Contacts of the helix formed by residues 409 - 429 (chain D) in PDB entry 6F0X
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 GLY 409 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405D VAL* 5.3 3.4 - - - -
406D THR* 3.1 12.3 + - - -
407D ILE 3.0 7.9 + - - -
408D GLU* 1.3 75.2 - - - +
410D PHE* 1.3 65.8 + - - +
412D GLN* 3.1 35.1 + - - +
413D ALA* 3.8 4.9 + - - +
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Residues in contact with PHE 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 4.6 4.9 - - + -
338D LEU* 4.0 16.4 - - + -
344D ILE* 3.8 14.4 - - + -
392D PRO* 3.6 44.2 - - + -
395D ALA* 4.6 2.8 - - + +
396D HIS* 4.2 21.3 - + + -
400D VAL* 4.7 15.3 - - + -
405D VAL* 4.8 6.9 - - + +
406D THR 3.1 7.1 + - - +
407D ILE* 3.5 36.6 - - + -
408D GLU 3.7 1.3 - - - +
409D GLY* 1.3 79.0 - - - +
411D LEU* 1.3 64.5 + - + +
413D ALA* 3.5 5.4 + - - +
414D LEU* 2.9 49.0 + - + +
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D LEU* 4.8 8.5 - - + -
369D LEU 4.3 15.7 - - - +
372D LEU* 4.1 20.0 - - + -
373D LEU* 4.6 17.9 - - + +
376D ILE* 4.2 12.9 - - + +
407D ILE* 4.2 6.5 - - + -
408D GLU* 3.4 43.5 - - + +
409D GLY 3.1 1.8 - - - -
410D PHE* 1.3 97.9 - - + +
412D GLN* 1.3 60.0 + - - +
414D LEU* 3.2 21.2 - - + +
415D SER* 2.9 29.1 + - - -
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Residues in contact with GLN 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D LEU* 5.2 5.9 - - + +
408D GLU 4.4 5.4 + - - +
409D GLY* 3.1 27.3 + - - +
411D LEU* 1.3 78.1 - - - +
413D ALA* 1.3 67.3 + - + +
415D SER* 3.2 9.0 + - - -
416D LEU* 3.0 32.6 + - + +
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Residues in contact with ALA 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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395D ALA* 4.5 4.5 - - + +
399D TYR* 3.6 36.1 - - + +
400D VAL* 5.5 4.9 - - + -
409D GLY 4.5 5.4 - - - +
410D PHE* 3.5 7.5 + - - +
411D LEU 3.3 0.2 - - - -
412D GLN* 1.3 81.6 - - + +
414D LEU* 1.3 66.0 + - - +
416D LEU* 3.1 19.1 + - + +
417D ALA* 2.9 22.5 + - - +
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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
----------------------------------------------------------
331D TYR* 5.4 8.7 - - + -
335D LEU* 6.1 0.7 - - + -
373D LEU* 4.9 6.5 - - + -
376D ILE* 4.3 17.0 - - + -
391D LEU* 4.2 11.2 - - + -
392D PRO* 3.7 40.2 - - + -
395D ALA* 3.7 15.6 - - + +
410D PHE* 2.9 27.2 + - + +
411D LEU* 3.2 32.1 + - + +
413D ALA* 1.3 75.9 - - - +
415D SER* 1.3 57.5 + - - +
417D ALA* 3.0 6.3 + - + +
418D VAL* 2.9 35.6 + - + +
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Residues in contact with SER 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D ILE* 4.7 10.3 - - - +
379D LYS* 2.7 37.2 + - - +
411D LEU 2.9 12.2 + - - -
412D GLN* 3.2 12.3 + - - -
414D LEU* 1.3 77.5 - - - +
416D LEU* 1.3 62.0 + - - +
418D VAL* 3.1 11.8 + - - +
419D ASP* 2.9 29.0 + - - +
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Residues in contact with LEU 416 (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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399D TYR* 4.5 25.2 + - + +
412D GLN* 3.0 20.0 + - + +
413D ALA* 3.1 26.5 - - + +
415D SER* 1.3 78.2 - - - +
417D ALA* 1.3 57.3 + - - +
419D ASP* 3.2 10.9 + - + +
420D LYS* 2.9 26.2 + - - +
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Residues in contact with ALA 417 (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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391D LEU* 4.8 9.0 - - + -
394D LEU* 5.2 4.9 - - + -
395D ALA* 4.1 20.9 - - + +
398D LEU* 5.7 1.3 - - + -
399D TYR* 4.0 19.0 - - + -
413D ALA 2.9 12.2 + - - +
414D LEU* 3.5 7.4 - - + +
416D LEU* 1.3 73.0 - - - +
418D VAL* 1.3 60.8 + - - +
420D LYS* 3.1 12.5 - - + +
421D GLN* 2.9 35.9 + - + +
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Residues in contact with VAL 418 (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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331D TYR* 5.1 0.4 - - - +
376D ILE* 4.6 15.3 - - + -
379D LYS* 4.5 14.4 - - + +
380D SER* 4.7 8.5 - - - +
383D LEU* 4.7 10.5 - - + -
391D LEU* 4.3 22.2 - - + -
414D LEU* 2.9 25.5 + - + +
415D SER* 3.1 15.2 + - - +
417D ALA* 1.3 76.0 - - - +
419D ASP* 1.3 66.8 + - - +
421D GLN* 3.1 10.9 + - - +
422D PHE* 3.0 47.1 + - + -
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Residues in contact with ASP 419 (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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379D LYS* 4.8 12.1 + - - +
415D SER* 2.9 26.9 + - - +
416D LEU* 3.6 13.8 - - + +
418D VAL* 1.3 77.5 - - - +
