Contacts of the helix formed by residues 400 - 418 (chain J) in PDB entry 3KDO
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 400 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TYR* 5.1 5.6 - - - -
395J LEU 4.4 2.2 - - - -
397J HIS* 3.1 20.0 + - - +
398J PRO 3.4 1.6 + - - -
399J ASP* 1.3 82.3 - - - +
401J PRO* 1.3 77.0 - - - +
402J ALA 3.6 1.6 - - - -
403J ALA* 3.3 1.6 + - - +
404J GLY 3.0 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 401 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TYR* 4.5 14.1 - - + -
61D TRP* 5.6 5.8 - - + -
176J LEU* 3.7 25.4 - - + -
179J ASP* 5.7 2.5 - - + -
180J LEU* 3.6 24.0 - - + +
394J THR 4.0 12.5 - - - +
395J LEU* 4.1 20.4 - - + +
400J GLY* 1.3 79.7 - - - +
402J ALA* 1.3 60.4 + - - +
404J GLY* 2.6 25.1 + - - -
405J ALA 2.9 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179J ASP* 4.5 18.5 - - + +
180J LEU* 4.2 4.0 - - - +
183J ASN* 3.3 39.9 - - - +
400J GLY 3.6 0.6 - - - -
401J PRO* 1.3 79.1 - - - +
403J ALA* 1.3 62.3 + - - +
405J ALA 3.5 0.7 + - - -
406J ARG* 3.3 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397J HIS* 4.2 7.4 - - + +
399J ASP* 3.4 34.2 + - + +
400J GLY 3.3 10.4 + - - +
401J PRO 3.0 0.6 - - - -
402J ALA* 1.3 76.6 - - - +
404J GLY* 1.3 67.4 + - - +
406J ARG* 3.2 23.6 + - - +
407J ALA* 3.0 18.4 + - - +
430J GLU* 3.6 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J PRO* 5.1 0.6 - - - +
393J GLY 5.6 0.7 - - - -
394J THR* 3.7 21.3 - - - -
397J HIS* 3.7 18.9 - - - -
400J GLY 3.0 7.1 + - - -
401J PRO 2.6 14.1 + - - -
403J ALA* 1.3 71.3 - - - +
405J ALA* 1.3 61.1 + - - -
407J ALA* 3.1 4.2 + - - +
408J VAL* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J TYR* 3.4 25.6 - - + +
180J LEU* 4.0 23.8 - - + +
183J ASN* 3.5 22.0 - - + +
185J ALA* 4.8 0.7 - - + -
394J THR* 4.0 2.2 - - - +
401J PRO 2.9 8.7 + - - +
402J ALA 3.7 8.1 - - - +
404J GLY* 1.3 74.8 - - - +
406J ARG* 1.3 62.9 + - - +
408J VAL* 3.4 2.6 + - - +
409J ARG* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183J ASN* 2.4 61.4 + - + +
402J ALA* 3.3 12.9 + - - +
403J ALA* 3.2 30.9 + - - +
405J ALA* 1.3 78.3 - - - +
407J ALA* 1.3 59.9 + - - +
409J ARG* 3.6 6.3 + - - +
410J GLN* 2.9 33.0 + - - +
430J GLU* 3.5 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J PRO* 4.6 4.7 - - + -
397J HIS* 4.3 4.9 - - + -
403J ALA 3.0 10.3 + - - +
404J GLY* 3.3 12.1 - - - +
406J ARG* 1.3 74.2 - - - +
408J VAL* 1.3 53.4 + - - +
410J GLN* 2.5 38.6 + - - +
411J ALA* 2.7 17.9 + - - +
430J GLU* 3.4 30.5 - - - +
431J LEU* 3.8 6.0 - - - +
434J ALA* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J TYR* 3.3 46.4 - - + +
372J PRO* 3.8 13.2 - - + -
375J ILE* 5.1 4.0 - - + -
388J LEU* 6.1 0.2 - - + -
390J LEU* 3.8 29.6 - - + -
393J GLY 4.6 0.9 - - - +
394J THR* 3.8 6.5 - - - +
404J GLY 2.9 18.8 + - - +
405J ALA 3.6 6.5 - - - +
407J ALA* 1.3 74.1 - - - +
409J ARG* 1.3 52.9 + - - +
411J ALA* 2.9 10.1 + - - +
412J ILE* 2.8 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J ARG* 3.1 51.1 - - - +
158J TYR* 3.9 13.7 - - + -
183J ASN 4.5 1.3 - - - +
184J GLY* 2.8 47.3 + - - +
186J ASP* 4.4 0.4 + - - -
222J GLU* 3.9 18.0 + - - -
