Contacts of the helix formed by residues 419 - 434 (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 419 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K LYS* 5.4 2.0 - - - +
409K LYS* 6.2 0.2 - - - +
416K ASP 5.4 1.1 - - - +
417K ALA 3.5 5.6 + - - +
418K PHE* 1.3 73.7 - - - +
420K SER* 1.3 65.4 + - - +
421K TYR* 3.0 32.1 - - + -
422K HIS* 2.7 53.2 + - - +
423K VAL 4.4 0.3 + - - -
475K LEU* 5.6 6.7 - - - -
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Residues in contact with SER 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K LYS* 4.1 19.6 - - - +
402K LYS* 4.0 11.2 - - - -
419K CYS* 1.3 75.1 - - - +
421K TYR* 1.3 62.4 + - - +
422K HIS 3.1 0.4 - - - -
423K VAL* 3.0 26.3 - - - +
424K LYS* 2.3 44.6 + - - +
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Residues in contact with TYR 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205K LYS* 3.4 33.8 - - - -
215K MET* 5.2 8.5 - - - +
364K ARG* 2.9 45.6 + - - -
371K GLU* 4.9 16.8 - - - -
419K CYS* 3.0 27.4 + - + -
420K SER* 1.3 78.6 - - - +
422K HIS* 1.3 56.3 + - - +
424K LYS* 3.9 7.6 - - + +
425K THR* 2.8 38.9 + - - +
467K HIS* 5.9 7.4 - - + +
475K LEU* 6.5 1.3 - - + -
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Residues in contact with HIS 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405K LEU* 6.1 3.8 - - + -
417K ALA 3.7 5.5 + - - -
418K PHE* 3.5 28.1 - + + -
419K CYS* 2.7 59.5 + - - +
421K TYR* 1.3 77.3 - - + +
423K VAL* 1.3 61.5 + - - +
425K THR* 3.4 4.5 + - - -
426K ALA* 3.0 24.9 + - - +
456K PHE* 6.1 5.6 - - + -
465K LEU* 5.6 2.3 - - - +
475K LEU* 3.4 25.1 - - + +
476K PHE* 3.2 40.2 - + + -
481K ILE* 5.3 3.2 - - - +
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Residues in contact with VAL 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398K LEU* 3.8 18.6 - - + -
401K MET* 4.1 25.8 - - + -
402K LYS* 4.1 22.9 - - + +
405K LEU* 4.7 15.0 - - + +
419K CYS 4.4 0.2 + - - -
420K SER* 3.0 29.8 + - - +
422K HIS* 1.3 77.3 - - - +
424K LYS* 1.3 71.0 + - + +
426K ALA* 3.8 5.1 - - + +
427K ILE* 2.9 31.8 + - + +
452K LEU* 6.5 0.4 - - + -
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Residues in contact with LYS 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K GLU 5.5 6.4 + - - -
371K GLU* 5.2 7.9 - - + +
375K LEU* 6.5 0.4 - - - -
398K LEU* 4.5 18.8 - - + +
399K LYS* 4.7 2.2 - - - +
402K LYS* 3.4 31.9 - - - +
420K SER* 2.3 45.5 + - - +
421K TYR* 3.9 10.1 - - + +
422K HIS 3.4 0.2 - - - -
423K VAL* 1.3 87.5 - - + +
425K THR* 1.3 57.6 + - - +
427K ILE* 3.2 9.0 - - + +
428K PHE* 2.8 52.8 + - + -
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Residues in contact with THR 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421K TYR* 2.8 26.1 + - - +
422K HIS* 3.8 5.1 - - - -
424K LYS* 1.3 76.6 - - - +
426K ALA* 1.3 62.6 + - - +
428K PHE* 3.2 9.7 + - - +
429K HIS* 2.8 37.7 + - + +
465K LEU* 5.1 9.6 - - + +
466K ASP 3.2 27.4 - - - +
467K HIS* 4.2 14.0 + - - -
468K TYR* 3.8 11.9 + - - +
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Residues in contact with ALA 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422K HIS 3.0 17.6 + - - +
423K VAL* 3.8 6.7 - - + +
425K THR* 1.3 76.0 - - - +
427K ILE* 1.3 57.8 + - - +
429K HIS* 3.3 4.3 + - - -
430K MET* 2.9 22.7 + - - +
455K PHE* 3.2 32.4 - - + -
456K PHE* 5.5 11.2 - - + -
459K CYS* 5.4 0.2 - - - -
465K LEU* 4.8 16.3 - - + +
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Residues in contact with ILE 427 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397K CYS* 3.5 17.3 - - - -