420D LYS* 1.3 66.2 + - - +
422D PHE* 3.2 18.2 + - - +
423D GLU* 3.0 26.7 + - + +
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Residues in contact with LYS 420 (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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398D LEU* 3.6 29.0 - - + +
399D TYR* 3.4 25.9 + - + +
416D LEU 2.9 14.2 + - - +
417D ALA* 3.1 12.8 - - + +
418D VAL 3.1 0.2 - - - -
419D ASP* 1.3 73.4 - - - +
421D GLN* 1.3 67.2 + - - +
423D GLU* 2.8 10.3 + - - +
424D GLU* 2.8 51.0 + - + +
148E HIS* 4.2 23.3 + - - +
315E ILE* 5.0 10.5 - - - +
316E LYS 5.4 0.4 - - - -
317E GLN* 5.0 11.5 + - - -
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Residues in contact with GLN 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D LEU* 5.0 13.0 - - + -
387D VAL* 3.7 24.6 - - + +
391D LEU* 3.6 21.1 - - + +
394D LEU* 4.1 11.9 - - - +
398D LEU* 6.3 0.6 - - - +
417D ALA* 2.9 21.6 + - - +
418D VAL* 3.3 8.5 - - - +
420D LYS* 1.3 71.9 - - - +
422D PHE* 1.3 66.5 + - - +
424D GLU* 2.8 38.2 + - - +
425D ARG* 3.0 26.8 + - - +
313E ALA 4.7 6.5 - - - +
314E ASP 3.8 19.4 + - - -
315E ILE* 5.1 2.0 - - - +
316E LYS* 5.3 5.2 - - - +
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Residues in contact with PHE 422 (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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379D LYS* 3.1 29.6 - - + -
381D GLU 4.3 12.3 - - - -
382D GLY* 5.3 2.9 - - - -
383D LEU* 4.4 24.9 - - + +
418D VAL* 3.0 45.6 + - + -
419D ASP* 3.3 17.3 - - - +
421D GLN* 1.3 78.9 - - - +
423D GLU* 1.3 61.4 + - + +
425D ARG* 3.1 9.9 + - - +
426D LYS* 2.9 25.2 + - - +
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Residues in contact with GLU 423 (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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419D ASP* 3.0 12.9 + - + +
420D LYS* 2.8 11.7 + - - +
422D PHE* 1.3 78.9 - - + +
424D GLU* 1.3 57.2 + - - +
426D LYS* 3.2 28.6 + - + +
427D LYS* 2.9 38.2 + - + +
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Residues in contact with GLU 424 (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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420D LYS* 2.8 49.1 + - + +
421D GLN* 2.8 51.1 + - - +
423D GLU* 1.3 72.3 - - - +
425D ARG* 1.3 66.5 + - - +
427D LYS* 3.1 8.6 + - - +
428D LEU* 3.0 19.8 + - - +
313E ALA 5.7 0.2 - - - +
315E ILE* 5.3 1.9 - - - +
316E LYS* 3.5 50.0 + - + +
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Residues in contact with ARG 425 (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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382D GLY 2.7 27.9 + - - -
383D LEU* 3.0 39.8 - - - +
384D SER* 3.5 9.7 - - - +
387D VAL* 5.2 4.0 - - - +
421D GLN* 3.0 12.4 + - - +
422D PHE* 3.5 9.4 - - - +
424D GLU* 1.3 77.3 - - - +
426D LYS* 1.3 65.1 + - - +
427D LYS 3.1 0.2 + - - -
429D ALA* 2.8 30.7 + - - +
311E ASP* 3.9 25.6 + - - +
316E LYS* 2.9 27.0 - - - +
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Residues in contact with LYS 426 (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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422D PHE 2.9 12.6 + - - +
423D GLU* 3.2 32.8 + - + +
425D ARG* 1.3 76.9 - - - +
427D LYS* 1.3 69.0 + - + +
429D ALA* 4.5 6.9 - - - +
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Residues in contact with LYS 427 (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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423D GLU* 2.9 22.3 + - + +
424D GLU* 3.1 7.8 + - - +
426D LYS* 1.3 87.2 - - + +
428D LEU* 1.3 66.4 + - - +
429D ALA* 4.7 0.7 - - - +
178E HIS* 5.3 2.0 - - + +
302E THR* 4.0 12.3 - - - +
318E TYR* 4.2 42.4 - - + -
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Residues in contact with LEU 428 (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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424D GLU 3.0 15.1 + - - +
427D LYS* 1.3 82.1 - - - +
429D ALA* 1.3 70.1 + - - +
178E HIS* 3.9 26.5 - - + +
302E THR* 3.6 20.7 - - - +
303E GLU* 3.6 14.4 - - - +
305E ILE* 5.7 6.3 - - + -
310E VAL* 5.4 6.7 - - + -
316E LYS* 4.5 14.6 - - + +
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Residues in contact with ALA 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ARG* 2.8 24.9 + - - +
426D LYS* 4.5 6.7 - - - +
427D LYS 4.7 0.4 - - - +
428D LEU* 1.3 82.2 - - - +
303E GLU* 3.2 37.4 - - - +
304E LYS 4.8 2.2 + - - -
305E ILE* 6.1 3.8 - - - -
306E ASP 5.2 8.4 - - - +
310E VAL* 5.6 8.7 - - - +
316E LYS* 5.1 1.7 - - - +
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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