Contacts of the helix formed by residues 393 - 412 (chain K) in PDB entry 6X5A
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 CYS 393 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K CYS* 1.3 74.0 - - - +
394K ARG* 1.3 54.6 + - - +
396K GLU* 3.2 17.9 - - + -
397K CYS* 2.6 37.5 + - + +
440K TRP* 3.4 17.2 - - - -
441K ASP 2.9 44.8 - - - +
442K PRO* 3.8 8.3 - - + -
444K ASN 4.0 2.5 - - - -
445K LEU* 4.1 11.7 - - + -
448K CYS* 3.5 20.4 - - - -
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Residues in contact with ARG 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331K TRP* 5.4 3.4 - - - +
378K HIS* 3.4 39.6 + - + -
379K GLY* 4.0 12.3 - - - -
380K ILE* 4.7 7.3 - - - +
381K GLU* 3.9 6.5 + - - -
392K CYS* 3.4 24.0 - - - +
393K CYS* 1.3 74.1 - - - +
395K LYS* 1.3 66.0 + - - +
397K CYS* 2.9 26.0 - - - -
398K LEU* 2.9 5.5 + - - +
431K TRP* 3.3 43.2 - - + +
434K ASP* 3.1 25.7 + - - +
436K GLN 3.6 8.1 + - - -
437K ASP* 3.9 21.2 + - - +
440K TRP* 3.5 31.6 + - + +
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Residues in contact with LYS 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154K LEU* 6.4 0.7 - - + -
158K ARG* 6.1 1.4 - - - +
200K TYR* 6.3 1.2 - - - -
202K GLU* 3.1 36.0 + - - +
375K LEU* 5.3 3.8 - - + -
378K HIS* 4.5 5.7 - - + +
385K CYS* 3.4 33.9 - - - -
391K LYS* 5.0 4.4 - - - +
394K ARG* 1.3 77.8 - - - +
396K GLU* 1.3 82.8 + - - +
398K LEU* 3.3 7.0 + - - +
399K LYS* 3.0 34.1 + - - +
431K TRP* 4.4 4.4 - - - -
601K ZN 3.4 13.7 - - - -
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Residues in contact with GLU 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K LYS* 6.0 4.5 - - + -
154K LEU* 4.2 24.5 - - + +
391K LYS* 2.3 35.8 + - - +
392K CYS 2.7 19.1 - - - +
393K CYS* 3.2 10.6 - - + +
395K LYS* 1.3 93.7 + - - +
397K CYS* 1.3 57.2 + - - +
399K LYS* 3.3 6.3 + - - +
400K LEU* 2.8 35.3 + - + +
442K PRO* 5.5 3.4 - - + -
445K LEU* 3.9 25.6 - - + -
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Residues in contact with CYS 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393K CYS* 2.6 19.0 + - + +
394K ARG* 2.9 24.9 - - - -
396K GLU* 1.3 73.1 - - - +
398K LEU* 1.3 63.4 + - - +
400K LEU* 3.6 13.5 - - + +
401K MET* 3.0 26.7 + - - +
427K ILE* 3.5 18.6 - - - -
431K TRP* 4.2 1.6 - - - -
440K TRP* 3.2 37.2 - - + -
445K LEU 5.6 1.1 - - - +
448K CYS* 5.6 0.2 - - + -
449K PHE* 4.8 11.1 - - + +
452K LEU* 4.0 10.5 - - + +
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Residues in contact with LEU 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K GLU* 5.3 1.1 - - - +
375K LEU* 3.6 35.4 - - + -
394K ARG 2.9 14.5 + - - +
395K LYS* 3.6 5.6 - - - +
397K CYS* 1.3 76.9 - - - +
399K LYS* 1.3 78.9 + - - +
401K MET* 4.1 1.5 - - - +
402K LYS* 2.9 36.5 + - + +
423K VAL* 3.8 29.4 - - + -
424K LYS* 4.5 17.9 - - + -
427K ILE* 3.5 32.1 - - + -
431K TRP* 4.6 3.8 - - + -
