Contacts of the helix formed by residues 391 - 404 (chain K) in PDB entry 3FKS
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 SER 391 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389K ALA 2.8 7.9 + - - -
390K GLY* 1.3 73.7 - - - +
392K LEU* 1.3 61.1 + - - +
393K LYS* 3.1 5.4 - - - +
394K LEU* 3.6 9.3 + - - +
395K PHE* 3.2 22.3 + - - +
425O THR 4.1 10.3 + - - -
426O GLY* 4.5 6.7 - - - -
427O ILE* 3.4 28.1 - - - +
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Residues in contact with LEU 392 (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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157K ALA* 4.6 12.6 - - + +
158K LEU* 3.8 19.3 - - + -
389K ALA* 3.4 32.8 + - + -
390K GLY 3.2 3.6 - - - -
391K SER* 1.3 76.7 - - - +
393K LYS* 1.3 63.5 + - - +
395K PHE* 3.5 9.5 + - + +
396K LEU* 3.3 25.4 + - + +
426K LEU* 3.9 36.1 - - + -
430K LEU* 5.1 8.3 - - + -
447K ILE* 4.2 19.1 - - + -
451K VAL* 4.4 15.0 - - + -
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Residues in contact with LYS 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158K LEU* 3.6 35.1 - - + +
369K VAL* 3.3 36.9 + - + +
372K SER 4.6 12.1 + - - +
373K VAL* 4.5 22.7 - - + +
374K SER 5.7 0.2 - - - +
391K SER* 3.1 3.0 - - - +
392K LEU* 1.3 78.6 - - - +
394K LEU* 1.3 84.7 + - + +
396K LEU 3.2 3.3 + - - -
397K ALA* 3.0 22.9 + - - +
345O TYR* 5.6 6.9 + - - -
424O PHE* 4.0 22.9 - - - +
425O THR* 5.2 5.8 - - - +
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Residues in contact with LEU 394 (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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391K SER* 3.6 12.6 + - - +
393K LYS* 1.3 100.1 - - - +
395K PHE* 1.3 63.3 + - - +
396K LEU 3.3 0.2 - - - -
397K ALA* 3.4 17.3 + - + +
398K GLN* 3.4 27.5 + - - +
343O GLY* 5.8 0.9 - - - -
345O TYR* 5.3 12.6 - - + -
425O THR* 3.9 32.1 - - + +
427O ILE* 4.0 16.4 - - + -
455O HIS* 5.5 0.3 + - - -
458O TYR* 3.8 30.5 - - + +
459O MET* 5.2 8.5 - - + -
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Residues in contact with PHE 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390K GLY 5.4 0.9 - - - +
391K SER 3.2 18.0 + - - +
392K LEU* 3.7 11.7 - - + +
393K LYS 3.2 0.6 - - - -
394K LEU* 1.3 79.1 - - - +
396K LEU* 1.3 65.0 + - + +
398K GLN* 3.6 4.5 + - - +
399K TYR* 3.1 29.0 + - + +
419K THR* 4.5 35.9 - - + -
422K ARG* 4.8 9.0 - - + -
423K GLY* 4.8 5.2 - - - -
426K LEU* 3.7 31.2 - - + -
450K GLY 5.9 3.8 - - - -
451K VAL* 5.9 5.2 - - - -
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Residues in contact with LEU 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158K LEU* 3.9 28.7 - - + -
369K VAL* 4.0 19.6 - - + +
392K LEU* 3.3 23.5 + - + +
393K LYS 3.2 5.2 + - - +
395K PHE* 1.3 77.4 - - + +
397K ALA* 1.3 60.3 + - - +
398K GLN 3.1 6.1 + - - -
399K TYR* 3.7 26.2 - - + +
400K ARG* 3.4 23.6 + - - +
423K GLY* 5.2 0.7 - - - -
426K LEU* 3.5 26.0 - - + -
427K THR* 4.2 11.9 - - - +
430K LEU* 4.0 16.8 - - + -
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Residues in contact with ALA 397 (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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369K VAL* 4.7 15.9 - - - +
370K GLY* 5.1 8.1 - - - +
393K LYS* 3.0 17.4 + - - +
394K LEU* 3.7 26.5 - - + +
395K PHE 3.3 0.6 - - - -
396K LEU* 1.3 76.8 - - - +
398K GLN* 1.3 69.4 + - + +
400K ARG* 4.6 2.3 - - - +
401K GLU* 4.2 13.7 + - - +
