Contacts of the helix formed by residues 400 - 418 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B LEU 4.2 0.9 - - - -
397B HIS* 3.2 20.0 + - - +
398B PRO 3.4 0.6 - - - -
399B ASP* 1.3 81.0 - - - +
401B PRO* 1.3 78.4 - - - +
402B ALA* 3.3 2.7 - - - -
403B ALA* 2.9 14.6 + - - +
404B GLY 3.1 8.7 + - - -
59G TYR* 4.3 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.7 32.1 - - + -
179B ASP* 5.7 3.4 - - + -
180B LEU* 3.6 18.1 - - + +
394B THR 3.9 12.1 - - - +
395B LEU* 4.0 15.8 - - + +
400B GLY* 1.3 82.2 - - - +
402B ALA* 1.3 64.1 + - - +
404B GLY* 2.8 13.5 + - - -
405B ALA 3.2 10.6 + - - -
59G TYR* 3.5 38.6 - - + -
61G TRP* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ASP* 4.8 14.9 - - + +
180B LEU* 4.4 3.8 - - - +
183B ASN* 2.6 48.0 + - - +
400B GLY 3.3 1.0 - - - -
401B PRO* 1.3 80.5 - - - +
403B ALA* 1.3 62.1 + - - +
404B GLY 3.5 0.2 + - - -
405B ALA 3.6 0.2 + - - -
406B ARG* 3.5 17.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B HIS* 3.8 12.3 - - + -
399B ASP* 3.6 30.7 + - + +
400B GLY 2.9 11.4 + - - +
402B ALA* 1.3 75.8 - - - +
404B GLY* 1.3 54.8 + - - +
406B ARG* 3.1 25.2 + - - +
407B ALA* 2.7 35.0 + - - +
430B GLU* 3.9 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 4.3 0.9 - - - -
393B GLY 5.3 0.7 - - - -
394B THR* 3.5 22.9 - - - -
397B HIS* 3.8 15.1 - - - -
400B GLY 3.1 4.2 + - - -
401B PRO 2.8 14.6 + - - -
403B ALA* 1.3 73.0 - - - +
405B ALA* 1.3 52.5 + - - -
407B ALA* 2.9 3.0 + - - +
408B VAL* 2.7 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.6 18.2 + - + +
180B LEU* 3.8 19.1 - - + +
183B ASN* 3.0 37.9 - - + +
185B ALA* 4.0 7.2 - - + +
394B THR* 4.1 2.0 - - - +
401B PRO 3.2 8.5 + - - +
402B ALA 3.8 1.6 - - - +
403B ALA 3.4 0.2 - - - -
404B GLY* 1.3 72.4 - - - +
406B ARG* 1.3 56.2 + - - +
408B VAL* 3.7 1.6 - - - +
409B ARG* 2.8 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 3.1 50.0 + - + +
402B ALA* 3.5 11.5 + - - +
403B ALA* 3.1 30.3 + - - +
405B ALA* 1.3 74.1 - - - +
407B ALA* 1.3 57.8 + - - +
409B ARG* 3.2 4.9 + - - +
410B GLN* 2.7 45.5 + - + +
430B GLU* 3.4 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO* 4.6 5.6 - - + -
397B HIS* 3.8 20.9 - - + -
403B ALA 2.7 16.5 + - - +
404B GLY* 3.2 8.1 - - - +
406B ARG* 1.3 72.4 - - - +
408B VAL* 1.3 61.9 + - - +
410B GLN* 3.2 15.9 + - - +
411B ALA 3.1 18.2 + - - -
430B GLU* 3.8 18.3 - - - +
431B LEU* 3.3 14.1 - - - +
434B ALA* 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 3.3 51.6 - - + +
372B PRO* 4.2 13.5 - - + -
375B ILE* 5.0 5.4 - - + -
388B LEU* 5.8 0.9 - - + -
390B LEU* 3.8 28.3 - - + -
393B GLY 4.4 3.8 - - - +
394B THR* 3.9 6.1 - - - +
404B GLY* 2.7 22.7 + - - +
405B ALA 3.7 0.2 - - - +
407B ALA* 1.3 68.2 - - - +
409B ARG* 1.3 65.6 + - - +
410B GLN 3.0 3.0 + - - -
411B ALA* 3.1 16.7 + - - +
412B ILE* 3.1 22.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ARG* 3.6 47.1 - - - +
158B TYR* 3.9 14.8 - - + -
184B GLY* 2.7 61.6 + - - -
