Contacts of the helix formed by residues 399 - 415 (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 GLN 399 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397N SER* 3.6 5.2 + - - +
398N GLU* 1.3 94.3 + - + +
400N ASP* 1.3 67.8 + - - +
402N LEU* 3.5 9.0 - - + +
403N THR* 3.1 26.5 + - - +
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Residues in contact with ASP 400 (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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384N LEU* 4.9 14.8 - - + +
395N GLU 5.1 0.9 - - - +
396N LEU* 3.8 19.0 - - + +
397N SER* 2.8 40.9 + - - +
398N GLU 3.4 0.2 - - - -
399N GLN* 1.3 77.6 - - - +
401N LYS* 1.3 64.2 + - - +
402N LEU 3.0 5.0 + - - -
403N THR* 3.2 5.0 + - - -
404N VAL* 3.0 27.9 + - + +
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Residues in contact with LYS 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393N MET* 5.3 9.4 - - + +
396N LEU* 3.8 26.6 - - + +
397N SER 3.2 18.1 + - - +
398N GLU* 4.2 16.8 - - - +
400N ASP* 1.3 79.6 - - - +
402N LEU* 1.3 64.7 + - - +
404N VAL* 3.8 9.6 - - - +
405N GLU* 3.3 22.2 + - - +
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Residues in contact with LEU 402 (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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398N GLU* 3.4 31.0 - - - +
399N GLN* 3.5 12.1 + - + +
400N ASP 3.0 0.6 - - - -
401N LYS* 1.3 86.6 - - + +
403N THR* 1.3 63.2 + - + +
405N GLU* 3.7 8.9 + - - +
406N ARG* 2.9 44.4 + - - +
450N ASP* 4.8 8.1 - - - +
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Residues in contact with THR 403 (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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377N THR* 3.7 25.5 - - + +
380N THR* 5.0 6.7 + - - -
384N LEU* 5.9 0.9 - - - +
399N GLN 3.1 15.5 + - - +
400N ASP* 3.2 7.3 + - - -
402N LEU* 1.3 81.3 - - + +
404N VAL* 1.3 64.7 + - - +
405N GLU 3.2 0.7 - - - -
406N ARG* 3.4 20.4 + - - +
407N ALA* 3.2 18.7 + - - +
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Residues in contact with VAL 404 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381N TYR* 4.3 21.7 - - + -
384N LEU* 3.5 31.2 - - + -
388N ILE* 5.1 6.1 - - + -
393N MET* 6.2 0.4 - - + -
396N LEU* 4.3 18.6 - - + -
400N ASP 3.0 27.9 + - - +
401N LYS* 3.8 9.4 - - - +
402N LEU 3.3 0.2 - - - -
403N THR* 1.3 77.6 - - - +
405N GLU* 1.3 64.4 + - - +
406N ARG 3.4 0.3 + - - -
407N ALA* 3.5 14.6 + - - +
408N ARG* 3.5 14.6 + - + +
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Residues in contact with GLU 405 (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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401N LYS 3.3 13.8 + - - +
402N LEU* 3.8 8.8 - - - +
403N THR 3.2 0.4 - - - -
404N VAL* 1.3 81.4 - - - +
406N ARG* 1.3 62.5 + - - +
409N LYS* 3.1 51.7 + - - +
450N ASP* 3.4 34.9 - - - +
454N GLU* 3.6 15.0 - - - +
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Residues in contact with ARG 406 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N THR* 5.1 5.4 - - + -
402N LEU* 2.9 45.3 + - - +
403N THR* 3.4 20.9 + - - +
404N VAL 3.2 0.6 - - - -
405N GLU* 1.3 86.2 - - - +
407N ALA* 1.3 53.2 + - - +
408N ARG 3.2 0.4 - - - -
409N LYS* 3.0 10.6 + - + +
410N ILE* 2.7 45.9 + - + +
444N VAL* 4.0 22.0 + - + +
445N LEU* 3.3 35.6 + - + -
447N GLY* 3.3 21.0 - - - +
449N TYR 6.1 0.2 - - - +
450N ASP* 3.5 23.5 + - - +
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Residues in contact with ALA 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N THR* 4.1 18.8 - - + +
378N LEU* 4.1 8.6 - - + +
381N TYR* 3.7 36.8 - - + -
403N THR 3.2 15.7 + - - +
404N VAL* 3.9 4.5 - - - +
405N GLU 3.5 0.6 - - - -
406N ARG* 1.3 77.4 - - - +
408N ARG* 1.3 58.5 + - - +
410N ILE* 4.1 5.1 - - - +
411N GLN* 3.0 32.3 + - - +
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Residues in contact with ARG 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381N TYR* 3.2 34.2 + - + +
404N VAL* 3.5 12.0 + - + +
