Contacts of the helix formed by residues 422 - 437 (chain C) in PDB entry 5KX8
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 ASP 422 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C TRP* 4.5 3.8 + - - -
420C ASP 3.5 6.5 + - - +
421C ALA* 1.3 72.4 - - - +
423C SER* 1.4 63.3 + - - +
424C THR* 3.3 14.3 + - - +
425C SER* 2.9 41.3 + - - -
426C VAL* 3.2 22.0 + - - +
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Residues in contact with SER 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411C GLU* 2.7 32.6 + - - -
414C ILE* 5.2 1.8 - - - -
421C ALA 3.9 1.6 + - - -
422C ASP* 1.4 68.4 - - - +
424C THR* 1.3 61.8 + - - +
426C VAL* 3.9 5.6 - - - +
427C GLU* 2.9 47.2 + - - +
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Residues in contact with THR 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422C ASP* 3.3 10.3 + - - -
423C SER* 1.3 79.3 - - - +
425C SER* 1.4 59.3 + - - +
427C GLU* 3.3 9.0 + - - +
428C ALA* 2.9 28.7 + - + +
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Residues in contact with SER 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C TRP* 2.8 32.3 + - - -
289C CYS* 5.2 1.3 - - - -
422C ASP* 2.9 27.1 + - - -
424C THR* 1.4 75.7 - - - +
426C VAL* 1.3 60.9 + - - +
428C ALA* 3.2 9.5 + - - +
429C MET 2.9 24.4 + - - -
457C MET* 3.7 31.3 - - - +
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Residues in contact with VAL 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C TRP* 3.6 29.8 - - + -
381C ILE* 3.9 19.1 - - + +
410C ILE* 4.1 10.3 - - + -
414C ILE* 3.6 40.2 - - + -
421C ALA* 4.0 18.6 - - + -
422C ASP 3.2 17.7 + - - +
423C SER 3.9 3.8 - - - +
425C SER* 1.3 76.7 + - - +
427C GLU* 1.4 51.2 + - - +
429C MET* 3.0 4.9 + - - +
430C TYR* 2.8 32.6 + - - +
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Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C ILE* 3.7 26.6 - - + +
411C GLU* 5.2 3.3 - - - +
423C SER* 2.9 34.8 + - - +
424C THR* 3.6 7.0 - - - +
426C VAL* 1.4 76.3 - - + +
428C ALA* 1.3 57.8 + - - +
430C TYR* 3.3 10.0 + - + +
431C SER* 2.8 30.0 + - - -
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Residues in contact with ALA 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C THR* 2.9 16.3 + - + +
425C SER* 3.4 10.3 - - - +
427C GLU* 1.3 76.4 - - - +
429C MET* 1.4 60.3 + - - +
431C SER* 3.4 8.8 + - - -
432C VAL* 3.3 24.3 + - - +
453C LEU 5.9 0.7 - - - +
457C MET* 4.0 24.2 - - + -
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Residues in contact with MET 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C TRP* 3.6 30.1 - - + -
289C CYS* 4.1 10.1 - - - -
292C ALA* 3.8 22.2 - - + -
377C LEU* 4.2 24.2 - - + +
380C ILE* 3.8 22.4 - - + -
381C ILE* 3.8 15.0 - - + -
425C SER 2.9 9.8 + - - +
426C VAL 3.0 7.2 + - - +
428C ALA* 1.4 72.0 - - - +
430C TYR* 1.3 66.7 + - - +
432C VAL* 3.2 9.8 + - - +
433C ALA* 3.0 19.9 + - - +
454C LEU* 4.4 4.3 - - + -
457C MET* 3.7 30.9 - - + -
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Residues in contact with TYR 430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C LEU* 3.7 28.3 - - + -
381C ILE* 3.7 8.6 - - + +
399C ILE* 5.5 1.1 - - + -
