Contacts of the helix formed by residues 444 - 462 (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 ASN 444 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438K SER 3.9 8.3 + - - -
439K GLN* 4.6 9.3 + - - +
441K ASP 2.5 16.8 + - - +
443K ARG* 1.3 99.8 - - - +
445K LEU* 1.3 54.8 + - - -
446K SER 3.2 2.7 - - - -
447K SER* 2.9 27.3 - - - +
448K CYS* 2.7 55.6 + - - -
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Residues in contact with LEU 445 (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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147K PRO* 3.6 29.6 - - + +
150K LEU* 3.5 38.6 - - + -
151K LYS* 5.5 7.4 - - + +
393K CYS* 4.1 13.4 - - + -
396K GLU* 3.9 26.0 - - + -
397K CYS* 5.6 2.0 - - + +
400K LEU* 3.6 22.3 - - + +
441K ASP 3.3 1.0 + - - -
442K PRO* 3.1 22.5 + - + +
443K ARG 3.4 1.8 + - - -
444K ASN* 1.3 76.3 - - - +
446K SER* 1.3 60.7 + - - +
448K CYS* 4.1 0.9 - - - +
449K PHE* 2.9 30.8 + - - +
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Residues in contact with SER 446 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146K GLU 3.9 21.9 + - - -
147K PRO* 4.6 12.4 - - - +
150K LEU* 5.7 2.5 - - - +
444K ASN 3.2 0.6 - - - -
445K LEU* 1.3 82.0 - - - +
447K SER* 1.3 60.5 - - - +
449K PHE* 3.6 8.5 - - - +
450K ASP* 2.8 33.0 + - - +
501K PHE* 5.4 6.6 - - - -
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Residues in contact with SER 447 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444K ASN* 2.9 28.2 + - - -
446K SER* 1.3 74.9 - - - +
448K CYS* 1.3 63.0 + - - +
450K ASP* 2.3 31.8 + - - +
451K LYS* 2.9 12.0 + - - +
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Residues in contact with CYS 448 (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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393K CYS* 3.5 14.6 - - - -
397K CYS* 5.6 0.4 - - + -
439K GLN* 2.9 26.7 - - - -
440K TRP* 3.4 25.5 - - + -
444K ASN* 2.7 53.1 + - - +
445K LEU 4.2 1.1 - - - +
447K SER* 1.3 73.5 - - - +
449K PHE* 1.3 56.9 + - - +
451K LYS* 3.3 16.2 - - - +
452K LEU* 2.8 27.9 + - - +
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Residues in contact with PHE 449 (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* 5.0 7.2 - - + -
397K CYS* 4.8 9.2 - - + +
400K LEU* 4.2 27.6 - - + -
401K MET* 4.0 22.7 - - + -
404K LEU* 4.3 13.5 - - + -
440K TRP* 4.9 0.6 - - - -
445K LEU* 2.9 22.7 + - + +
446K SER* 3.6 8.3 - - - +
447K SER 3.2 0.2 - - - -
448K CYS* 1.3 77.9 - - - +
450K ASP* 1.3 58.1 + - + +
452K LEU* 3.1 27.7 + - + +
453K LEU* 2.8 55.2 + - + +
501K PHE* 3.3 40.8 - + - -
504K PHE* 6.3 0.9 - + - -
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Residues in contact with ASP 450 (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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446K SER* 2.8 23.8 + - - +
447K SER* 2.3 40.6 + - - +
449K PHE* 1.3 70.3 - - + +
451K LYS* 1.3 65.1 + - - +
453K LEU* 3.1 20.9 + - + +
454K ALA* 2.8 28.1 + - - +
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Residues in contact with LYS 451 (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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430K MET* 3.6 28.1 - - + +
439K GLN* 3.0 53.5 + - + +
440K TRP* 3.4 21.4 - - - +
447K SER 2.9 9.8 + - - +
448K CYS* 3.3 24.9 - - - +
450K ASP* 1.3 84.3 + - - +
452K LEU* 1.3 55.4 + - - +
454K ALA* 3.2 10.2 + - - +
455K PHE* 2.9 25.6 + - - +
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Residues in contact with LEU 452 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397K CYS* 4.0 32.8 - - + +
401K MET* 3.5 37.0 - - + -
423K VAL* 6.5 0.4 - - + -
427K ILE* 4.4 16.6 - - + -
430K MET* 5.1 10.3 - - + -
440K TRP* 4.0 11.7 - - + -
448K CYS 2.8 14.9 + - - +
449K PHE* 3.3 25.8 - - + +
450K ASP 3.1 0.2 - - - -
451K LYS* 1.3 74.7 - - - +
453K LEU* 1.3 60.7 + - - +
455K PHE* 3.1 14.9 + - + +
456K PHE* 2.9 26.2 + - + +
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Residues in contact with LEU 453 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401K MET* 3.6 16.4 - - + -
404K LEU* 5.5 4.5 - - + -
449K PHE* 2.8 53.6 + - + +
450K ASP* 3.3 26.7 - - + +
452K LEU* 1.3 77.4 - - - +
454K ALA* 1.3 56.8 + - - +
456K PHE* 3.1 3.6 + - - +
