Contacts of the helix formed by residues 433 - 447 (chain W) 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 ARG 433 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135W GLU* 2.8 39.7 + - + +
137W GLY* 4.8 3.4 - - - -
177W ALA* 5.4 16.3 + - + +
178W HIS* 5.8 0.6 - - - -
431W LEU* 3.9 21.7 - - + +
432W VAL* 1.3 74.3 - - - +
434W LEU* 1.3 67.8 + - - +
435W LYS* 3.1 18.0 + - + +
436W ASP* 3.3 9.5 + - + +
437W THR* 2.9 21.5 + - - -
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Residues in contact with LEU 434 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133W ILE* 4.7 27.1 - - + -
135W GLU* 3.7 31.3 + - + +
142W ASP* 3.5 34.4 + - + +
143W LEU* 5.1 0.7 - - - -
363W VAL* 5.6 5.2 - - + +
367W HIS* 3.3 38.6 - - + +
432W VAL 4.1 0.4 + - - -
433W ARG* 1.3 72.6 - - - +
435W LYS* 1.3 73.4 + - + +
437W THR* 3.3 13.9 + - - -
438W VAL* 3.3 14.3 + - + +
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Residues in contact with LYS 435 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135W GLU* 4.6 7.7 + - - +
433W ARG* 3.1 19.6 + - + +
434W LEU* 1.3 87.2 - - + +
436W ASP* 1.3 63.1 + - - +
438W VAL* 3.3 12.6 + - - +
439W ALA* 3.6 11.3 + - - +
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Residues in contact with ASP 436 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432W VAL* 4.3 8.3 - - + +
433W ARG* 3.3 11.3 + - + +
435W LYS* 1.3 79.4 - - - +
437W THR* 1.3 58.0 - - - +
439W ALA* 3.5 8.9 + - - +
440W SER* 2.7 37.6 + - - -
462W GLY* 3.8 13.7 - - - -
463W ILE* 4.4 1.9 - - - +
464W GLU* 3.1 37.8 - - - +
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Residues in contact with THR 437 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139W LYS* 4.1 19.8 - - + +
142W ASP* 5.0 2.9 + - + -
143W LEU* 3.9 30.2 - - + +
413W PHE* 6.3 0.2 - - - -
432W VAL* 3.1 21.6 + - - +
433W ARG 2.9 16.9 + - - -
434W LEU* 3.5 14.2 - - + -
435W LYS 3.2 0.2 - - - -
436W ASP* 1.3 78.6 - - - +
438W VAL* 1.3 62.8 + - + +
440W SER* 3.4 4.2 + - - -
441W PHE* 3.2 38.6 + - + +
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Residues in contact with VAL 438 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143W LEU* 4.9 7.6 - - + -
366W GLU* 4.0 37.7 - - + +
367W HIS* 3.5 36.1 - - + +
370W VAL* 3.9 21.3 - - + +
434W LEU* 3.3 17.1 + - + +
435W LYS* 3.3 8.0 + - - +
437W THR* 1.3 78.2 - - - +
439W ALA* 1.3 62.7 + - - +
442W LYS* 3.0 24.2 + - - +
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Residues in contact with ALA 439 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366W GLU* 5.7 2.5 - - - +
435W LYS 3.6 7.9 + - - +
436W ASP* 3.5 13.2 + - - +
437W THR 3.4 0.2 - - - -
438W VAL* 1.3 79.9 - - - +
440W SER* 1.3 63.0 + - - +
442W LYS* 3.8 9.1 - - - +
443W ALA* 3.1 26.7 + - - +
463W ILE* 5.7 1.3 - - + -
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Residues in contact with SER 440 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413W PHE* 3.7 23.5 - - - -
432W VAL* 5.7 0.2 - - - +
436W ASP* 2.7 24.9 + - - -
437W THR* 3.6 7.1 - - - -
438W VAL 3.3 0.2 - - - -
439W ALA* 1.3 79.0 - - - +
441W PHE* 1.3 63.7 + - - +
443W ALA* 3.4 3.9 + - - +
