Contacts of the helix formed by residues 439 - 451 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149T GLN* 5.7 1.6 - - - -
190T ARG* 3.5 21.5 - - - +
191T TRP* 6.5 0.4 - - - -
438T LEU* 1.3 75.3 - - - +
440T THR* 1.3 60.2 + - - +
441T GLU* 3.1 28.5 - - - +
442T GLU* 2.9 42.5 + - + +
443T GLN* 3.2 17.0 + - - +
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Residues in contact with THR 440 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149T GLN* 3.3 33.7 + - - +
382T VAL* 4.0 24.1 - - + +
384T ALA* 4.8 2.7 - - + -
385T LEU* 3.8 30.1 - - + +
438T LEU 4.1 0.6 + - - -
439T ALA* 1.3 72.6 - - - +
441T GLU* 1.3 67.3 + - - +
443T GLN* 3.4 12.5 + - - +
444T VAL* 3.3 29.4 + - + +
485T ILE* 5.1 3.1 - - + -
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Residues in contact with GLU 441 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439T ALA* 3.1 24.6 - - + +
440T THR* 1.3 83.8 + - - +
442T GLU* 1.3 65.2 + - + +
444T VAL* 3.2 11.9 - - - +
445T PRO* 3.1 22.0 - - - +
474T LEU* 5.6 0.3 - - - +
482T LEU* 4.1 30.9 - - + +
485T ILE* 3.8 29.7 - - + +
486T ARG* 3.7 39.7 + - - +
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Residues in contact with GLU 442 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T ARG* 4.5 4.7 + - - -
438T LEU* 3.8 24.0 - - + +
439T ALA* 2.9 37.1 + - + +
441T GLU* 1.3 81.2 - - + +
443T GLN* 1.3 61.4 + - - +
445T PRO* 3.2 15.7 - - - +
446T LEU* 3.4 21.6 - - + +
471T LEU* 3.5 31.6 - - + +
474T LEU* 5.6 6.5 - - + -
482T LEU* 5.3 7.6 - - + -
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Residues in contact with GLN 443 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151T GLY* 4.0 13.5 - - - -
152T LEU 4.1 2.5 - - - +
153T LYS* 4.6 23.5 - - + +
156T ASP* 3.7 26.4 + - - +
157T ALA* 5.3 0.5 + - - +
385T LEU* 3.9 19.6 - - + +
438T LEU* 3.3 39.3 + - + +
439T ALA 3.2 15.1 + - - +
440T THR* 3.4 7.2 + - - +
442T GLU* 1.3 78.4 - - - +
444T VAL* 1.3 59.4 + - - +
445T PRO* 3.2 0.7 - - - -
446T LEU* 3.2 9.5 + - - +
447T ILE* 3.0 38.5 + - + +
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Residues in contact with VAL 444 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384T ALA* 3.4 42.6 - - + +
385T LEU* 3.6 14.4 - - + +
388T VAL* 3.2 32.6 - - + +
440T THR 3.3 15.2 + - - +
441T GLU* 3.2 17.9 - - - +
443T GLN* 1.3 78.2 - - - +
445T PRO* 1.3 74.6 - - + +
448T TYR* 3.3 10.2 + - - +
485T ILE* 3.7 21.8 - - + -
491T LEU* 5.3 3.6 - - + -
499T LEU* 5.2 1.4 - - - +
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Residues in contact with PRO 445 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441T GLU 3.1 23.8 - - - +
442T GLU* 3.2 17.7 - - - +
444T VAL* 1.3 91.2 - - + +
446T LEU* 1.3 60.8 + - + +
448T TYR* 3.2 6.9 + - + +
449T ALA* 2.8 29.6 + - - +
470T PHE* 4.7 24.9 - - + -
474T LEU* 5.6 3.8 - - + -
485T ILE* 5.5 2.5 - - + -
499T LEU* 4.8 19.5 - - + -
503T THR* 5.6 7.1 - - + +
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Residues in contact with LEU 446 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153T LYS* 4.4 13.5 - - + -
429T LEU* 3.8 32.8 - - + +
438T LEU* 5.3 3.1 - - + -
442T GLU* 3.4 21.3 - - + +
443T GLN* 3.2 9.1 + - - +
445T PRO* 1.3 78.8 - - + +
447T ILE* 1.3 67.9 + - + +
449T ALA* 3.3 8.2 + - + +
450T GLY* 3.1 17.2 + - - -
455T LEU* 4.9 11.7 - - + -
466T PHE* 5.1 7.2 - - + -
467T GLU* 3.8 49.1 - - + +
470T PHE* 6.1 5.4 - - + -
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Residues in contact with ILE 447 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153T LYS* 5.2 4.0 - - + +
157T ALA* 4.3 19.7 - - + -
385T LEU* 4.5 9.2 - - + -
388T VAL* 3.7 16.4 - - + +
389T ALA* 3.6 38.4 - - + +
392T LEU* 4.9 12.6 - - + -
426T LEU* 5.7 1.4 - - - +
429T LEU* 6.3 0.7 - - + -
430T LEU* 4.4 19.3 - - + -
443T GLN* 3.0 24.3 + - + +
444T VAL 4.1 0.2 - - - +
446T LEU* 1.3 79.7 - - + +
448T TYR* 1.3 63.2 + - - +
450T GLY* 3.0 10.4 + - - -
451T VAL* 3.1 19.0 + - + +
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Residues in contact with TYR 448 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388T VAL* 4.0 20.4 - - + +
444T VAL 3.3 15.9 + - - +
445T PRO 3.2 5.3 + - - +
447T ILE* 1.3 76.8 - - - +
449T ALA* 1.3 65.5 + - - +
450T GLY 3.2 0.9 + - - -
451T VAL* 3.6 28.2 + - + +
454T HIS* 3.6 31.7 + + - -
496T LEU* 4.8 15.3 + - + +
499T LEU* 3.5 35.4 - - + -
500T LYS* 3.8 35.6 - - + +
503T THR* 4.8 9.6 - - + -
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Residues in contact with ALA 449 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429T LEU* 5.4 0.4 - - + -
445T PRO 2.8 14.2 + - - +
446T LEU* 3.4 12.6 - - + +
447T ILE 3.3 0.2 - - - -
448T TYR* 1.3 77.7 - - - +
450T GLY* 1.3 57.2 + - - +
453T GLY* 3.7 0.3 - - - -
454T HIS* 2.8 43.8 + - + +
455T LEU* 3.7 34.1 + - + +
466T PHE* 5.9 0.9 - - + -
503T THR* 5.8 7.0 - - + -
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Residues in contact with GLY 450 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422T ARG* 4.6 5.0 + - - +
426T LEU* 4.0 26.5 - - - -
429T LEU* 5.4 3.6 - - - -
446T LEU 3.1 9.1 + - - -
447T ILE 3.0 9.0 + - - -
449T ALA* 1.3 75.1 - - - +
451T VAL* 1.3 64.7 + - - -
453T GLY* 3.1 19.2 + - - -
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Residues in contact with VAL 451 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388T VAL 3.5 25.1 - - - +
389T ALA* 4.7 0.2 - - - -
390T GLY* 4.5 13.5 - - - +
392T LEU* 4.3 24.0 - - + -
422T ARG* 4.3 5.2 + - - -
426T LEU* 4.9 1.3 - - + +
447T ILE* 3.1 15.1 + - + +
448T TYR* 3.6 28.0 - - + +
450T GLY* 1.3 79.6 - - - +
453T GLY 3.3 19.0 + - - -
454T HIS* 5.3 2.7 - - - -
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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