Contacts of the helix formed by residues 422 - 437 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B TRP* 4.6 4.0 + - - -
414B ILE* 5.9 0.2 - - - -
420B ASP 3.5 6.1 + - - +
421B ALA* 1.3 72.5 - - - +
423B SER* 1.4 63.5 + - - +
424B THR* 3.3 13.7 + - - +
425B SER* 2.9 39.9 + - - -
426B VAL* 3.2 22.5 + - - +
206D ASN* 4.2 28.9 + - + +
207D ASN* 4.1 19.5 - - - +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLU* 3.0 33.0 + - - -
414B ILE* 5.2 4.0 - - - +
421B ALA 3.9 2.0 + - - -
422B ASP* 1.4 72.0 - - - +
424B THR* 1.3 59.9 + - - +
426B VAL* 3.9 5.1 - - - +
427B GLU* 2.9 49.3 + - - +
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Residues in contact with THR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ASP* 3.3 11.3 + - - -
423B SER* 1.3 79.3 - - - +
425B SER* 1.4 60.2 - - - +
427B GLU* 3.3 8.6 + - - +
428B ALA* 2.9 28.0 + - + +
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Residues in contact with SER 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 2.8 31.8 + - - -
289B CYS* 5.2 1.6 - - - -
422B ASP* 2.9 27.0 + - - -
424B THR* 1.4 75.5 - - - +
426B VAL* 1.3 61.1 + - - +
428B ALA* 3.2 9.4 + - - +
429B MET 2.9 24.6 + - - -
457B MET* 3.7 30.1 - - - +
458B THR* 6.1 0.2 - - - -
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 3.6 31.6 - - + -
381B ILE* 3.9 19.8 - - + +
410B ILE* 4.4 10.1 - - + -
414B ILE* 3.6 39.3 - - + -
421B ALA* 4.0 18.6 - - + -
422B ASP 3.2 17.1 + - - +
423B SER 3.9 3.4 - - - +
425B SER* 1.3 76.4 + - - +
427B GLU* 1.3 51.8 + - + +
429B MET* 3.0 5.2 + - - +
430B TYR* 2.8 31.9 + - - +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B THR* 5.8 0.2 + - - -
410B ILE* 3.8 23.1 - - + +
411B GLU* 5.2 4.5 - - - +
423B SER* 2.9 35.0 + - - +
424B THR* 3.6 7.0 - - - +
426B VAL* 1.3 75.0 - - + +
428B ALA* 1.3 55.5 + - - +
430B TYR* 3.3 9.9 + - + +
431B SER* 2.8 29.9 + - - -
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B THR* 2.9 15.6 + - + +
425B SER* 3.2 10.7 + - - +
427B GLU* 1.3 76.2 - - - +
429B MET* 1.4 61.3 + - - +
431B SER* 3.4 9.3 + - - -
432B VAL* 3.3 24.8 + - - +
453B LEU 5.9 0.4 - - - +
457B MET* 4.0 24.9 - - + +
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Residues in contact with MET 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TRP* 3.6 31.4 - - + -
288B ARG 4.1 3.4 - - - +
289B CYS* 4.1 10.3 - - - -
292B ALA* 3.8 22.7 - - + -
377B LEU* 4.1 24.6 - - + +
380B ILE* 3.8 18.2 - - + -
381B ILE* 3.8 14.8 - - + -
425B SER 2.9 9.0 + - - +
426B VAL 3.5 6.5 - - - +
428B ALA* 1.4 71.7 - - - +
430B TYR* 1.3 65.6 + - - +
432B VAL* 3.2 9.2 + - - +
433B ALA* 3.0 20.1 + - - +
454B LEU* 4.4 4.5 - - + -
457B MET* 3.7 32.5 - - + -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 3.8 26.5 - - + -
381B ILE* 3.7 8.2 - - + +
399B ILE* 4.9 0.7 - - + -
400B LYS* 3.4 36.2 + - + +
