Contacts of the helix formed by residues 421 - 437 (chain B) in PDB entry 5FLZ
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 TRP 421 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352B LYS* 5.7 5.2 - - - -
413B GLU* 4.4 2.9 - - - -
417B LYS* 3.5 42.6 - - + +
418B GLU* 3.1 32.4 + - + +
419B VAL* 3.1 31.8 + - + -
420B GLN* 1.4 68.1 + - - +
422B THR* 1.3 74.3 + - - +
423B ASN* 3.0 7.0 + - - -
424B GLU* 2.8 61.6 + - - +
425B PHE* 3.5 29.1 - + + -
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Residues in contact with THR 422 (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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421B TRP* 1.3 80.6 - - - +
423B ASN* 1.4 57.4 + - - +
425B PHE* 3.3 24.6 + - + +
426B SER* 3.1 32.1 + - - +
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR* 4.8 4.9 + - - -
420B GLN* 3.0 51.1 + - - +
421B TRP 3.0 3.3 + - - -
422B THR* 1.4 74.9 + - - +
424B GLU* 1.4 76.0 + - - +
426B SER* 3.3 11.2 + - - -
427B LYS* 3.1 21.5 + - - +
452B GLN* 6.1 2.6 - - - +
456B ILE* 5.7 5.5 - - - +
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Residues in contact with GLU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B THR* 3.8 13.7 - - - +
352B LYS* 3.5 28.1 - - - +
409B TYR* 2.8 32.6 + - + +
419B VAL* 3.3 1.7 - - - +
420B GLN 3.2 5.1 - - - +
421B TRP* 2.8 61.1 + - - +
423B ASN* 1.4 82.3 - - - +
425B PHE* 1.4 65.8 + - + +
427B LYS* 3.1 10.6 - - - +
428B LYS* 2.9 37.4 + - - +
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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
----------------------------------------------------------
352B LYS* 6.3 0.2 - - + -
421B TRP* 3.5 39.7 - + + -
422B THR* 3.3 28.4 + - + +
424B GLU* 1.4 89.7 - - + +
426B SER* 1.4 63.0 + - - +
428B LYS* 3.2 27.5 + - + +
429B TYR* 3.1 20.3 + - - +
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B THR* 3.1 19.6 + - - +
423B ASN* 3.4 13.8 - - - -
425B PHE* 1.4 74.2 - - - +
427B LYS* 1.4 51.6 + - - +
429B TYR* 3.1 11.3 + - - +
430B HIS* 2.9 56.6 + - - -
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Residues in contact with LYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 5.4 7.9 - - + +
351B THR* 4.1 16.6 - - + -
423B ASN 3.1 10.4 + - - +
424B GLU* 3.1 16.2 - - - +
426B SER* 1.4 74.0 - - - +
428B LYS* 1.3 63.2 + - - +
430B HIS* 3.1 15.0 + - - +
431B VAL* 3.0 37.9 + - - +
448B ILE* 3.7 51.0 - - + +
449B ILE* 3.7 24.1 - - - +
452B GLN* 3.9 26.9 - - + -
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B MET* 3.8 27.2 - - + +
351B THR* 3.5 33.8 - - + +
352B LYS* 4.1 17.5 - - - +
424B GLU* 2.9 47.3 + - - +
425B PHE* 3.2 30.6 + - + +
427B LYS* 1.3 75.1 - - - +
429B TYR* 1.3 64.1 + - - +
431B VAL* 3.4 1.3 + - - +
432B LEU* 3.2 23.9 + - - +
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Residues in contact with TYR 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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425B PHE 3.1 8.6 + - - +
426B SER* 3.1 11.8 + - - +
428B LYS* 1.3 80.2 - - - +
430B HIS* 1.4 78.3 + + - +
432B LEU* 3.2 22.5 - - + +
433B TYR* 2.7 57.5 + + + +
436B ASN* 5.4 1.3 - - - -
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Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B SER* 2.9 43.2 + - - -
427B LYS* 3.1 21.5 + - - +
429B TYR* 1.4 96.1 - + - +
431B VAL* 1.4 64.8 + - - +
433B TYR* 3.1 17.0 + - + +
434B GLN 3.1 10.9 + - - -
448B ILE* 3.8 31.8 - - + +
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 4.1 11.7 - - + +
347B MET* 3.6 43.3 - - + -
350B LEU* 5.5 4.3 - - + -
351B THR* 4.9 6.1 - - + -
427B LYS* 3.0 28.1 + - - +
428B LYS 3.9 1.3 - - - +
430B HIS* 1.4 72.8 - - - +
432B LEU* 1.3 66.0 + - - +
434B GLN* 3.2 4.9 + - - +
435B SER* 3.1 32.0 + - - +
445B PHE* 3.8 34.1 - - + -
448B ILE* 4.7 1.6 - - - -
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Residues in contact with LEU 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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347B MET* 5.2 9.4 - - + -
428B LYS 3.2 12.2 + - - +
429B TYR* 3.2 31.4 - - + +
431B VAL* 1.3 76.4 - - - +
433B TYR* 1.4 59.0 + - - +
435B SER* 3.3 9.3 + - - -
436B ASN* 2.8 58.9 + - - +
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Residues in contact with TYR 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B TYR* 2.7 40.1 + + + +
430B HIS* 3.1 17.0 + - + +
432B LEU* 1.4 75.0 - - - +
434B GLN* 1.4 63.6 + - - +
436B ASN* 3.1 35.7 + - + +
437B SER* 3.8 18.7 + - - -
439B ARG* 5.7 3.4 - - - -
444B ASN* 6.3 0.9 - - - -
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Residues in contact with GLN 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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343B TYR* 3.4 38.6 + - - -
430B HIS 3.1 11.7 + - - +
431B VAL 3.2 6.0 + - - +
433B TYR* 1.4 78.1 - - - +
435B SER* 1.4 51.5 + - - +
436B ASN 3.2 0.3 + - - -
438B TYR* 2.9 32.6 + - - +
439B ARG* 2.9 38.2 + - - +
440B GLY* 3.4 19.5 + - - -
441B ILE* 3.5 26.8 - - + +
444B ASN* 4.8 11.2 - - - +
445B PHE* 4.5 25.0 - - + +
448B ILE* 5.4 2.9 - - + -
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Residues in contact with SER 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B TYR* 3.3 31.6 - - - +
431B VAL* 3.1 16.0 + - - +
432B LEU* 3.3 14.5 - - - -
434B GLN* 1.4 78.3 + - - +
436B ASN* 1.3 56.4 + - - +
437B SER 3.4 0.2 - - - -
438B TYR* 3.2 35.0 - - - -
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Residues in contact with ASN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B TYR* 5.4 1.6 - - - -
432B LEU* 2.8 51.6 + - - +
433B TYR* 3.1 31.5 + - + +
435B SER* 1.3 78.5 - - - +
437B SER* 1.3 58.0 + - - +
438B TYR* 5.0 1.7 - - - -
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Residues in contact with SER 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B TYR* 3.8 17.6 + - - -
434B GLN 3.5 1.8 + - - -
436B ASN* 1.3 77.4 - - - +
438B TYR* 1.4 63.1 + - - +
439B ARG* 2.9 41.4 + - - +
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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