Contacts of the helix formed by residues 439 - 452 (chain L) 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 ALA 439 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149L GLN* 5.1 3.4 - - - +
187L ASN* 6.1 0.2 - - - +
190L ARG* 3.3 35.9 - - - +
191L TRP* 6.1 1.6 - - + -
438L LEU* 1.3 77.2 - - - +
440L THR* 1.3 61.4 + - - +
441L GLU* 3.2 29.4 - - + +
442L GLU* 2.8 30.6 + - - +
443L GLN* 3.1 8.0 + - - +
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Residues in contact with THR 440 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L GLN* 2.8 37.2 + - - +
382L VAL* 3.9 32.9 - - + +
385L LEU* 4.8 10.3 - - + +
438L LEU 3.8 0.4 + - - -
439L ALA* 1.3 73.1 - - - +
441L GLU* 1.3 62.3 + - - +
443L GLN* 2.9 28.2 + - + +
444L VAL* 3.0 30.1 + - + +
485L ILE* 4.8 7.0 - - + +
486L ARG* 6.4 0.4 - - - -
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Residues in contact with GLU 441 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439L ALA* 3.6 23.2 - - + +
440L THR* 1.3 81.0 + - - +
442L GLU* 1.3 66.0 + - + +
443L GLN 3.4 0.2 - - - -
445L PRO* 3.0 19.7 - - - +
482L LEU* 3.3 47.9 - - + +
485L ILE* 3.7 18.3 - - + +
486L ARG* 3.3 42.0 - - - +
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Residues in contact with GLU 442 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L ARG* 5.1 2.3 + - - -
437L PRO 4.8 0.3 - - - +
438L LEU* 3.2 34.3 - - + +
439L ALA* 2.8 25.0 + - + +
441L GLU* 1.3 86.8 - - + +
443L GLN* 1.3 61.7 + - - +
444L VAL 3.7 0.2 - - - -
445L PRO* 3.8 3.9 - - - +
446L LEU* 3.2 27.6 - - - +
471L LEU* 3.9 26.2 - - + +
475L LYS* 3.3 34.4 + - - -
482L LEU* 5.3 5.4 - - + -
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Residues in contact with GLN 443 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLN* 6.1 0.6 - - - +
151L GLY* 3.5 15.2 + - - -
152L LEU 4.5 0.2 - - - -
153L LYS* 4.1 25.1 - - + +
156L ASP* 3.6 33.6 + - - +
157L ALA* 5.2 1.2 - - - +
385L LEU* 4.2 18.3 - - + +
438L LEU* 2.7 31.5 + - + +
439L ALA 3.4 12.1 + - - +
440L THR* 2.9 13.3 + - - +
442L GLU* 1.3 79.1 - - - +
444L VAL* 1.3 66.2 + - - +
445L PRO 3.4 0.2 - - - -
446L LEU* 3.3 7.4 + - - +
447L ILE* 2.9 32.5 + - + +
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Residues in contact with VAL 444 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384L ALA* 3.8 33.9 - - + +
385L LEU* 4.0 8.7 - - + +
388L VAL* 3.4 27.6 - - + +
440L THR* 3.0 24.5 + - + +
443L GLN* 1.3 76.2 - - - +
445L PRO* 1.3 66.2 - - + +
447L ILE* 3.4 0.5 + - - +
448L TYR* 2.9 27.4 + - - +
485L ILE* 4.1 17.3 - - + -
491L LEU* 3.6 20.9 - - + -
499L LEU* 4.5 4.3 - - + -
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Residues in contact with PRO 445 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441L GLU 3.0 24.2 - - - +
442L GLU* 3.8 6.3 - - - +
443L GLN 3.5 3.8 - - - -
444L VAL* 1.3 95.9 - - + +
446L LEU* 1.3 58.0 + - + +
448L TYR* 3.0 9.0 + - + +
449L ALA* 2.9 31.0 + - - +
470L PHE* 3.9 12.5 - - + -
471L LEU* 5.8 0.7 - - + -
474L LEU* 3.6 32.8 - - + -
482L LEU* 4.0 6.3 - - + -
485L ILE* 4.4 7.2 - - + -
499L LEU* 4.6 15.3 - - + -
503L THR* 5.4 0.9 + - - -