403B ILE* 3.6 36.2 - - + +
404B GLU* 5.2 2.1 - - + +
410B ILE* 3.5 43.3 - - + -
426B VAL 2.8 15.8 + - - +
427B GLU* 3.6 9.4 - - + +
429B MET* 1.3 73.0 - - - +
431B SER* 1.3 57.2 + - - +
433B ALA* 3.1 3.5 + - - +
434B SER* 2.8 48.3 + - - -
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Residues in contact with SER 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU 2.8 20.9 + - - -
428B ALA* 3.5 9.6 - - - -
429B MET 3.3 0.4 - - - -
430B TYR* 1.3 75.8 - - - +
432B VAL* 1.3 62.4 + - - +
434B SER* 3.2 8.2 + - - -
435B GLN* 3.0 45.1 + - - +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.6 20.6 - - + -
428B ALA 3.3 13.0 + - - +
429B MET 3.2 8.6 + - - +
431B SER* 1.3 75.1 - - - +
433B ALA* 1.3 57.8 + - - +
435B GLN* 3.3 11.2 + - - +
436B CYS* 2.9 31.0 + - - -
445B PRO* 6.1 0.4 - - + -
450B VAL* 4.0 29.2 - - + +
453B LEU* 3.6 36.8 - - + -
454B LEU* 4.2 17.9 - - + -
457B MET* 6.2 0.4 - - + -
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLY* 3.8 19.7 - - - +
377B LEU* 3.9 18.1 - - + +
378B LEU* 3.8 22.7 - - + -
429B MET 3.0 13.3 + - - +
430B TYR* 3.4 9.9 - - - +
432B VAL* 1.3 75.4 - - - +
434B SER* 1.3 57.0 + - - +
436B CYS* 3.3 5.2 + - - +
437B LEU* 2.9 35.6 + - - +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LYS* 2.9 50.8 + - - +
404B GLU* 4.1 9.2 + - - +
430B TYR* 2.8 34.4 + - - -
431B SER* 3.5 11.0 - - - -
433B ALA* 1.3 72.0 - - - +
435B GLN* 1.3 63.3 + - - +
437B LEU* 3.2 6.3 + - - -
438B HIS* 3.5 2.1 + - - +
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Residues in contact with GLN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B SER* 3.0 41.3 + - - +
432B VAL* 3.6 8.5 - - - +
434B SER* 1.3 77.3 - - - +
436B CYS* 1.3 61.8 + - - +
438B HIS* 3.4 21.9 + - - +
443B LYS 5.0 0.3 - - - +
444B ARG* 3.8 1.4 - - - -
445B PRO* 3.3 33.0 - - + +
449B LYS* 5.6 0.9 - - - +
453B LEU* 3.8 28.6 - - - +
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Residues in contact with CYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ILE* 3.4 41.3 - - - +
371B TYR* 3.4 11.9 + - - -
373B PHE* 4.6 5.4 - - - -
374B GLY* 3.6 15.5 - - - -
377B LEU* 4.8 0.4 - - - -
432B VAL* 2.9 27.4 + - - +
433B ALA* 3.5 6.1 - - - +
435B GLN* 1.3 75.2 - - - +
437B LEU* 1.3 57.4 + - - +
438B HIS 3.2 4.2 + - - -
444B ARG* 3.4 21.8 - - - -
445B PRO* 4.3 1.6 - - - -
450B VAL* 3.6 25.1 - - - -
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B TYR* 3.4 35.2 - - + +
374B GLY 4.1 7.2 - - - +
375B VAL* 3.7 19.5 - - + +
378B LEU* 3.5 36.1 - - + -
397B LEU* 3.7 18.6 - - + +
400B LYS* 3.3 36.5 + - + +
433B ALA 2.9 21.2 + - - +
434B SER* 3.2 0.8 + - - -
436B CYS* 1.3 73.5 - - - +
438B HIS* 1.3 63.9 + - - +
439B GLU* 3.3 18.8 + - - +
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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