224J LYS* 5.2 0.4 - - - +
405J ALA 3.2 13.5 + - - +
406J ARG* 3.7 9.0 - - - +
408J VAL* 1.3 78.8 - - - +
410J GLN* 1.3 56.7 + - + +
412J ILE* 3.4 11.8 + - - +
413J ASP* 2.8 46.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 410 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406J ARG* 2.9 27.6 + - - +
407J ALA* 2.5 19.3 + - - +
409J ARG* 1.3 68.2 - - + +
411J ALA* 1.3 63.0 + - - +
412J ILE 3.0 1.6 - - - -
413J ASP* 2.9 11.9 + - - +
414J ALA* 2.8 22.3 + - - +
424J TYR* 3.6 17.2 - - + +
428J HIS* 3.3 28.3 - - + +
430J GLU* 2.8 33.7 + - - +
431J LEU* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J PRO* 3.8 35.4 - - + +
375J ILE* 3.9 13.7 - - + -
407J ALA 2.7 12.1 + - - +
408J VAL 3.3 7.9 - - - +
410J GLN* 1.3 72.8 - - - +
412J ILE* 1.3 58.3 + - - +
414J ALA* 3.7 3.4 + - - +
415J ILE* 2.8 36.5 + - + +
421J LEU* 6.0 3.1 - - + -
431J LEU* 4.3 14.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J ARG* 4.6 13.7 - - + +
156J PRO* 4.2 26.7 - - + +
158J TYR* 4.0 26.5 - - + -
375J ILE* 4.2 13.9 - - + -
379J ILE* 5.1 3.8 - - + -
388J LEU* 4.7 13.7 - - + -
408J VAL* 2.8 24.9 + - + +
409J ARG* 3.5 19.1 - - - +
411J ALA* 1.3 76.1 - - - +
413J ASP* 1.3 57.6 + - - +
415J ILE* 3.1 6.3 + - - +
416J MET* 2.7 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 413 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J ARG* 5.8 2.9 - - - -
409J ARG* 2.8 38.9 + - - +
410J GLN* 2.9 11.9 + - - +
412J ILE* 1.3 79.5 - - - +
414J ALA* 1.3 57.0 + - - +
416J MET* 3.3 6.2 + - - +
417J GLN* 2.9 31.7 + - - +
424J TYR* 3.6 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410J GLN 2.8 9.6 + - - +
411J ALA* 3.9 7.2 - - - +
413J ASP* 1.3 76.6 - - - +
415J ILE* 1.3 55.0 + - + +
417J GLN* 3.2 3.9 + - - -
418J GLY 2.7 29.3 + - - -
419J ILE* 2.8 32.2 + - - +
420J PRO 4.7 0.4 - - - +
421J LEU* 4.9 6.1 - - - -
424J TYR* 3.4 37.4 - - + -
431J LEU* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372J PRO 5.8 0.9 - - - +
375J ILE* 3.5 36.3 - - + +
376J GLN* 3.8 18.2 - - + +
379J ILE* 3.6 40.8 - - + -
411J ALA* 2.8 25.4 + - + +
412J ILE 3.1 3.6 + - - +
414J ALA* 1.3 74.1 - - + +
416J MET* 1.3 66.6 + - + +
417J GLN 3.4 0.3 + - - -
418J GLY* 3.4 10.8 + - - +
419J ILE 5.1 0.7 - - - +
421J LEU* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 416 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ASP* 4.2 11.9 - - + +
155J ARG* 3.7 29.2 - - + +
156J PRO* 4.0 10.8 - - - -
379J ILE* 5.9 2.9 - - + -
384J THR* 4.0 25.6 - - + -
412J ILE* 2.7 37.4 + - + +
413J ASP* 3.7 6.5 - - - +
415J ILE* 1.3 74.3 - - + +
417J GLN* 1.3 60.2 + - - +
418J GLY 3.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413J ASP 2.9 18.5 + - - +
414J ALA* 3.7 5.4 - - - +
416J MET* 1.3 78.9 - - - +
418J GLY* 1.3 58.6 + - - +
419J ILE* 3.7 25.5 + - + +
424J TYR* 5.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414J ALA 2.7 5.1 + - - -
415J ILE* 3.4 8.4 + - - -
416J MET 3.4 2.8 - - - -
417J GLN* 1.3 79.9 - - - +
419J ILE* 1.3 60.0 + - - +
420J PRO* 3.4 10.7 - - - +
----------------------------------------------------------
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