Contacts of the helix formed by residues 391 - 402 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390J GLY* 1.3 76.1 - - - +
392J LEU* 1.3 65.0 + - - +
393J LYS* 3.1 2.5 - - - +
394J LEU* 3.2 39.1 + - - -
395J PHE* 3.2 29.1 + - - -
451J VAL* 5.1 8.9 - - - +
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Residues in contact with LEU 392 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J ALA* 4.7 9.4 - - + -
158J LEU* 4.3 18.6 - - + -
389J ALA* 3.6 34.5 + - + +
391J SER* 1.3 74.8 - - - +
393J LYS* 1.3 65.7 + - - +
395J PHE* 3.9 5.7 - - + +
396J LEU* 3.1 43.1 + - + +
426J LEU* 4.1 29.6 - - + -
430J LEU* 5.0 12.1 - - + -
447J ILE* 4.3 12.6 - - + -
451J VAL* 4.1 20.5 - - + +
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Residues in contact with LYS 393 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J LEU* 3.6 39.7 - - + +
159J VAL* 5.7 0.9 - - - -
369J VAL* 3.6 38.0 + - + +
370J GLY* 4.8 6.3 + - - -
372J SER 5.2 1.3 - - - -
373J VAL* 4.8 14.6 - - - +
389J ALA 5.0 1.2 + - - -
390J GLY 5.9 0.7 - - - +
391J SER* 3.1 0.8 - - - -
392J LEU* 1.3 80.8 - - - +
394J LEU* 1.3 64.1 + - + +
396J LEU* 3.9 2.1 - - - +
397J ALA* 2.9 36.6 + - + +
337N ARG* 5.6 6.8 - - - +
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Residues in contact with LEU 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390J GLY 4.6 3.8 - - - +
391J SER* 3.2 35.8 + - - +
393J LYS* 1.3 81.9 - - + +
395J PHE* 1.3 68.4 + - + +
397J ALA* 2.9 17.1 + - - +
398J GLN* 3.0 26.1 + - - +
341N GLU* 3.7 35.8 - - + +
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Residues in contact with PHE 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391J SER* 3.2 26.1 + - - +
392J LEU* 3.9 8.3 - - + +
394J LEU* 1.3 79.9 - - + +
396J LEU* 1.3 63.6 + - - +
398J GLN* 3.2 15.1 + - - +
399J TYR* 3.0 22.4 + - - +
418J GLN* 6.2 1.3 - - + -
419J THR* 4.7 22.2 - - + +
422J ARG* 3.9 46.9 - - + -
426J LEU* 4.8 15.0 - - + -
451J VAL* 5.2 13.7 - - + -
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Residues in contact with LEU 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J LEU* 3.7 31.6 - - + -
369J VAL* 5.2 11.4 - - + -
392J LEU* 3.1 37.3 + - + +
393J LYS* 4.0 3.4 - - - +
395J PHE* 1.3 79.2 - - - +
397J ALA* 1.3 63.1 + - - +
399J TYR* 3.4 10.6 + - + +
400J ARG* 3.3 22.0 + - - +
423J GLY* 4.9 6.1 - - - +
426J LEU* 4.2 26.5 - - + -
427J THR* 4.3 14.4 - - + +
430J LEU* 3.9 17.7 - - + -
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Residues in contact with ALA 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393J LYS* 2.9 24.1 + - + +
394J LEU* 2.9 13.0 + - - +
396J LEU* 1.3 78.2 - - - +
398J GLN* 1.3 63.0 + - + +
400J ARG* 3.3 16.1 + - - +
401J GLU* 3.8 10.2 + - - +
341N GLU* 5.0 7.6 - - - +
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Residues in contact with GLN 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394J LEU* 3.0 28.7 + - - +
395J PHE* 3.5 21.9 - - - +
397J ALA* 1.3 74.4 - - + +
399J TYR* 1.3 59.9 + - - +
401J GLU* 2.9 25.2 - - + +
402J VAL* 2.9 35.1 + - + +
419J THR* 4.7 12.5 - - + +
341N GLU* 5.5 7.2 + - - +
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Residues in contact with TYR 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J PHE 3.0 16.6 + - - +
396J LEU* 3.7 13.5 - - + +
397J ALA 3.3 0.2 - - - -
398J GLN* 1.3 76.9 - - - +
400J ARG* 1.3 67.2 + - + +
401J GLU 3.3 0.3 + - - -
402J VAL* 3.4 27.9 + - - +
403J ALA* 3.7 12.8 + - + +
419J THR* 4.1 17.8 - - + +
420J LEU* 4.4 13.7 - - + -
423J GLY* 3.5 24.0 - - - -
424J GLU* 3.4 39.2 - - + +
427J THR* 4.0 20.2 + - + -
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Residues in contact with ARG 400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355J GLU* 5.2 2.6 + - - -
358J LEU* 4.8 16.2 - - - +
367J ILE 4.2 4.0 + - - -
368J ASN* 3.4 32.5 + - - +
369J VAL* 3.9 18.0 - - - +
370J GLY* 4.2 17.7 - - - +
396J LEU 3.3 11.2 + - - +
397J ALA* 3.6 12.8 - - - +
398J GLN 3.2 1.0 - - - -
399J TYR* 1.3 84.0 - - + +
401J GLU* 1.3 58.6 + - - +
403J ALA* 4.2 11.6 - - - +
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Residues in contact with GLU 401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397J ALA 3.8 5.1 - - - +
398J GLN* 2.9 43.9 - - - +
400J ARG* 1.3 79.6 - - - +
402J VAL* 1.3 61.2 + - + +
403J ALA 3.2 9.8 + - - -
404J ALA* 4.4 6.1 + - - +
405J PHE* 4.9 5.4 - - - -
18P LYS* 5.8 5.2 - - - +
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Residues in contact with VAL 402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398J GLN* 2.9 23.5 + - + +
399J TYR* 3.4 18.3 + - - +
401J GLU* 1.3 82.9 - - + +
403J ALA* 1.3 58.2 + - - +
404J ALA 3.6 0.7 - - - -
405J PHE* 3.5 38.1 - - + -
416J THR* 4.4 32.3 - - + +
419J THR* 5.6 9.0 - - + -
420J LEU* 4.6 18.3 - - + +
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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