400C LYS* 3.4 35.9 + - + +
403C ILE* 3.5 41.8 - - + +
404C GLU* 5.1 2.2 - - + +
410C ILE* 3.5 36.3 - - + -
426C VAL 2.8 13.1 + - - +
427C GLU* 3.6 9.9 - - + +
429C MET* 1.3 73.8 - - - +
431C SER* 1.3 57.5 + - - +
433C ALA* 3.1 3.2 + - - +
434C SER* 2.8 48.3 + - - -
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Residues in contact with SER 431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLU 2.8 20.9 + - - -
428C ALA* 3.5 10.3 - - - -
429C MET 3.3 0.2 - - - -
430C TYR* 1.3 73.7 - - - +
432C VAL* 1.3 63.3 + - - +
434C SER* 3.2 8.6 + - - -
435C GLN* 3.0 44.0 + - - +
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Residues in contact with VAL 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 3.6 20.6 - - + -
428C ALA 3.6 13.0 - - - +
429C MET 3.2 8.3 + - - +
431C SER* 1.3 75.1 - - - +
433C ALA* 1.3 55.7 + - - +
435C GLN* 3.3 10.9 + - - +
436C CYS* 2.9 31.4 + - - -
445C PRO* 6.1 0.4 - - + -
450C VAL* 4.0 28.7 - - + +
453C LEU* 3.6 37.5 - - + +
454C LEU* 4.2 19.7 - - + -
457C MET* 6.2 0.2 - - - -
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Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C GLY* 3.8 14.1 - - - +
377C LEU* 3.8 16.8 - - + +
378C LEU* 3.8 27.8 - - + +
429C MET 3.0 12.9 + - - +
430C TYR* 3.1 9.6 + - - +
432C VAL* 1.3 77.6 - - - +
434C SER* 1.4 56.7 + - - +
436C CYS* 3.3 5.0 + - - +
437C LEU* 2.9 36.7 + - - +
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Residues in contact with SER 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C LYS* 3.5 35.4 + - - +
404C GLU* 4.1 8.5 + - - +
430C TYR* 2.8 34.7 + - - -
431C SER* 3.5 11.7 - - - -
433C ALA* 1.4 69.9 - - - +
435C GLN* 1.3 65.7 + - - +
437C LEU* 3.2 13.4 + - - -
438C HIS* 3.4 9.9 + - - +
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Residues in contact with GLN 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C SER* 3.0 40.1 + - - +
432C VAL* 3.6 8.5 - - - +
434C SER* 1.3 76.9 - - - +
436C CYS* 1.3 60.7 + - - +
438C HIS* 3.4 21.8 + - - +
443C LYS 5.0 0.3 - - - +
444C ARG* 3.8 1.6 - - - -
445C PRO* 3.3 32.3 - - + +
449C LYS* 5.6 1.4 - - - +
453C LEU* 3.8 28.8 - - - +
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Residues in contact with CYS 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C ILE* 3.4 32.5 - - - +
371C TYR* 3.4 12.1 + - - -
373C PHE* 4.6 5.6 - - - -
374C GLY* 3.6 15.7 - - - -
377C LEU* 4.8 0.4 - - - -
432C VAL* 2.9 30.6 + - - +
433C ALA 3.5 5.6 - - - +
434C SER 3.3 0.4 - - - -
435C GLN* 1.3 74.8 - - - +
437C LEU* 1.3 57.0 + - - +
438C HIS 3.2 5.0 + - - -
444C ARG* 3.4 21.0 - - - -
445C PRO* 4.2 1.6 - - - -
450C VAL* 3.6 33.2 - - - -
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C TYR* 3.4 43.5 + - + +
374C GLY 4.1 7.9 - - - +
375C VAL* 3.7 19.1 - - + +
378C LEU* 3.5 37.2 - - + -
397C LEU* 3.7 18.6 - - + +
400C LYS* 3.4 24.9 + - + +
433C ALA 2.9 20.8 + - - +
434C SER* 3.2 8.4 + - - +
436C CYS* 1.3 74.1 - - - +
438C HIS* 1.4 63.7 + - - +
439C GLU* 3.2 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
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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