444W VAL* 3.2 26.0 + - - +
462W GLY* 4.3 1.2 - - - -
463W ILE* 3.3 43.1 + - - +
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Residues in contact with PHE 441 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139W LYS* 4.6 7.9 - - + -
143W LEU* 3.6 19.3 - - + -
370W VAL* 3.8 18.2 - - + -
374W VAL* 3.9 19.5 - - + -
410W ILE* 3.6 38.4 - - + -
413W PHE* 3.3 41.5 - + - -
414W LEU* 3.5 28.5 - - + -
437W THR* 3.2 28.3 + - + +
440W SER* 1.3 77.8 - - - +
442W LYS* 1.3 65.6 + - - +
444W VAL* 3.1 7.0 + - - +
445W LEU* 2.9 26.9 + - - +
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Residues in contact with LYS 442 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366W GLU* 2.7 39.3 + - - +
370W VAL* 3.5 31.7 - - + +
438W VAL* 3.0 19.7 + - - +
439W ALA* 3.8 7.6 - - - +
441W PHE* 1.3 76.2 - - - +
443W ALA* 1.3 63.2 + - - +
444W VAL 3.1 0.2 + - - -
445W LEU* 3.2 6.0 + - - +
446W GLU* 3.0 50.5 + - + +
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Residues in contact with ALA 443 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W ALA 3.1 17.1 + - - +
440W SER* 3.6 5.4 - - - +
442W LYS* 1.3 79.6 - - - +
444W VAL* 1.3 59.6 + - - +
446W GLU* 3.7 5.3 + - - +
447W GLY 3.3 4.0 + - - -
448W LYS* 3.2 54.3 + - - +
449W TYR* 4.0 20.4 - - + -
463W ILE* 5.7 0.9 - - + -
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Residues in contact with VAL 444 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406W ARG* 4.1 14.2 + - + +
409W LYS* 5.1 12.8 - - + +
410W ILE* 3.5 27.8 - - + -
413W PHE* 5.4 7.9 - - + -
440W SER 3.2 17.7 - - - +
441W PHE* 3.1 9.2 + - - +
443W ALA* 1.3 75.9 - - - +
445W LEU* 1.3 65.3 + - - +
447W GLY* 3.0 15.1 + - - -
448W LYS 4.9 1.6 - - - +
449W TYR* 4.6 12.6 - - + +
450W ASP* 4.1 8.6 - - - +
457W PHE* 4.6 17.3 - - + -
463W ILE* 4.5 17.5 - - + -
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Residues in contact with LEU 445 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370W VAL* 3.3 34.5 - - + +
373W LYS* 3.5 31.6 - - + +
374W VAL* 3.8 16.2 - - + +
377W THR* 3.6 27.4 - - + +
406W ARG* 3.9 20.3 + - + -
410W ILE* 4.5 17.3 - - + -
441W PHE 2.9 18.8 + - - +
442W LYS* 3.7 5.2 - - - +
444W VAL* 1.3 76.2 - - - +
446W GLU* 1.3 63.8 + - + +
447W GLY 3.5 0.3 + - - -
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Residues in contact with GLU 446 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373W LYS* 6.0 3.8 - - - +
406W ARG* 4.2 4.2 + - - -
442W LYS* 3.0 44.8 + - + +
443W ALA* 3.7 5.1 - - - +
445W LEU* 1.3 79.7 - - + +
447W GLY* 1.3 56.6 + - - +
448W LYS* 3.1 35.4 + - + +
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Residues in contact with GLY 447 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406W ARG* 3.5 20.0 - - - -
443W ALA 3.3 0.6 + - - -
444W VAL 3.0 10.1 + - - -
446W GLU* 1.3 80.0 - - - +
448W LYS* 1.3 64.9 + - - +
449W TYR 3.4 2.0 - - - -
450W ASP* 3.6 15.0 + - - +
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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
------------------------------------------------------------
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