457K LEU* 2.9 28.8 + - + +
493K ILE* 5.1 0.9 - - + -
497K ARG* 3.0 64.7 + - + +
501K PHE* 4.9 5.6 - - + -
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Residues in contact with ALA 454 (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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450K ASP 2.8 13.1 + - - +
451K LYS* 3.3 13.5 - - - +
453K LEU* 1.3 74.8 - - - +
455K PHE* 1.3 57.4 + - - +
457K LEU* 3.1 24.3 - - + +
458K GLU* 2.9 30.6 + - - +
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Residues in contact with PHE 455 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426K ALA* 3.2 36.8 - - + -
429K HIS* 3.6 27.6 - + + -
430K MET* 3.8 34.3 - - + -
433K GLN* 4.9 15.5 - - - -
451K LYS 2.9 13.7 + - - +
452K LEU* 3.1 16.8 + - + +
454K ALA* 1.3 75.1 - - - +
456K PHE* 1.3 59.7 + - + +
458K GLU* 3.0 25.4 - - + +
459K CYS* 2.9 54.2 + - - -
465K LEU* 5.4 1.6 - - + -
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Residues in contact with PHE 456 (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* 3.4 26.5 - - + -
405K LEU* 4.2 29.4 - - + -
418K PHE* 6.2 1.8 - + - -
422K HIS* 6.1 5.6 - - + -
426K ALA* 5.5 6.7 - - + -
452K LEU 2.9 12.7 + - - +
453K LEU 3.1 7.6 + - - +
455K PHE* 1.3 82.1 - - + +
457K LEU* 1.3 58.1 + - - +
459K CYS* 3.3 8.2 + - + +
460K LEU* 2.9 36.9 + - + +
465K LEU* 5.1 4.0 - - + -
476K PHE* 5.0 19.1 - + - -
489K LEU* 4.0 31.2 - - + -
493K ILE* 4.6 6.5 - - + -
497K ARG* 4.3 7.2 - - - +
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Residues in contact with LEU 457 (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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453K LEU* 2.9 13.5 + - + +
454K ALA* 3.1 32.8 - - + +
456K PHE* 1.3 76.6 - - - +
458K GLU* 1.3 59.8 + - + +
460K LEU* 3.0 22.8 - - + +
461K ARG* 2.9 71.0 + - - +
490K SER* 5.9 0.7 - - - +
497K ARG* 3.4 30.2 - - - +
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Residues in contact with GLU 458 (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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454K ALA 2.9 18.4 + - - +
455K PHE* 3.0 42.7 - - + +
457K LEU* 1.3 76.6 - - + +
459K CYS* 1.3 85.4 + - - +
461K ARG* 3.3 31.1 + - - +
462K THR* 3.5 20.9 + - + +
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Residues in contact with CYS 459 (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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426K ALA* 5.4 0.2 - - - -
455K PHE* 2.9 51.3 + - - +
456K PHE* 3.5 7.2 - - + +
458K GLU* 1.3 93.7 - - - +
460K LEU* 1.3 65.9 + - - +
461K ARG 3.4 0.2 + - - -
462K THR* 3.8 2.1 + - - -
463K GLU* 3.8 9.0 + - - -
464K LYS 3.7 16.9 + - - +
465K LEU* 3.4 46.2 - - + +
476K PHE* 5.0 1.4 - - - -
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Residues in contact with LEU 460 (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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456K PHE* 2.9 27.4 + - + +
457K LEU* 3.0 36.1 - - + +
459K CYS* 1.3 75.7 - - - +
461K ARG* 1.3 76.7 + - + +
463K GLU* 3.4 3.6 + - - -
465K LEU* 5.2 0.4 - - - +
476K PHE* 5.4 9.2 - - + -
483K ARG* 3.1 32.1 + - - +
486K LYS* 5.3 4.9 - - + +
487K GLU* 4.5 13.7 - - - +
489K LEU* 5.1 7.9 - - + -
490K SER* 4.0 38.1 - - - +
493K ILE* 6.0 3.4 - - + -
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Residues in contact with ARG 461 (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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457K LEU* 2.9 53.0 + - + +
458K GLU* 3.5 20.0 - - - +
459K CYS 3.2 1.0 - - - -
460K LEU* 1.3 88.5 - - + +
462K THR* 1.3 66.5 + - + +
463K GLU* 3.2 2.5 + - - +
483K ARG* 4.5 4.6 + - - +
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Residues in contact with THR 462 (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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458K GLU* 3.5 18.7 + - + +
459K CYS* 4.1 4.5 + - - -
460K LEU 3.4 0.4 - - - -
461K ARG* 1.3 80.8 - - + +
463K GLU* 1.3 69.5 + - - +
464K LYS* 3.5 15.4 + - - +
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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
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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