Contacts of the helix formed by residues 406 - 423 (chain R) in PDB entry 5IJO
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 ASP 406 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405R ALA* 1.3 87.6 - - + +
407R GLU* 1.3 62.9 + - - +
409R GLN* 3.0 21.5 + - - +
410R LEU* 3.2 9.8 + - - +
343S ALA* 5.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 407 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403R ILE* 4.4 9.4 - - + +
404R GLN* 4.2 20.3 - - + -
405R ALA* 3.0 2.2 - - - +
406R ASP* 1.3 78.8 - - - +
408R GLU* 1.3 59.1 + - - +
410R LEU* 3.2 10.1 + - + +
411R ARG* 2.8 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 408 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404R GLN* 4.9 8.5 - - + +
405R ALA 3.5 12.9 + - - +
406R ASP 3.3 0.8 - - - -
407R GLU* 1.3 79.0 - - - +
409R GLN* 1.4 41.8 + - - +
411R ARG* 3.1 9.6 + - + +
412R VAL* 2.5 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 409 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405R ALA 4.4 2.1 + - - +
406R ASP* 3.0 15.7 + - - +
408R GLU* 1.4 71.6 - - - +
410R LEU* 1.3 68.5 + - - +
411R ARG 3.1 0.7 - - - -
412R VAL* 3.9 8.1 - - - +
413R GLN* 3.2 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406R ASP 3.2 5.4 + - - +
407R GLU* 3.2 14.9 + - + +
409R GLN* 1.3 81.3 - - - +
411R ARG* 1.3 65.6 + - + +
413R GLN* 3.2 6.5 + - - +
414R LEU* 3.0 23.0 + - - +
343S ALA* 6.2 4.5 - - + -
346S PHE* 5.8 5.6 - - + -
347S ARG* 5.2 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 411 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407R GLU* 2.8 18.1 + - + +
408R GLU* 3.1 11.4 + - + +
410R LEU* 1.3 80.2 - - - +
412R VAL* 1.4 53.5 + - - +
414R LEU* 3.7 7.8 - - - +
415R ASP* 3.0 27.7 + - - +
433T THR* 6.1 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408R GLU 2.5 18.0 + - - +
409R GLN* 3.9 9.6 - - - +
410R LEU 3.3 0.8 - - - -
411R ARG* 1.4 69.8 - - - +
413R GLN* 1.4 60.7 + - - +
415R ASP* 3.3 7.0 + - - +
416R THR* 3.2 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 413 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409R GLN 3.2 9.6 + - - +
410R LEU* 3.2 10.9 + - - +
412R VAL* 1.4 72.1 - - - +
414R LEU* 1.3 66.8 + - - +
416R THR* 3.2 6.7 + - - -
417R ILE* 3.1 22.7 + - - +
350S VAL* 4.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410R LEU 3.0 13.7 + - - +
411R ARG* 3.7 10.1 - - - +
413R GLN* 1.3 79.3 - - - +
415R ASP* 1.4 61.2 + - - +
417R ILE* 3.5 5.1 + - - +
418R GLN* 3.0 24.4 + - - +
350S VAL* 5.7 2.9 - - - +
437T ALA* 5.6 11.7 - - + -
440T ILE* 5.8 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 415 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411R ARG 3.0 14.3 + - - +
412R VAL* 3.6 10.1 - - - +
413R GLN 3.2 0.2 - - - -
414R LEU* 1.4 72.3 - - - +
416R THR* 1.4 70.3 - - - +
418R GLN* 3.1 12.1 + - - +
419R GLY 3.5 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412R VAL 3.2 11.1 + - - -
413R GLN* 3.8 7.9 - - - -
414R LEU 3.2 0.2 - - - -
415R ASP* 1.4 81.5 - - - +
417R ILE* 1.4 64.5 + - - +
418R GLN 3.1 0.2 + - - -
419R GLY 3.9 0.2 + - - -
420R GLU* 3.3 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413R GLN 3.1 13.4 + - - +
414R LEU* 4.0 4.9 - - - +
416R THR* 1.4 77.9 - - - +
418R GLN* 1.3 66.7 + - - +
420R GLU* 3.1 21.2 + - - +
421R LEU* 3.2 7.3 + - - +
354S GLU* 6.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 418 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414R LEU 3.0 18.0 + - - +
415R ASP* 3.1 5.6 + - - +
416R THR 3.1 2.6 - - - -
417R ILE* 1.3 75.1 - - - +
419R GLY* 1.3 67.7 + - - +
420R GLU 3.0 1.2 + - - -
421R LEU* 3.2 18.6 - - - +
422R ASN* 3.3 3.6 + - - +
440T ILE* 4.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 419 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415R ASP 3.5 8.7 + - - -
416R THR 4.3 0.2 - - - -
418R GLN* 1.3 78.9 - - - +
420R GLU* 1.5 64.0 + - - +
421R LEU 2.9 0.4 - - - -
422R ASN* 3.0 18.5 - - - +
423R ALA* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416R THR 3.3 14.4 + - - +
417R ILE* 3.1 16.5 + - - +
418R GLN 3.0 2.2 - - - -
419R GLY* 1.5 67.7 - - - +
421R LEU* 1.4 67.6 - - - +
423R ALA 2.7 12.0 + - - -
424R PRO 4.1 2.1 - - - -
425R THR 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417R ILE 3.7 6.7 - - - +
418R GLN* 3.2 12.8 - - - +
420R GLU* 1.4 78.0 - - - +
422R ASN* 1.4 69.6 - - - +
423R ALA* 2.6 0.9 + - - -
424R PRO 3.8 2.3 - - - -
425R THR 4.2 0.5 + - - -
426R GLN* 4.0 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 422 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418R GLN 3.3 2.2 + - - +
419R GLY* 3.0 24.7 - - - +
420R GLU 2.9 0.2 - - - -
421R LEU* 1.4 86.2 - - - +
423R ALA* 1.3 98.6 - - + +
425R THR 3.8 1.2 + - - -
426R GLN* 4.0 3.1 + - - +
427R PHE* 4.2 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 423 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419R GLY 3.1 3.6 + - - +
420R GLU 2.7 8.7 + - - -
421R LEU 2.6 4.6 + - - -
422R ASN* 1.3 114.9 - - + +
424R PRO* 1.3 73.9 - - + +
426R GLN 3.8 0.7 + - - -
427R PHE* 3.8 9.4 + - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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