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Residues in contact with LYS 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154K LEU* 5.2 15.3 - - + -
202K GLU* 3.3 53.6 + - + +
395K LYS 3.0 17.6 + - - +
396K GLU* 3.8 5.2 - - - +
398K LEU* 1.3 99.7 - - - +
400K LEU* 1.3 57.0 + - + +
402K LYS* 3.3 31.8 - - + +
403K TYR* 2.8 70.4 + - + +
424K LYS* 4.7 2.0 - - - +
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Residues in contact with LEU 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LEU* 3.4 50.3 - - + +
153K VAL* 5.2 0.9 - - + -
154K LEU* 6.5 0.4 - - + -
396K GLU* 2.8 25.2 + - + +
397K CYS* 3.2 13.9 + - - +
399K LYS* 1.3 75.9 - - + +
401K MET* 1.3 57.6 + - - +
403K TYR* 4.9 0.2 - - - -
404K LEU* 2.9 33.2 + - - +
445K LEU* 3.6 37.0 - - + +
449K PHE* 4.2 25.6 - - + -
504K PHE* 3.9 13.1 - - + -
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Residues in contact with MET 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397K CYS 3.0 15.6 + - - +
398K LEU* 5.2 0.2 - - - -
400K LEU* 1.3 74.3 - - - +
402K LYS* 1.3 66.4 + - - +
404K LEU* 4.5 5.4 - - - -
405K LEU* 2.9 62.0 + - + +
423K VAL* 4.1 15.7 - - + -
449K PHE* 4.0 8.5 - - + -
452K LEU* 3.5 36.6 - - + -
453K LEU* 3.6 25.1 - - + -
456K PHE* 3.4 35.4 - - + -
493K ILE* 5.7 2.0 - - + -
497K ARG* 4.5 0.4 - - - +
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Residues in contact with LYS 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201K TYR* 3.2 27.5 + - - +
204K VAL 4.5 5.9 + - - -
206K ILE* 5.5 7.7 + - - +
398K LEU* 2.9 21.7 + - + +
399K LYS* 3.3 25.1 - - + +
401K MET* 1.3 78.2 - - - +
403K TYR* 1.3 73.3 + - + +
405K LEU* 3.8 3.8 - - - +
406K GLU* 2.9 32.1 + - + +
420K SER* 4.0 9.6 - - - +
423K VAL* 4.1 22.6 - - + +
424K LYS* 3.4 30.1 - - - +
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Residues in contact with TYR 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K VAL* 6.2 3.4 - - + -
154K LEU* 5.7 5.4 - - + -
157K LEU* 3.4 38.0 - - + +
201K TYR* 3.2 41.0 - - + +
206K ILE* 6.5 0.9 - - + -
399K LYS* 2.8 53.5 + - + +
400K LEU* 4.1 1.8 - - - +
402K LYS* 1.3 90.8 - - + +
404K LEU* 1.3 64.5 + - - +
406K GLU* 3.2 12.2 + - + +
407K GLN* 2.8 46.8 + - - +
504K PHE* 5.0 6.5 - + + -
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Residues in contact with LEU 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400K LEU 2.9 20.7 + - - +
401K MET* 3.9 7.4 - - - +
403K TYR* 1.3 77.4 - - - +
405K LEU* 1.3 63.8 + - + +
407K GLN* 3.3 2.5 + - - +
408K LEU* 2.9 27.8 + - + +
449K PHE* 4.3 13.2 - - + -
453K LEU* 5.5 3.1 - - + -
493K ILE* 6.0 2.2 - - + -
496K GLU* 3.4 44.4 - - + +
501K PHE* 4.1 29.2 - - + -
503K ILE* 4.3 8.7 - - + -
504K PHE* 3.5 28.3 - - + -
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Residues in contact with LEU 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K MET* 2.9 55.5 + - + +
402K LYS* 3.9 3.1 - - - +
404K LEU* 1.3 79.0 - - + +
406K GLU* 1.3 57.6 + - - +
408K LEU* 4.7 4.3 - - + -
409K LYS* 2.8 40.7 + - + +