405N GLU 4.3 0.2 - - - +
406N ARG 3.2 0.4 - - - -
407N ALA* 1.3 78.1 - - - +
409N LYS* 1.3 57.9 + - - +
411N GLN* 4.3 12.1 - - - +
412N ARG* 3.2 58.7 + - - +
454N GLU* 3.1 35.5 + - - +
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Residues in contact with LYS 409 (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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405N GLU* 3.1 41.9 + - - +
406N ARG* 3.0 14.5 + - + +
408N ARG* 1.3 78.4 - - - +
410N ILE* 1.3 61.2 + - + +
412N ARG* 3.4 1.4 + - - -
413N PHE* 2.9 28.6 + - - +
444N VAL* 5.3 5.8 - - + -
449N TYR 3.4 6.1 + - - +
450N ASP* 3.2 43.0 + - - +
452N ILE 3.7 16.0 + - - -
454N GLU* 3.5 24.2 - - + -
457N PHE* 3.6 38.6 - - + +
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Residues in contact with ILE 410 (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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374N VAL* 4.0 24.5 - - + +
377N THR* 6.2 3.4 - - + -
378N LEU* 4.8 7.6 - - + -
406N ARG* 2.7 29.1 + - + +
407N ALA* 4.1 6.1 - - - +
409N LYS* 1.3 70.9 - - - +
411N GLN* 1.3 67.4 + - - +
413N PHE* 2.9 18.1 + - + +
414N LEU* 3.0 17.5 + - + +
441N PHE* 3.4 41.3 - - + +
444N VAL* 3.8 31.9 - - + -
445N LEU* 5.3 11.2 - - + -
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Residues in contact with GLN 411 (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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339N ILE* 5.6 6.4 - - + +
342N LEU* 3.7 28.4 - - - +
344N ILE* 3.9 26.7 - - + +
350N PRO* 6.0 3.9 - - + +
378N LEU* 4.1 16.3 - - + +
381N TYR* 4.0 25.1 + - - -
407N ALA 3.0 18.8 + - - +
408N ARG* 4.5 10.2 - - - +
410N ILE* 1.3 77.5 - - - +
412N ARG* 1.3 63.4 + - + +
414N LEU* 3.6 27.1 - - + +
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Residues in contact with ARG 412 (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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342N LEU 5.9 0.6 + - - -
344N ILE* 4.7 14.6 - - + +
408N ARG* 3.2 52.5 + - + +
409N LYS 3.4 4.1 + - - +
410N ILE 3.1 0.4 - - - -
411N GLN* 1.3 78.4 - - + +
413N PHE* 1.3 61.9 + - - +
414N LEU 3.1 2.0 - - - -
415N SER* 2.6 27.9 + - - -
454N GLU* 4.3 24.0 + - - +
455N HIS* 5.0 11.1 + - - +
457N PHE* 3.2 10.8 - - + +
458N TYR* 3.6 43.7 - - + +
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Residues in contact with PHE 413 (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* 2.7 43.7 + - + -
409N LYS 2.9 17.9 + - - +
410N ILE* 2.9 12.9 + - + +
412N ARG* 1.3 75.9 - - - +
414N LEU* 1.3 58.1 + - - +
440N SER* 4.1 17.0 - - - -
441N PHE* 3.3 43.1 - + - -
444N VAL* 5.3 5.2 - - + -
457N PHE* 3.5 33.8 + + + -
460N VAL* 4.0 5.4 - - + -
462N GLY* 3.7 23.1 - - - -
463N ILE* 4.1 9.9 - - + -
466N VAL* 3.4 26.0 - - + -
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Residues in contact with LEU 414 (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* 3.6 12.8 - - - +
140N VAL* 3.5 46.5 - - + +
143N LEU* 4.8 4.9 - - + -
144N LEU* 4.5 11.4 - - + -
344N ILE* 5.1 4.3 - - + -
346N PRO* 4.7 0.3 - - - +
348N VAL 5.8 0.4 - - - +
350N PRO* 4.1 30.7 - - + -
374N VAL* 5.4 0.9 - - + -
378N LEU* 4.5 9.2 - - + -
410N ILE* 3.0 17.1 + - + +
411N GLN* 3.6 22.0 - - + +
412N ARG 3.1 0.2 - - - -
413N PHE* 1.3 74.5 - - - +
415N SER* 1.3 68.8 + - - +
416N GLN* 3.6 2.9 + - - +
441N PHE* 3.6 28.3 - - + -
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Residues in contact with SER 415 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139N LYS* 2.9 18.7 + - - -
344N ILE* 3.7 23.4 - - - +
345N TYR 3.0 24.9 - - - -
346N PRO* 4.4 1.3 - - - -
411N GLN 4.2 1.2 + - - -
412N ARG 2.6 23.5 + - - +
413N PHE 3.3 1.4 - - - +
414N LEU* 1.3 81.4 - - - +
416N GLN* 1.3 56.2 + - - +
458N TYR* 4.1 8.5 - - - -
459N MET* 3.1 23.4 + - - -
460N VAL 3.9 4.9 + - - +
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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
------------------------------------------------------------
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