186B ASP* 4.1 0.8 + - - -
222B GLU* 4.5 19.2 + - - -
224B LYS* 5.0 0.2 - - - +
405B ALA 2.8 27.8 + - - +
406B ARG* 3.6 7.2 - - - +
408B VAL* 1.3 72.5 - - - +
410B GLN* 1.3 59.8 + - - +
412B ILE* 3.8 9.0 + - - +
413B ASP* 3.0 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ARG* 2.7 28.7 + - + +
407B ALA* 3.3 6.4 - - - +
408B VAL 3.0 0.2 - - - -
409B ARG* 1.3 76.0 - - - +
411B ALA* 1.3 67.1 + - - +
413B ASP* 2.9 11.9 + - - +
414B ALA 2.9 19.6 + - - -
424B TYR* 3.6 14.4 - - + +
428B HIS* 3.7 31.2 - - + +
430B GLU* 3.3 24.9 + - - +
431B LEU* 2.8 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO* 4.1 13.9 - - + +
375B ILE* 3.9 21.3 - - + -
407B ALA 3.1 5.4 + - - +
408B VAL 3.1 7.6 + - - +
410B GLN* 1.3 77.6 - - - +
412B ILE* 1.3 58.2 + - - +
414B ALA* 3.2 5.1 + - - +
415B ILE* 2.9 38.9 + - + +
421B LEU* 6.2 3.6 - - + -
431B LEU* 3.6 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ARG* 4.4 16.8 - - + +
156B PRO* 3.6 35.0 - - + +
158B TYR* 3.9 23.8 - - + -
375B ILE* 4.6 6.3 - - + -
379B ILE* 5.1 3.1 - - + -
388B LEU* 3.8 28.9 - - + -
408B VAL* 3.1 21.4 + - + +
409B ARG* 3.9 13.0 - - - +
411B ALA* 1.3 77.0 - - - +
413B ASP* 1.3 51.9 + - - +
415B ILE* 3.7 7.1 - - - +
416B MET* 2.7 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ARG* 5.3 6.1 - - - -
409B ARG* 3.0 28.6 + - - +
410B GLN* 2.9 11.1 + - - +
412B ILE* 1.3 79.5 - - - +
414B ALA* 1.3 55.1 + - - +
416B MET* 3.1 8.3 + - - +
417B GLN* 2.6 39.1 + - - +
424B TYR* 3.7 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B GLN 2.9 7.5 + - - +
411B ALA* 3.5 11.4 - - - +
413B ASP* 1.3 74.6 - - - +
415B ILE* 1.3 52.4 - - + +
417B GLN* 2.9 3.7 + - - -
418B GLY 2.4 35.2 + - - -
419B ILE 3.0 27.2 + - - +
420B PRO 4.5 1.8 - - - +
421B LEU* 5.2 3.6 - - + -
424B TYR* 3.5 39.1 - - + -
431B LEU* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B PRO 5.9 0.4 - - - +
375B ILE* 4.3 10.5 - - + -
376B GLN* 3.5 48.0 - - + +
379B ILE* 4.0 41.1 - - + -
380B GLU 5.9 0.2 - - - +
411B ALA* 2.9 23.5 + - + +
412B ILE* 3.8 3.6 - - - +
414B ALA* 1.3 77.0 - - + +
416B MET* 1.3 68.2 + - - +
418B GLY* 3.1 14.7 + - - +
419B ILE 4.2 2.4 + - - +
421B LEU* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP* 4.4 11.4 - - + +
155B ARG* 3.8 26.2 - - + +
156B PRO* 3.8 18.6 - - - -
379B ILE* 5.8 1.8 - - + -
384B THR* 4.0 20.0 - - + -
412B ILE* 2.7 43.9 + - + +
413B ASP* 3.5 9.0 - - - +
415B ILE* 1.3 79.1 - - + +
417B GLN* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP 2.6 20.7 + - - +
414B ALA* 3.5 1.6 - - - +
416B MET* 1.3 75.1 - - - +
418B GLY* 1.3 56.4 + - - +
419B ILE* 3.1 28.0 - - + +
424B TYR* 5.5 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ALA 2.4 16.3 + - - -
415B ILE* 3.1 12.0 + - - -
417B GLN* 1.3 75.8 - - - +
419B ILE* 1.3 58.7 + - - -
420B PRO* 3.2 13.7 - - - +
----------------------------------------------------------
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