422K HIS* 6.1 3.4 - - + -
423K VAL* 4.7 15.0 - - + +
456K PHE* 4.2 19.7 - - + -
489K LEU* 5.7 4.0 - - + -
493K ILE* 3.5 31.6 - - + -
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Residues in contact with GLU 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K ILE 5.0 4.0 - - - +
207K SER* 4.8 13.7 - - - -
402K LYS* 2.9 21.8 + - + +
403K TYR* 3.4 15.9 - - + +
405K LEU* 1.3 74.7 - - - +
407K GLN* 1.3 58.5 + - + +
409K LYS* 2.9 37.5 + - - +
410K LYS* 3.0 43.5 + - - +
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Residues in contact with GLN 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K LEU* 6.0 2.8 - - - +
403K TYR* 2.8 47.1 + - - +
404K LEU* 3.9 1.7 - - - +
406K GLU* 1.3 77.8 - - + +
408K LEU* 1.3 62.5 + - - +
410K LYS* 3.0 38.4 - - - +
411K GLU* 3.0 13.8 + - - +
503K ILE* 3.4 38.9 - - + +
504K PHE* 4.4 14.9 - - - -
506K LYS* 3.2 24.6 + - - +
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Residues in contact with LEU 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404K LEU* 2.9 17.9 + - + +
405K LEU* 4.1 4.7 - - + +
407K GLN* 1.3 76.6 - - - +
409K LYS* 1.3 62.4 + - + +
411K GLU* 3.0 25.4 + - - +
412K PHE* 3.2 43.0 - - + -
489K LEU* 6.0 0.9 - - + -
492K LYS* 3.6 30.7 - - + +
493K ILE* 3.6 31.4 - - + -
495K TYR* 4.0 7.4 - - + -
496K GLU* 3.1 37.5 - - + +
503K ILE* 4.6 1.9 - - - +
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Residues in contact with LYS 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405K LEU* 2.8 32.2 + - + +
406K GLU* 2.9 34.2 + - - +
408K LEU* 1.3 73.3 - - + +
410K LYS* 1.3 68.7 + - - +
412K PHE 2.8 24.4 - - - +
413K GLN* 3.7 3.3 + - - -
415K LEU* 3.9 23.7 - - + +
416K ASP* 3.6 21.2 + - - +
418K PHE* 4.3 21.7 + - + +
489K LEU* 6.2 4.5 - - + -
492K LYS* 3.6 12.8 - - - +
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Residues in contact with LYS 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406K GLU* 3.0 36.7 + - + +
407K GLN* 3.0 53.7 - - - +
409K LYS* 1.3 83.8 - - - +
411K GLU* 1.3 61.7 + - + +
413K GLN* 3.3 24.0 + - - +
506K LYS* 4.4 7.6 - - - +
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Residues in contact with GLU 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407K GLN 3.0 14.6 + - - +
408K LEU* 3.0 26.0 - - - +
410K LYS* 1.3 78.9 - - + +
412K PHE* 1.3 99.9 + - + +
413K GLN* 3.1 15.0 + - - +
495K TYR* 4.5 3.9 + - - -
496K GLU* 4.1 0.3 - - - +
503K ILE* 3.1 36.7 - - + +
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Residues in contact with PHE 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408K LEU* 3.2 35.7 + - + -
409K LYS 2.8 15.3 + - - +
410K LYS 3.2 0.4 - - - -
411K GLU* 1.3 113.0 - - - +
413K GLN* 1.3 58.1 + - - +
414K GLU* 3.1 11.2 + - + +
415K LEU* 3.5 11.8 + - + +
488K PHE* 4.8 9.2 - + + -
492K LYS* 3.2 38.4 + - + +
495K TYR* 4.6 17.0 - + - -
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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