Contacts of the helix formed by residues 391 - 402 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390U GLY* 1.3 81.3 + - - +
392U LEU* 1.3 62.6 + - - +
393U LYS* 3.1 4.0 - - - +
394U LEU* 3.0 28.8 + - - +
395U PHE* 2.9 27.4 + - - +
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Residues in contact with LEU 392 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157U ALA* 5.1 3.6 - - + -
158U LEU* 3.6 19.3 - - + -
389U ALA* 4.3 16.4 - - + +
390U GLY 4.0 1.2 - - - +
391U SER* 1.3 76.0 - - - +
393U LYS* 1.3 61.4 + - - +
395U PHE* 3.8 8.5 - - + -
396U LEU* 3.3 37.6 + - + +
426U LEU* 4.1 31.2 - - + -
430U LEU* 4.8 16.8 - - + -
447U ILE* 4.4 31.0 - - + -
451U VAL* 4.0 20.3 - - + +
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Residues in contact with LYS 393 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158U LEU* 3.2 40.1 + - + +
159U VAL* 4.5 3.6 - - - +
369U VAL* 3.1 37.5 - - + +
370U GLY 5.4 0.4 - - - -
372U SER 3.6 19.5 - - - -
373U VAL* 3.2 38.4 - - - +
374U SER 3.7 9.7 + - - +
391U SER* 3.1 1.5 - - - -
392U LEU* 1.3 79.1 - - - +
394U LEU* 1.3 66.2 + - + +
396U LEU 4.4 0.2 - - - -
397U ALA* 3.6 9.9 - - - +
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Residues in contact with LEU 394 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391U SER* 3.0 29.8 + - - +
393U LYS* 1.3 87.3 - - + +
395U PHE* 1.3 63.8 + - - +
396U LEU 3.3 0.7 - - - -
397U ALA* 3.3 4.1 + - + +
398U GLN* 3.1 37.9 + - - +
340V SER 3.7 24.0 - - - +
341V GLU* 3.7 19.7 - - + +
342V LEU 6.3 0.9 - - - -
344V ILE 6.1 1.3 - - - +
345V TYR* 4.7 22.0 - - + +
458V TYR* 5.7 4.0 - - - +
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Residues in contact with PHE 395 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391U SER 2.9 15.5 + - - +
392U LEU* 4.0 12.8 - - + +
393U LYS 3.5 0.2 - - - -
394U LEU* 1.3 77.6 - - - +
396U LEU* 1.3 59.7 + - + +
398U GLN* 3.5 15.9 + - - +
399U TYR* 3.2 21.4 + - + +
419U THR* 4.5 29.6 - - + -
422U ARG* 3.8 26.5 - - + -
423U GLY* 4.2 18.8 - - - -
426U LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 396 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158U LEU* 4.0 7.9 - - + -
369U VAL* 3.6 36.6 - - + -
392U LEU* 3.3 25.6 + - + +
394U LEU 3.3 0.4 - - - -
395U PHE* 1.3 81.1 - - + +
397U ALA* 1.3 65.6 + - - +
399U TYR* 3.0 21.2 + - + +
400U ARG* 3.0 14.6 + - - +
423U GLY 4.4 3.8 - - - +
426U LEU* 4.2 22.9 - - + -
427U THR* 4.1 22.7 - - + +
430U LEU* 3.9 26.0 - - + -
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Residues in contact with ALA 397 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369U VAL* 4.2 12.5 - - + +
370U GLY* 5.0 4.5 - - - +
393U LYS 3.6 15.3 + - - +
394U LEU* 3.3 12.3 + - + +
396U LEU* 1.3 80.2 - - - +
398U GLN* 1.3 60.0 + - - +
400U ARG* 3.5 7.9 + - - +
401U GLU* 3.4 18.0 + - - +
341V GLU* 4.0 36.7 - - + +
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Residues in contact with GLN 398 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394U LEU* 3.1 24.2 + - - +
395U PHE* 3.7 15.4 - - - +
396U LEU 3.2 0.2 - - - -
397U ALA* 1.3 74.2 - - - +
399U TYR* 1.3 64.9 + - - +
401U GLU* 3.1 27.0 - - - +
402U VAL* 3.5 13.0 + - - +
341V GLU 3.3 14.4 + - - +
342V LEU* 2.8 41.1 + - + -
412V ARG* 5.1 3.9 + - - +
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Residues in contact with TYR 399 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395U PHE* 3.2 15.6 + - + +
396U LEU* 3.0 17.6 + - + +
398U GLN* 1.3 75.1 - - - +
400U ARG* 1.3 68.1 + - + +
402U VAL* 3.1 29.0 + - + +
403U ALA* 4.9 0.5 - - - +
419U THR 3.6 14.6 - - - +
420U LEU* 3.8 20.3 + - + +
423U GLY* 3.4 26.0 - - - -
424U GLU* 3.1 49.9 + - - +
427U THR* 4.2 11.2 - - + -
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Residues in contact with ARG 400 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355U GLU* 5.1 5.5 + - - -
368U ASN* 3.9 34.7 + - - +
370U GLY* 6.0 1.6 - - - -
371U LEU* 5.8 2.2 - - - +
396U LEU 3.0 10.9 + - - +
397U ALA* 3.9 9.9 - - - +
398U GLN 3.4 0.2 - - - -
399U TYR* 1.3 79.6 - - + +
401U GLU* 1.3 64.4 + - - +
402U VAL 3.2 0.9 + - - -
403U ALA* 3.2 26.3 - - + +
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Residues in contact with GLU 401 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397U ALA 3.4 8.6 + - - +
398U GLN* 3.1 21.1 - - - +
399U TYR 3.1 0.2 - - - -
400U ARG* 1.3 81.2 - - - +
402U VAL* 1.3 59.7 + - + +
403U ALA 3.3 3.9 + - - -
404U ALA 5.2 0.3 + - - -
405U PHE* 4.0 11.1 + - - +
338V GLY 5.3 1.6 - - - +
342V LEU* 3.1 42.4 - - - +
385V GLN* 5.6 4.6 + - - -
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Residues in contact with VAL 402 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398U GLN 3.6 15.0 - - - +
399U TYR* 3.1 19.3 + - + +
400U ARG 3.1 1.0 - - - -
401U GLU* 1.3 81.2 - - + +
403U ALA* 1.3 59.8 + - - +
405U PHE* 3.7 35.4 - - + -
406U ALA* 4.1 17.3 - - + +
416U THR* 5.5 16.2 - - + +
419U THR* 5.7 4.5 - - - +
420U LEU* 5.0 11.9 - - + +
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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