Contacts of the helix formed by residues 420 - 439 (chain B) in PDB entry 5DKB
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 GLY 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B VAL 3.1 2.0 + - - -
419B GLU* 1.3 73.1 - - - +
421B MET* 1.3 62.8 + - - +
422B VAL* 3.2 11.8 + - - +
423B GLU* 3.6 16.2 + - - +
424B ILE* 4.6 1.4 + - - +
601B 5C9 4.1 9.1 - - - -
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Residues in contact with MET 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B MET* 4.4 14.4 - - + -
343B MET* 4.8 0.4 - - - +
346B LEU* 4.0 20.6 - - + -
402B LEU* 5.8 0.4 - - + -
404B PHE* 3.9 29.8 - - + -
410B LEU* 6.0 0.4 - - + -
415B GLY* 3.3 24.9 - - - +
418B VAL* 3.2 23.9 + - + +
419B GLU 3.4 1.4 + - - -
420B GLY* 1.3 74.3 - - - +
422B VAL* 1.3 58.8 + - - +
423B GLU 3.0 4.0 + - - -
424B ILE* 3.1 11.7 + - + +
425B PHE* 2.9 38.9 + - + +
428B LEU* 5.9 0.7 - - + -
601B 5C9 3.8 42.6 - - + +
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Residues in contact with VAL 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 4.5 23.8 - - + +
415B GLY 4.2 2.2 + - - -
416B LYS* 3.6 42.6 - - + +
420B GLY* 3.2 8.7 - - - +
421B MET* 1.3 78.2 - - - +
423B GLU* 1.3 65.4 + - + +
425B PHE* 3.6 9.0 - - - +
426B ASP* 3.1 31.7 + - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG 5.2 9.4 - - - +
420B GLY* 3.6 11.3 + - - +
421B MET 3.0 1.0 + - - -
422B VAL* 1.3 85.3 - - + +
424B ILE* 1.3 63.3 + - - +
426B ASP* 3.5 5.5 + - - +
427B MET* 3.4 38.4 + - + +
516B HIS* 5.7 1.7 - - - -
520B LYS* 5.0 12.5 - - - +
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Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B MET* 3.7 14.8 - - + -
420B GLY 4.6 1.0 + - - +
421B MET* 3.1 27.7 + - + +
423B GLU* 1.3 77.2 - - - +
425B PHE* 1.3 68.5 + - - +
427B MET* 3.5 20.8 + - + +
428B LEU* 3.1 37.9 + - + +
517B MET* 3.3 31.0 - - + +
520B LYS* 4.3 5.8 - - + -
521B GLY* 3.6 22.7 - - - +
601B 5C9 4.7 22.7 - - + +
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Residues in contact with PHE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B LEU* 3.7 27.4 - - + -
404B PHE* 4.5 5.6 - + - -
410B LEU* 3.2 34.5 - - + -
411B ASP* 3.2 20.2 - - - -
412B ARG* 3.4 22.7 - - + -
415B GLY* 4.0 22.4 - - - -
421B MET* 2.9 27.7 + - + +
422B VAL* 3.6 11.9 - - - +
423B GLU 3.2 0.2 - - - -
424B ILE* 1.3 80.2 - - - +
426B ASP* 1.3 57.0 + - - +
428B LEU* 3.2 4.7 + - - +
429B LEU* 2.9 54.4 + - + +
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Residues in contact with ASP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR 5.0 1.3 - - - +
412B ARG* 3.4 46.7 + - - +
422B VAL* 3.1 18.6 + - - +
423B GLU* 3.9 6.1 - - - +
424B ILE 3.4 0.2 - - - -
425B PHE* 1.3 79.8 - - - +
427B MET* 1.3 57.7 + - + +
429B LEU* 3.4 14.9 + - - +
430B ALA* 2.9 30.5 + - - +
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Residues in contact with MET 427 (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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459A TYR* 4.8 6.7 - - + +
460A THR* 4.2 24.5 - - + -
423B GLU* 3.4 27.2 + - + +
424B ILE* 3.6 35.9 - - + +
425B PHE 3.2 0.4 - - - -
426B ASP* 1.3 78.4 - - + +
428B LEU* 1.3 53.2 + - - +
430B ALA* 3.4 6.3 + - - +
431B THR* 2.6 37.1 + - - -
516B HIS* 3.7 32.5 - - + +
517B MET* 3.5 24.2 - - + +
520B LYS* 4.5 10.8 - - + -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B MET* 4.1 23.6 - - + -
391B LEU* 3.9 13.5 - - + -
392B VAL* 3.7 23.3 - - + +
402B LEU* 3.8 23.8 - - + -
404B PHE* 5.4 0.2 - - + -
421B MET* 5.9 1.1 - - + -
424B ILE* 3.1 30.8 + - + +
425B PHE* 3.6 4.9 - - - +
427B MET* 1.3 74.3 - - - +
429B LEU* 1.3 65.9 + - - +
431B THR* 3.2 4.6 + - - -
432B SER* 2.9 24.3 + - - -
517B MET* 3.8 20.9 - - + -
601B 5C9 3.5 28.3 - - + -
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Residues in contact with LEU 429 (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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400B GLY* 3.6 39.9 - - - +
401B LYS 3.6 7.2 - - - +
402B LEU* 3.7 20.4 - - + -
412B ARG* 4.6 10.5 - - + -
425B PHE* 2.9 40.5 + - + +
426B ASP* 3.6 21.1 - - - +
428B LEU* 1.3 76.5 - - - +
430B ALA* 1.3 51.9 + - - +
432B SER* 3.2 5.3 + - - -
433B SER* 2.8 37.1 + - - -
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Residues in contact with ALA 430 (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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459A TYR* 3.6 38.0 - - + +
