Contacts of the helix formed by residues 391 - 402 (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 SER 391 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389T ALA 3.2 6.3 + - - -
390T GLY* 1.3 77.2 - - - +
392T LEU* 1.3 63.8 + - - +
393T LYS* 3.1 4.5 + - - +
394T LEU* 3.6 12.6 + - - +
395T PHE* 3.8 11.3 + - - +
425X THR 3.8 17.3 - - - -
426X GLY* 3.2 34.0 + - - -
427X ILE* 4.1 13.3 - - - +
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Residues in contact with LEU 392 (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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157T ALA* 4.8 13.7 - - + +
158T LEU* 3.7 23.6 - - + -
389T ALA* 4.5 17.5 + - + +
390T GLY 3.3 3.4 - - - +
391T SER* 1.3 76.0 - - - +
393T LYS* 1.3 62.1 + - - +
395T PHE* 3.7 9.3 + - + +
396T LEU* 3.3 31.4 + - + +
426T LEU* 3.9 35.0 - - + -
430T LEU* 4.8 11.4 - - + -
447T ILE* 4.9 16.2 - - + -
451T VAL* 4.3 20.9 - - + -
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Residues in contact with LYS 393 (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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158T LEU* 3.6 37.8 - - + +
159T VAL* 5.0 0.7 - - + -
369T VAL* 3.2 40.9 + - + +
370T GLY 5.5 0.2 + - - -
372T SER 3.7 21.9 + - - +
373T VAL* 3.8 28.2 - - + +
374T SER 5.2 0.7 - - - +
391T SER* 3.1 1.7 - - - -
392T LEU* 1.3 80.7 - - - +
394T LEU* 1.3 78.8 + - + +
397T ALA* 3.2 15.3 + - - +
345X TYR* 4.0 15.4 + - - -
424X PHE* 4.4 22.2 - - - +
425X THR* 5.5 4.3 - - - +
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Residues in contact with LEU 394 (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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391T SER* 3.6 8.9 + - - +
392T LEU 3.5 0.2 - - - -
393T LYS* 1.3 93.8 - - - +
395T PHE* 1.3 61.1 + - - +
397T ALA* 3.6 10.5 + - + +
398T GLN* 3.1 30.0 + - - +
343X GLY 4.5 0.7 - - - +
345X TYR* 4.0 25.1 - - + -
425X THR* 3.5 38.4 - - + +
427X ILE* 4.2 16.6 - - + -
458X TYR* 3.6 28.5 + - + +
459X MET* 3.9 15.7 - - + -
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Residues in contact with PHE 395 (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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391T SER 3.8 10.4 + - - +
392T LEU* 3.7 12.1 + - + +
393T LYS 3.3 0.4 - - - -
394T LEU* 1.3 75.3 - - - +
396T LEU* 1.3 63.9 + - + +
397T ALA 3.1 1.1 - - - -
398T GLN* 2.9 11.5 + - + +
399T TYR* 2.9 33.5 + + + +
419T THR* 4.5 31.9 - - + -
422T ARG* 4.9 7.2 - - + -
423T GLY* 4.7 10.8 - - - -
426T LEU* 4.1 28.0 - - + -
455X HIS* 5.0 16.6 - + - -
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Residues in contact with LEU 396 (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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158T LEU* 4.0 23.3 - - + -
369T VAL* 4.0 23.2 - - + +
392T LEU* 3.3 37.3 + - + +
395T PHE* 1.3 81.8 - - + +
397T ALA* 1.3 60.5 + - - +
399T TYR* 4.0 14.9 - - + +
400T ARG* 3.1 27.0 + - - +
423T GLY* 4.9 0.7 - - - -
426T LEU* 3.6 30.3 - - + -
427T THR* 3.8 22.4 - - + +
430T LEU* 4.7 9.0 - - + -
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Residues in contact with ALA 397 (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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369T VAL* 4.2 12.3 - - + +
370T GLY* 4.8 14.4 - - - +
393T LYS* 3.2 19.1 + - - +
394T LEU* 3.6 20.0 - - + +
395T PHE 3.1 0.6 - - - -
396T LEU* 1.3 77.1 - - - +
398T GLN* 1.3 61.1 + - - +
400T ARG* 4.6 3.3 - - - +
401T GLU* 3.4 23.0 + - - +
341X GLU 4.8 3.5 - - - +
342X LEU 4.0 5.5 - - - +
343X GLY* 4.6 14.6 - - - -
345X TYR* 6.2 0.2 - - + -
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Residues in contact with GLN 398 (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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394T LEU 3.1 15.6 + - - +
395T PHE* 2.9 11.6 + - + +
397T ALA* 1.3 78.5 - - - +
399T TYR* 1.3 64.1 + - - +
400T ARG 3.2 2.4 + - - -
401T GLU* 3.2 25.6 + - - +
402T VAL* 3.4 9.3 - - - +
342X LEU 3.9 10.3 + - - -
343X GLY* 4.1 1.8 + - - -
412X ARG* 2.7 35.5 + - - +
455X HIS* 4.4 25.4 - - + +
458X TYR* 3.1 48.7 + - + +
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Residues in contact with TYR 399 (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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395T PHE* 2.9 26.2 + + + +
396T LEU* 3.5 13.0 + - + +
398T GLN* 1.3 77.0 - - - +
400T ARG* 1.3 67.6 + - + +
402T VAL* 3.5 19.0 + - - +
419T THR* 4.2 9.2 - - - -
420T LEU* 3.3 47.3 + - + +
423T GLY* 3.6 31.9 - - - -
424T GLU* 3.4 21.5 + - - +
427T THR* 4.3 10.5 - - - -
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Residues in contact with ARG 400 (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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355T GLU* 2.9 30.4 + - - -
357T GLU* 4.9 5.1 - - - +
358T LEU* 3.3 37.7 - - + +
368T ASN* 2.9 32.1 + - - +
369T VAL* 5.7 8.1 - - + +
370T GLY 5.8 1.3 - - - +
396T LEU 3.1 18.0 + - - +
397T ALA* 4.6 4.5 - - - +
398T GLN 3.2 0.2 - - - -
399T TYR* 1.3 83.1 - - + +
401T GLU* 1.3 59.8 + - - +
402T VAL 3.1 11.6 + - - +
403T ALA* 5.2 2.8 - - - +
341X GLU* 5.9 0.6 + - - -
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Residues in contact with GLU 401 (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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397T ALA 3.4 17.4 + - - +
398T GLN* 3.2 15.0 - - - +
400T ARG* 1.3 79.0 - - - +
402T VAL* 1.3 82.1 + - - +
403T ALA* 3.9 3.1 + - - +
341X GLU 5.1 3.1 - - - +
342X LEU* 4.0 31.6 - - + +
408X ARG* 3.3 22.9 + - - -
412X ARG* 3.5 26.8 + - - +
454X GLU* 5.2 1.4 - - - +
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Residues in contact with VAL 402 (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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398T GLN* 3.4 11.2 + - + +
399T TYR* 3.5 16.5 - - - +
400T ARG 3.1 5.3 - - - +
401T GLU* 1.3 98.9 - - - +
403T ALA* 1.3 73.0 + - - +
416T THR* 6.4 1.8 - - - -
420T LEU* 5.1 17.3 - - + +
408X ARG* 5.4 6.3 - - - +
454X GLU* 5.6 4.5 - - - +
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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