Contacts of the helix formed by residues 433 - 445 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135N GLU* 2.8 46.8 + - - -
137N GLY* 5.7 0.4 - - - -
177N ALA* 4.4 25.1 + - - +
178N HIS* 5.1 1.4 - - - -
431N LEU* 4.0 22.0 - - + +
432N VAL* 1.3 76.8 - - - +
434N LEU* 1.3 63.7 + - - +
435N LYS* 4.6 12.2 - - + +
436N ASP* 3.3 10.0 + - + +
437N THR* 2.6 29.0 + - - -
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Residues in contact with LEU 434 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133N ILE* 5.3 20.0 - - + -
135N GLU* 3.1 34.2 + - + +
142N ASP* 3.3 40.4 + - + +
146N PRO* 6.5 0.2 - - + -
363N VAL* 5.8 7.6 - - + +
367N HIS* 4.1 17.3 - - + +
432N VAL 4.0 0.2 + - - -
433N ARG* 1.3 70.7 - - - +
435N LYS* 1.3 71.6 + - + +
437N THR* 2.9 17.2 + - - -
438N VAL* 3.0 24.8 + - + +
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Residues in contact with LYS 435 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135N GLU* 4.7 0.4 + - - +
433N ARG* 3.4 11.8 - - + +
434N LEU* 1.3 85.1 - - + +
436N ASP* 1.3 62.1 + - - +
438N VAL* 3.7 6.4 + - - +
439N ALA* 3.4 19.9 + - - +
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Residues in contact with ASP 436 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432N VAL* 4.1 7.9 - - + +
433N ARG* 3.3 14.1 + - + +
434N LEU 3.2 0.6 - - - -
435N LYS* 1.3 77.2 - - - +
437N THR* 1.3 57.0 + - - +
439N ALA* 3.4 6.1 + - - +
440N SER* 2.6 45.0 + - - -
462N GLY* 4.0 16.6 - - - -
463N ILE* 4.0 4.2 + - - +
464N GLU* 3.4 33.1 - - - +
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Residues in contact with THR 437 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N LYS* 4.1 39.6 - - + +
142N ASP* 5.1 9.5 - - + +
143N LEU* 4.5 10.7 - - + +
432N VAL* 3.1 19.1 + - - +
433N ARG 2.6 23.5 + - - -
434N LEU* 2.9 9.4 + - - -
436N ASP* 1.3 77.3 - - - +
438N VAL* 1.3 64.2 + - - +
440N SER* 3.3 13.4 + - - -
441N PHE* 3.4 27.1 + - + -
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Residues in contact with VAL 438 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143N LEU* 4.8 7.2 - - + -
366N GLU* 4.6 15.5 - - + +
367N HIS* 3.6 55.2 - - + +
370N VAL* 4.1 15.0 - - + +
434N LEU* 3.0 26.4 + - + +
435N LYS* 4.0 5.6 - - - +
437N THR* 1.3 77.6 - - - +
439N ALA* 1.3 61.5 + - - +
440N SER 3.3 0.9 + - - -
441N PHE 3.5 0.3 + - - -
442N LYS* 3.3 23.1 + - - +
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Residues in contact with ALA 439 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435N LYS 3.4 13.9 + - - +
436N ASP* 3.4 8.1 + - - +
438N VAL* 1.3 80.5 - - - +
440N SER* 1.3 62.5 + - - +
442N LYS* 4.0 12.6 - - - +
443N ALA* 3.3 24.4 + - - +
463N ILE* 5.8 0.7 - - - -
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Residues in contact with SER 440 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413N PHE* 4.1 18.6 - - - -
432N VAL* 5.3 1.3 - - - +
436N ASP* 2.6 27.7 + - - -
437N THR* 3.5 9.1 - - - -
438N VAL 3.1 0.2 - - - -
439N ALA* 1.3 80.3 - - - +
441N PHE* 1.3 61.0 + - - +
443N ALA* 3.7 3.5 + - - +
444N VAL* 3.2 25.7 + - - +
462N GLY* 4.6 1.2 - - - -
463N ILE* 3.1 44.0 + - - +
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Residues in contact with PHE 441 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139N LYS* 4.8 7.6 - - + -
143N LEU* 3.8 20.2 - - + -
370N VAL* 3.7 21.1 - - + -
374N VAL* 3.8 15.0 - - + -
410N ILE* 3.4 46.0 - - + -
413N PHE* 3.3 34.8 - + + -
414N LEU* 3.6 27.1 - - + -
437N THR* 3.4 28.9 + - + +
440N SER* 1.3 77.4 - - - +
442N LYS* 1.3 65.8 + - - +
444N VAL* 3.3 7.7 + - - +
445N LEU* 3.2 25.8 + - - +
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Residues in contact with LYS 442 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366N GLU* 2.7 46.9 + - - +
370N VAL* 3.8 24.1 - - + +
438N VAL* 3.3 18.8 + - - +
439N ALA* 4.0 12.1 - - - +
440N SER 3.4 0.2 - - - -
441N PHE* 1.3 78.3 - - - +
443N ALA* 1.3 64.7 + - - +
445N LEU* 3.2 23.3 + - + +
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Residues in contact with ALA 443 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439N ALA 3.3 16.0 + - - +
440N SER* 3.8 5.2 - - - +
442N LYS* 1.3 81.8 - - - +
444N VAL* 1.3 63.7 + - + +
445N LEU 4.2 2.1 - - - -
448N LYS* 3.5 45.2 + - - +
449N TYR* 3.9 23.6 - - + +
463N ILE* 5.5 4.7 - - + -
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Residues in contact with VAL 444 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ARG* 4.0 18.9 + - + +
409N LYS* 5.3 6.7 - - + -
410N ILE* 3.8 26.7 - - + -
413N PHE* 5.3 9.4 - - + -
440N SER 3.2 19.1 - - - +
441N PHE* 3.5 9.9 - - - +
442N LYS 3.2 0.6 - - - -
443N ALA* 1.3 76.6 - - + +
445N LEU* 1.3 65.3 + - + +
447N GLY* 3.3 16.5 - - - -
448N LYS 3.9 0.5 + - - -
449N TYR* 4.5 25.7 + - + +
450N ASP* 4.2 3.2 - - - +
457N PHE* 4.9 18.6 - - + -
463N ILE* 5.4 5.4 - - + -
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Residues in contact with LEU 445 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370N VAL* 4.1 20.4 - - + +
373N LYS* 3.5 46.7 - - + +
374N VAL* 4.5 8.3 - - + +
377N THR* 4.5 14.8 - - + +
406N ARG* 3.3 24.4 + - + +
410N ILE* 5.3 13.9 - - + -
441N PHE 3.2 14.9 + - - +
442N LYS* 3.2 16.9 + - - +
443N ALA 4.2 2.0 - - - -
444N VAL* 1.3 83.0 - - + +
447N GLY* 2.9 29.3 + - - -
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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