Contacts of the helix formed by residues 406 - 414 (chain D) 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 406 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D LYS* 3.4 25.3 - - - +
377D THR* 3.2 35.8 + - + -
402D LEU* 3.4 10.5 + - - +
403D THR* 3.4 30.8 + - - +
404D VAL 3.5 0.6 - - - -
405D GLU* 1.3 97.5 - - - +
407D ALA* 1.3 56.9 + - - +
408D ARG 3.3 0.4 - - - -
409D LYS* 3.7 8.7 - - + -
410D ILE* 2.8 39.7 + - + +
444D VAL* 4.3 16.8 - - + +
445D LEU* 3.3 43.8 + - - +
447D GLY* 5.0 8.8 - - - +
450D ASP* 4.9 3.6 - - - +
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Residues in contact with ALA 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D THR* 4.1 18.8 - - - +
378D LEU* 4.6 12.1 - - + +
380D THR* 6.2 0.2 - - + -
381D TYR* 4.3 26.7 - - + -
403D THR 3.9 2.9 + - - +
404D VAL* 3.6 17.2 + - - +
405D GLU 2.9 0.2 - - - -
406D ARG* 1.3 80.5 - - - +
408D ARG* 1.3 57.4 + - + +
409D LYS 3.1 1.3 + - - -
411D GLN* 3.0 35.4 + - - +
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Residues in contact with ARG 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 5.3 8.1 + - - -
342D LEU* 5.9 1.2 - - - +
381D TYR* 4.8 21.6 + - + -
404D VAL 5.0 5.2 - - - +
405D GLU* 3.1 12.4 + - - +
407D ALA* 1.3 80.3 - - + +
409D LYS* 1.3 59.0 + - - +
411D GLN* 5.2 0.2 - - - -
412D ARG* 3.4 61.0 - - - +
454D GLU* 4.6 22.8 + - - +
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Residues in contact with LYS 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405D GLU* 3.5 17.8 + - - +
406D ARG* 3.3 11.2 + - + +
407D ALA 3.1 0.4 - - - -
408D ARG* 1.3 81.9 - - - +
410D ILE* 1.3 68.5 + - + +
411D GLN 3.3 0.7 - - - -
412D ARG* 3.4 6.6 + - - +
413D PHE* 3.1 21.3 + - - +
444D VAL* 5.2 10.1 - - + -
449D TYR 3.7 19.5 - - - +
450D ASP* 2.7 44.9 + - - +
452D ILE 3.9 19.3 + - - +
453D PRO* 4.5 10.4 - - - +
454D GLU 5.0 6.7 - - - +
457D PHE* 4.1 22.7 - - + +
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Residues in contact with ILE 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D VAL* 4.1 20.6 - - + +
377D THR* 5.2 3.8 - - + -
378D LEU* 4.9 10.5 - - + -
406D ARG* 2.8 30.1 + - + +
407D ALA 4.9 0.2 - - - +
409D LYS* 1.3 73.4 - - + +
411D GLN* 1.3 67.4 - - - +
413D PHE* 3.0 18.8 + - + +
414D LEU* 3.2 16.8 + - + +
441D PHE* 3.5 34.9 - - + -
444D VAL* 3.5 32.3 - - + -
445D LEU* 4.2 19.1 - - + -
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Residues in contact with GLN 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D ILE* 4.7 18.2 - - + +
342D LEU* 4.0 22.5 - - - +
344D ILE* 3.2 27.2 - - + +
350D PRO* 5.4 10.0 - - + +
378D LEU* 4.8 15.0 - - + +
381D TYR* 6.0 2.4 - - - -
407D ALA* 3.0 22.1 + - - +
409D LYS 3.3 0.4 - - - -
410D ILE* 1.3 78.9 - - - +
412D ARG* 1.3 78.7 + - - +
414D LEU* 3.7 26.0 + - + +
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Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 5.1 2.8 + - - -
342D LEU* 3.7 33.2 + - - +
344D ILE* 3.9 20.1 - - + +
408D ARG* 3.4 65.2 - - - +
409D LYS* 3.4 8.9 + - - +
410D ILE 3.1 0.4 - - - -
411D GLN* 1.3 96.5 + - - +
413D PHE* 1.3 57.5 + - - +
414D LEU 3.1 5.3 + - - -
415D SER* 2.9 28.1 + - - -
454D GLU* 4.7 28.3 + - - +
457D PHE* 3.2 9.8 - - + +
458D TYR* 4.0 28.3 - - + -
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Residues in contact with PHE 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LYS* 3.1 28.4 + - + +
409D LYS 3.1 9.6 + - - +
410D ILE* 3.0 14.1 + - + +
412D ARG* 1.3 74.4 - - - +
414D LEU* 1.3 59.9 + - - +
415D SER 3.2 0.7 - - - -
437D THR* 5.7 0.2 - - + -
440D SER* 3.2 33.7 - - - -
441D PHE* 3.4 41.2 - + - -
444D VAL* 5.0 8.1 - - + -
457D PHE* 3.2 46.4 - + + +
460D VAL* 3.8 7.6 - - + -
461D GLY 4.4 1.8 - - - -
462D GLY* 3.5 15.0 - - - -
466D VAL* 3.5 24.7 - - + -
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Residues in contact with LEU 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LYS* 4.1 9.1 - - - +
140D VAL* 3.7 64.9 + - + +
143D LEU* 5.5 1.1 - - + -
144D LEU* 4.3 16.8 - - + -
344D ILE* 4.5 5.4 - - + -
345D TYR 4.5 0.7 - - - +
346D PRO* 4.8 0.2 - - - +
350D PRO* 4.1 19.3 - - + -
374D VAL* 5.3 1.8 - - + -
378D LEU* 5.1 5.2 - - + -
410D ILE* 3.2 21.1 + - + +
411D GLN* 3.7 20.4 - - + +
412D ARG 3.1 1.2 - - - -
413D PHE* 1.3 77.7 - - - +
415D SER* 1.3 62.7 + - - +
416D GLN* 3.5 2.6 + - - +
441D PHE* 3.6 26.2 - - + -
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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