398K LEU* 3.5 37.0 - - + -
401K MET* 6.4 0.2 - - + -
423K VAL* 2.9 18.8 + - + +
424K LYS* 3.2 17.0 - - + +
426K ALA* 1.3 74.3 - - - +
428K PHE* 1.3 74.0 + - + +
430K MET* 4.2 5.6 - - + -
431K TRP* 2.8 73.1 + - + +
452K LEU* 4.4 16.2 - - + -
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Residues in contact with PHE 428 (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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326K LEU* 5.9 0.2 - - + -
331K TRP* 5.6 0.5 - - - -
371K GLU* 3.4 42.8 - - + -
374K ILE* 3.5 39.6 - - + +
375K LEU* 4.8 4.3 - - + -
424K LYS* 2.8 35.7 + - + +
425K THR* 3.2 7.4 + - - +
427K ILE* 1.3 86.4 - - + +
429K HIS* 1.3 63.5 + - - +
431K TRP* 3.8 18.3 - + - +
432K THR* 2.9 26.4 + - - +
468K TYR* 3.8 37.7 - + + -
469K PHE* 3.8 12.6 - + - -
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Residues in contact with HIS 429 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K PRO* 6.2 0.2 - - + -
425K THR* 2.8 34.6 + - + +
426K ALA* 3.6 3.0 - - - +
428K PHE* 1.3 75.2 - - - +
430K MET* 1.3 57.4 + - - +
432K THR* 3.0 12.0 - - + +
433K GLN* 3.0 31.5 + - - +
455K PHE* 3.6 24.0 - + + -
465K LEU* 5.3 9.0 - - + +
466K ASP* 2.9 44.9 + - - +
468K TYR* 3.4 31.6 - + + -
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Residues in contact with MET 430 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426K ALA 2.9 17.4 + - - +
427K ILE* 3.8 9.9 - - + +
428K PHE 3.3 0.2 - - - -
429K HIS* 1.3 77.0 - - - +
431K TRP* 1.3 57.4 + - + +
433K GLN* 3.6 10.5 + - - +
434K ASP* 2.8 42.2 + - + +
439K GLN* 5.9 0.2 - - + -
440K TRP* 3.6 24.2 - - + -
451K LYS* 3.6 40.4 - - + +
452K LEU* 5.1 8.1 - - + -
455K PHE* 3.8 37.9 - - + -
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Residues in contact with TRP 431 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K TRP* 3.3 34.2 + - + -
374K ILE* 5.1 6.1 - - + -
375K LEU* 3.6 37.2 - - + -
378K HIS* 3.5 27.4 - + + +
394K ARG* 3.3 66.5 + - + +
397K CYS* 4.2 4.8 - - - -
398K LEU* 4.6 1.6 - - + -
427K ILE* 2.8 54.0 + - + +
428K PHE* 4.1 16.8 - + - +
430K MET* 1.3 75.0 - - - +
432K THR* 1.3 63.6 + - - +
434K ASP* 3.5 13.5 - - - +
440K TRP* 4.1 17.2 - + - -
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Residues in contact with THR 432 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K PRO* 3.3 11.6 + - + +
328K ILE* 4.5 0.5 - - - -
331K TRP* 3.7 40.1 - - - +
428K PHE 2.9 15.9 + - - +
429K HIS* 3.0 26.9 - - + +
431K TRP* 1.3 78.1 - - - +
433K GLN* 1.3 64.8 + - + +
434K ASP 3.4 2.3 + - - +
468K TYR* 3.1 31.8 + - + +
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Residues in contact with GLN 433 (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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429K HIS 3.0 18.3 + - - +
430K MET* 4.2 11.9 - - + +
432K THR* 1.3 79.7 - - + +
434K ASP* 1.3 61.8 + - - +
435K PRO* 3.1 13.9 - - - +
455K PHE* 4.9 17.4 - - - -
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Residues in contact with ASP 434 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331K TRP* 3.6 15.9 + - - -
394K ARG* 3.1 13.7 + - - -
430K MET* 2.8 29.3 + - + +
431K TRP* 3.5 17.4 - - - +
432K THR 3.2 0.8 - - - -
433K GLN* 1.3 74.6 - - - +
435K PRO* 1.3 65.6 - - - +
436K GLN 2.8 25.4 + - - +
439K GLN* 3.4 14.6 - - - +
440K TRP* 2.6 35.5 + - - +
451K LYS* 4.5 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
------------------------------------------------------------
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