472A LYS* 6.1 1.0 - - - -
426B ASP 2.9 21.4 + - - +
427B MET 3.7 4.7 - - - +
428B LEU 3.3 0.2 - - - -
429B LEU* 1.3 72.4 - - - +
431B THR* 1.3 57.6 + - - +
433B SER* 3.4 7.8 + - - -
434B ARG* 2.8 29.0 + - - +
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR* 5.4 7.6 - - + +
392B VAL* 3.7 24.0 - - + -
427B MET 2.6 20.9 + - - -
428B LEU 3.5 7.2 - - - -
430B ALA* 1.3 77.0 - - - +
432B SER* 1.3 56.8 + - - +
434B ARG* 3.1 8.6 + - - +
435B PHE* 2.9 32.2 + - + +
510B ILE* 3.8 28.5 - - + -
513B HIS* 5.1 5.4 - - + +
514B ILE* 4.5 4.7 - - + -
517B MET* 3.4 21.3 - - + +
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Residues in contact with SER 432 (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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392B VAL* 3.2 35.5 + - - +
395B SER* 3.2 28.5 + - - -
396B MET* 3.3 5.2 + - - +
401B LYS 5.7 0.7 - - - -
402B LEU* 5.1 2.0 - - - -
428B LEU 2.9 16.1 + - - -
429B LEU* 3.6 7.4 - - - -
431B THR* 1.3 72.2 - - - +
433B SER* 1.3 61.1 + - - +
435B PHE* 3.3 5.4 + - - +
436B ARG* 3.0 31.8 + - - +
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Residues in contact with SER 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LYS* 5.8 3.6 - - - -
429B LEU 2.8 17.9 + - - -
430B ALA* 3.5 8.8 + - - -
432B SER* 1.3 77.0 - - - +
434B ARG* 1.3 61.8 + - - +
436B ARG* 3.2 28.5 + - - +
437B MET* 3.0 28.1 + - - +
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Residues in contact with ARG 434 (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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459A TYR* 3.2 35.6 + - + +
472A LYS* 4.3 1.6 - - - +
476A HIS* 3.4 39.6 + - - +
430B ALA 2.8 14.9 + - - +
431B THR* 3.1 13.0 + - - +
433B SER* 1.3 77.4 + - - +
435B PHE* 1.3 60.6 + - - +
437B MET* 3.3 33.7 + - - +
438B MET* 3.1 48.1 + - - +
506B GLN* 3.7 40.8 + - - +
510B ILE* 3.6 18.9 - - + +
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Residues in contact with PHE 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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389B ILE* 4.1 24.7 - - + -
392B VAL* 3.4 31.4 - - + -
393B TRP* 4.7 5.2 - - + -
396B MET* 3.8 19.9 - - + +
431B THR* 2.9 11.8 + - + +
432B SER 3.6 8.3 - - - +
434B ARG* 1.3 76.5 - - - +
436B ARG* 1.3 57.1 + - - +
438B MET* 3.5 5.1 + - - -
439B ASN 2.9 21.5 + - - -
440B LEU* 3.0 49.2 + - + -
445B PHE* 5.4 0.2 - + - -
448B LEU* 4.2 19.5 - - + -
507B LEU* 4.5 3.1 - - + -
510B ILE* 3.6 42.4 - - + -
511B LEU* 6.0 0.4 - - + -
514B ILE* 4.9 0.4 - - + -
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Residues in contact with ARG 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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395B SER 4.5 1.0 + - - -
396B MET* 2.7 54.7 + - + +
397B GLU* 5.1 10.3 - - - +
398B HIS 5.1 0.2 + - - -
399B PRO* 3.8 39.5 - - - +
400B GLY 5.0 1.6 - - - +
432B SER* 3.0 19.9 + - - +
433B SER* 3.2 26.6 + - - +
435B PHE* 1.3 74.3 - - - +
437B MET* 1.3 61.2 + - - +
439B ASN* 3.0 18.5 + - - +
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Residues in contact with MET 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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472A LYS* 3.4 23.1 - - - +
473A ASP* 6.1 2.7 - - - +
476A HIS* 5.3 0.2 - - - +
433B SER* 3.0 14.7 + - - +
434B ARG* 3.3 44.6 - - - +
436B ARG* 1.3 77.7 - - - +
438B MET* 1.3 62.5 + - + +
439B ASN* 3.3 2.4 + - - +
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Residues in contact with MET 438 (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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434B ARG* 3.1 52.7 + - - +
435B PHE* 3.8 7.0 - - - +
437B MET* 1.3 75.4 - - + +
439B ASN* 1.3 70.2 + - - +
440B LEU* 4.5 3.4 - - + +
503B ARG* 2.9 40.5 + - + +
506B GLN* 3.3 31.9 - - + +
507B LEU* 3.6 28.7 - - + -
510B ILE* 3.8 21.3 - - - -
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Residues in contact with ASN 439 (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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396B MET* 5.0 4.6 - - - +
435B PHE 2.9 4.4 + - - -
436B ARG* 3.0 16.0 + - - +
437B MET 3.1 2.4 - - - +
438B MET* 1.3 82.3 - - - +
440B LEU* 1.3 67.5 + - - +
441B GLN* 3.4 22.7 + - - +
503B ARG* 3.3 8.0 + - - -
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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