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Residues in contact with LEU 446 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L LYS* 4.5 9.4 - - + -
429L LEU* 3.4 38.0 - - + +
438L LEU* 4.0 16.8 - - + -
442L GLU 3.2 19.1 - - - +
443L GLN* 3.3 8.6 + - - +
445L PRO* 1.3 82.4 - - + +
447L ILE* 1.3 64.1 + - + +
449L ALA* 3.5 12.7 + - + +
450L GLY 3.6 1.7 + - - -
455L LEU* 4.5 0.6 - - + +
466L PHE* 4.9 10.8 - - + -
467L GLU* 3.7 52.7 - - + +
470L PHE* 4.9 10.1 - - + -
471L LEU* 4.1 11.9 - - + -
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Residues in contact with ILE 447 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L LYS* 5.5 6.5 - - + +
157L ALA* 4.3 20.6 - - + -
385L LEU* 4.2 12.1 - - + -
388L VAL* 3.6 36.3 - - + +
389L ALA* 4.1 7.6 - - + +
392L LEU* 4.6 12.8 - - + -
426L LEU* 5.3 1.1 - - + +
429L LEU* 4.7 10.7 - - + +
430L LEU* 4.8 13.7 - - + -
443L GLN* 2.9 27.4 + - + +
444L VAL 3.8 3.6 - - - +
446L LEU* 1.3 74.7 - - + +
448L TYR* 1.3 61.1 + - - +
450L GLY* 3.0 2.9 + - - -
451L VAL* 2.9 34.9 + - + +
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Residues in contact with TYR 448 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388L VAL* 3.6 22.4 - - + +
444L VAL 2.9 17.3 + - - +
445L PRO* 3.0 5.8 + - + +
447L ILE* 1.3 73.1 - - - +
449L ALA* 1.3 58.1 + - - +
450L GLY 2.9 10.0 + - - -
451L VAL* 4.6 1.1 - - - +
452L ASN* 2.9 70.9 + - - +
454L HIS* 4.3 14.0 - + - -
496L LEU* 4.7 15.3 + - + -
499L LEU* 3.8 23.1 - - + -
500L LYS* 3.4 42.2 - - - +
503L THR* 4.0 18.6 - - - -
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Residues in contact with ALA 449 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445L PRO 2.9 15.6 + - - +
446L LEU* 3.9 8.7 - - - +
447L ILE 3.3 0.4 - - - -
448L TYR* 1.3 76.8 - - - +
450L GLY* 1.3 55.0 + - - +
454L HIS* 3.4 19.3 + - + -
455L LEU* 3.2 41.4 + - + +
466L PHE* 4.7 14.4 - - + -
470L PHE* 5.3 4.0 - - + -
503L THR* 4.2 18.4 - - + -
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Residues in contact with GLY 450 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422L ARG* 3.1 27.0 + - - +
426L LEU* 3.7 26.7 - - - +
429L LEU* 4.2 1.8 - - - -
446L LEU 3.6 1.8 + - - -
447L ILE 3.0 6.3 + - - -
448L TYR 2.9 1.0 - - - -
449L ALA* 1.3 80.0 - - - +
451L VAL* 1.3 60.6 + - - +
452L ASN 3.3 1.1 - - - -
453L GLY* 3.3 4.3 + - - -
454L HIS 4.9 0.2 - - - -
455L LEU* 4.1 12.3 - - - -
456L ASP* 4.8 0.9 - - - +
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Residues in contact with VAL 451 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388L VAL 3.2 28.5 - - - +
389L ALA* 4.8 2.0 - - - -
390L GLY* 4.9 8.1 - - - +
392L LEU* 4.7 23.6 - - + -
422L ARG* 3.0 16.0 + - - +
426L LEU* 5.1 5.4 - - + -
447L ILE* 2.9 22.2 + - + +
448L TYR* 5.0 0.2 - - - -
450L GLY* 1.3 76.4 - - - +
452L ASN* 1.3 67.5 + - - +
453L GLY 3.2 0.4 - - - -
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Residues in contact with ASN 452 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388L VAL* 5.4 2.0 + - - +
422L ARG* 3.7 3.9 + - - -
448L TYR* 2.9 61.0 + - + +
451L VAL* 1.3 89.5 + - - +
453L GLY* 1.3 64.8 + - - +
454L HIS* 3.4 19.7 + - + -
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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