 6.1 2.7 - - + -
374O PRO* 3.6 26.0 - - + +
377O ALA* 5.0 5.2 - - + -
378O SER* 3.7 17.9 - - - +
381O ILE* 3.8 28.3 - - + -
404O ASP* 3.6 8.1 + - - +
405O SER* 3.2 19.3 + - - +
407O LEU* 1.3 77.4 - - - +
409O HIS* 1.4 66.0 + - - +
411O LYS* 3.5 7.2 + - - +
412O HIS* 3.0 47.5 + - + +
414O LEU* 4.8 2.5 - - + -
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Residues in contact with HIS 409 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378O SER* 2.7 25.9 + - - -
382O GLN* 3.6 8.5 + - - -
405O SER* 2.6 47.7 + - - -
406O ASP* 3.2 30.8 + - - +
408O LEU* 1.4 76.0 - - - +
410O TRP* 1.3 53.5 + - - +
412O HIS 3.3 1.4 + - - -
413O SER* 2.7 34.1 + - - -
414O LEU* 3.5 19.8 + - + -
417O LEU* 3.9 13.0 - - + -
418O ILE* 3.6 33.6 + - + +
421O SER* 3.8 11.2 - - - -
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Residues in contact with TRP 410 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I GLN* 3.6 29.0 + - + +
349I ILE* 3.9 29.2 - - + +
401I ASN* 4.8 0.9 - - - -
404I LEU* 4.1 25.9 - - + +
405I GLN* 4.4 14.1 - - + -
408I ASP* 3.4 52.6 - - + +
406O ASP* 3.4 28.1 + - + +
407O LEU* 3.8 6.3 - - + +
408O LEU 3.4 0.2 - - - -
409O HIS* 1.3 78.9 - - - +
411O LYS* 1.3 64.3 + - - +
413O SER* 3.2 8.7 + - - +
418O ILE* 3.7 27.1 - - + +
422O ILE* 6.1 0.2 - - + -
448O MET* 3.7 31.9 - - + -
451O LEU* 4.2 15.0 - - + -
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Residues in contact with LYS 411 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345I GLN* 5.4 4.9 - - - -
407O LEU* 3.3 14.7 + - + +
408O LEU* 4.0 8.3 - - - +
409O HIS 3.3 0.8 - - - -
410O TRP* 1.3 80.0 - - - +
412O HIS* 1.3 92.2 + - + +
413O SER* 3.5 2.1 + - - -
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Residues in contact with HIS 412 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374O PRO* 3.5 37.5 - - + +
408O LEU* 3.0 32.0 + - + +
409O HIS 3.3 2.2 + - - -
411O LYS* 1.3 106.5 - - + +
413O SER* 1.3 67.7 + - - +
414O LEU* 3.2 24.9 + - + +
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Residues in contact with SER 413 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408I ASP* 3.9 20.9 - - - -
409O HIS 2.7 12.6 + - - -
410O TRP* 3.2 9.8 + - - +
411O LYS 4.7 1.8 - - - -
412O HIS* 1.3 81.7 + - - +
414O LEU* 1.3 55.3 + - - -
415O SER* 3.0 10.2 + - - -
418O ILE* 4.9 0.7 - - - -
451O LEU* 3.1 25.7 - - - +
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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