342O LEU 4.6 4.5 - - - +
343O GLY* 5.7 6.3 - - - -
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Residues in contact with GLN 398 (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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394K LEU 3.4 18.4 + - - +
395K PHE* 4.1 3.8 - - - +
396K LEU 3.1 0.2 - - - -
397K ALA* 1.3 89.0 + - - +
399K TYR* 1.3 63.0 + - - +
400K ARG 3.2 1.8 - - - -
401K GLU* 3.5 11.7 + - - +
402K VAL* 3.4 28.9 + - + +
342O LEU 4.3 4.6 + - - -
343O GLY* 5.0 0.8 - - - -
412O ARG* 3.0 32.3 + - - +
455O HIS* 3.8 34.5 - - + +
458O TYR* 3.4 31.7 + - + -
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Residues in contact with TYR 399 (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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395K PHE* 3.1 24.7 + + + +
396K LEU* 3.5 26.9 + - + -
398K GLN* 1.3 78.7 - - - +
400K ARG* 1.3 63.4 + - + +
402K VAL* 3.5 5.7 + - - +
403K ALA* 3.0 32.8 + - + +
419K THR* 4.0 10.5 - - - -
420K LEU* 3.9 33.0 + - + +
423K GLY* 3.4 37.9 + - - -
424K GLU* 3.4 10.6 + - - +
427K THR* 3.7 18.9 + - - -
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Residues in contact with ARG 400 (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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355K GLU* 2.9 30.9 + - - -
357K GLU* 5.2 3.8 - - - +
358K LEU* 4.2 25.3 - - - +
368K ASN* 3.0 33.2 + - - +
396K LEU 3.4 13.6 + - - +
397K ALA* 5.2 2.5 - - - +
398K GLN 3.2 0.4 - - - -
399K TYR* 1.3 84.0 - - + +
401K GLU* 1.3 58.9 + - - +
402K VAL 2.9 10.3 + - - -
403K ALA* 3.0 18.8 + - + +
404K ALA* 3.4 12.6 + - - +
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Residues in contact with GLU 401 (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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397K ALA 4.2 10.7 + - - +
398K GLN* 3.5 14.7 + - - +
399K TYR 3.5 0.4 - - - -
400K ARG* 1.3 78.7 - - - +
402K VAL* 1.3 61.0 + - + +
404K ALA* 4.6 3.7 - - - +
405K PHE* 4.3 12.5 + - - +
342O LEU* 3.2 41.0 - - + +
408O ARG* 3.8 17.3 + - - +
412O ARG* 3.2 34.9 + - - -
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Residues in contact with VAL 402 (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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398K GLN* 3.4 18.5 + - + +
399K TYR* 3.8 5.4 - - - +
400K ARG 2.9 0.8 - - - -
401K GLU* 1.3 80.5 - - + +
403K ALA* 1.3 64.7 + - - +
404K ALA 3.1 2.7 - - - -
405K PHE* 3.0 17.7 + - + +
406K ALA* 3.2 14.6 + - + +
416K THR* 5.1 18.8 - - + +
420K LEU* 4.5 15.0 - - + -
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Residues in contact with ALA 403 (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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399K TYR* 3.0 29.4 + - + +
400K ARG* 3.0 14.3 + - + +
402K VAL* 1.3 78.2 - - - +
404K ALA* 1.3 59.3 + - - +
406K ALA* 3.6 15.9 + - - +
420K LEU* 4.2 17.5 - - + +
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Residues in contact with ALA 404 (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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400K ARG 3.4 8.5 + - - +
401K GLU* 4.9 3.8 - - - +
402K VAL 3.1 0.8 - - - -
403K ALA* 1.3 75.9 - - - +
405K PHE* 1.3 61.2 - - - +
406K ALA* 3.0 9.6 + - - +
407K GLN* 4.8 5.5 + - - +
239P ASN* 5.4 1.2 - - - +
243P ASN* 6.0 0.3 + - - -
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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