Contacts of the helix formed by residues 434 - 446 (chain M) 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 LEU 434 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133M ILE* 4.1 30.3 - - + -
135M GLU* 2.7 35.3 + - + +
142M ASP* 3.4 40.6 - - + +
367M HIS* 3.8 20.4 - - + +
433M ARG* 1.3 70.6 - - - +
435M LYS* 1.3 89.7 + - + +
436M ASP 3.1 1.3 - - - -
437M THR* 3.2 13.9 + - - -
438M VAL* 3.5 13.1 + - + +
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Residues in contact with LYS 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133M ILE* 6.3 0.8 - - - +
135M GLU* 5.5 3.3 + - - +
433M ARG* 4.4 3.0 - - + +
434M LEU* 1.3 101.6 - - + +
436M ASP* 1.3 61.4 + - - +
438M VAL* 3.2 23.6 - - + +
439M ALA* 3.6 11.8 + - - +
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Residues in contact with ASP 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432M VAL* 4.5 8.5 - - + +
433M ARG* 4.1 22.6 + - + +
434M LEU 3.1 0.8 - - - -
435M LYS* 1.3 79.9 - - - +
437M THR* 1.3 58.9 + - - +
439M ALA* 4.6 3.0 - - - +
440M SER* 3.0 23.9 + - - -
462M GLY* 4.1 18.8 - - - -
463M ILE* 4.4 8.0 + - - +
464M GLU* 3.1 27.2 - - - +
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Residues in contact with THR 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M ILE 5.5 0.2 - - - -
139M LYS* 3.9 32.5 - - + +
142M ASP* 5.3 5.7 + - + +
143M LEU* 4.4 11.7 - - + +
432M VAL* 3.4 14.3 + - - +
433M ARG 2.7 22.9 + - - -
434M LEU* 3.2 9.1 + - - -
436M ASP* 1.3 77.0 - - - +
438M VAL* 1.3 61.7 + - - +
440M SER* 3.2 3.7 + - - -
441M PHE* 2.9 60.3 + - + -
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Residues in contact with VAL 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M LEU* 3.6 25.6 - - + -
366M GLU* 5.7 4.0 - - + -
367M HIS* 3.3 48.2 - - + +
370M VAL* 3.7 12.2 - - + +
434M LEU* 3.5 11.0 + - + +
435M LYS* 3.2 21.3 - - + +
437M THR* 1.3 75.3 - - - +
439M ALA* 1.3 64.3 + - + +
441M PHE 3.4 0.2 + - - -
442M LYS* 3.0 29.9 + - - +
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Residues in contact with ALA 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435M LYS 3.6 13.8 + - - +
436M ASP* 4.6 3.4 - - - +
437M THR 3.4 0.4 - - - -
438M VAL* 1.3 83.8 - - + +
440M SER* 1.3 62.0 + - - +
442M LYS* 3.5 10.0 + - - +
443M ALA* 3.2 21.0 + - - +
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Residues in contact with SER 440 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413M PHE* 3.4 17.8 - - - -
436M ASP 3.0 21.2 + - - -
437M THR* 3.2 7.8 + - - -
439M ALA* 1.3 80.2 - - - +
441M PHE* 1.3 63.1 + - - +
443M ALA* 3.1 19.8 + - - +
444M VAL* 3.3 9.9 + - - +
462M GLY* 5.3 1.1 - - - -
463M ILE* 3.0 47.9 + - - +
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Residues in contact with PHE 441 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139M LYS* 4.6 7.9 - - + -
143M LEU* 4.0 12.8 - - + -
370M VAL* 4.1 13.5 - - + -
374M VAL* 4.1 13.5 - - + -
410M ILE* 3.6 41.7 - - + -
413M PHE* 3.3 40.8 - + - -
414M LEU* 3.5 26.7 - - + -
437M THR* 2.9 47.5 + - + +
438M VAL 4.1 2.5 - - - +
440M SER* 1.3 73.8 - - - +
442M LYS* 1.3 60.0 + - - +
444M VAL* 3.1 7.0 + - - +
445M LEU* 2.9 35.7 + - - +
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Residues in contact with LYS 442 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366M GLU* 3.2 30.1 - - + +
370M VAL* 3.9 16.9 - - + +
438M VAL 3.0 17.7 + - - +
439M ALA* 3.7 10.8 - - - +
440M SER 3.3 0.2 - - - -
441M PHE* 1.3 76.8 - - - +
443M ALA* 1.3 61.8 + - - +
445M LEU* 3.7 11.8 - - + +
446M GLU* 2.7 57.4 + - + +
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Residues in contact with ALA 443 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439M ALA 3.2 9.8 + - - +
440M SER* 3.1 13.1 + - - +
441M PHE 3.1 0.4 - - - -
442M LYS* 1.3 81.8 - - - +
444M VAL* 1.3 61.7 + - - +
445M LEU 3.4 0.2 + - - -
446M GLU* 3.6 5.2 + - - -
448M LYS* 3.3 45.0 + - + +
449M TYR* 3.5 26.2 - - + +
463M ILE* 5.2 1.6 - - + -
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Residues in contact with VAL 444 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406M ARG* 4.1 11.6 - - + +
409M LYS* 5.3 10.3 - - + -
410M ILE* 3.5 29.6 - - + -
413M PHE* 4.8 11.7 - - + -
440M SER 3.7 12.8 - - - +
441M PHE* 3.1 9.9 + - - +
443M ALA* 1.3 76.1 - - - +
445M LEU* 1.3 63.8 + - - +
447M GLY* 3.1 13.9 + - - -
448M LYS 4.8 1.3 - - - +
449M TYR* 4.4 18.6 - - + +
450M ASP* 4.1 6.7 - - - +
457M PHE* 4.3 28.5 - - + -
463M ILE* 4.4 5.8 - - + -
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Residues in contact with LEU 445 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370M VAL* 3.7 37.7 - - + +
373M LYS* 3.8 28.3 - - + -
374M VAL* 4.2 14.4 - - + +
377M THR* 4.1 23.1 - - + +
406M ARG* 2.8 30.4 + - + +
410M ILE* 4.6 16.6 - - + -
441M PHE 2.9 24.3 + - - +
442M LYS* 3.7 8.1 - - + +
443M ALA 3.3 0.2 - - - -
444M VAL* 1.3 72.5 - - - +
446M GLU* 1.3 58.1 + - + +
447M GLY 2.9 5.2 - - - -
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Residues in contact with GLU 446 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406M ARG* 4.1 6.0 + - - -
442M LYS* 2.7 52.5 + - + +
443M ALA* 3.6 4.8 + - - +
444M VAL 3.4 0.6 - - - -
445M LEU* 1.3 75.8 - - + +
447M GLY* 1.3 62.8 + - - +
448M LYS* 3.1 32.5 + - + +
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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