Contacts of the helix formed by residues 404 - 417 (chain A) in PDB entry 4KJW
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 ALA 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A PHE* 4.6 3.1 - - + -
202A GLU* 3.3 20.6 - - - +
203A GLU* 4.3 20.0 - - + +
357A PHE* 6.2 0.4 - - + -
398A LEU* 3.6 8.9 + - - +
399A ALA* 4.2 3.2 - - - +
402A ILE* 3.3 19.7 - - + -
403A ARG* 1.3 78.7 - - - +
405A PRO* 1.3 63.9 - - - +
406A LEU 3.4 2.2 - - - -
407A THR* 3.5 8.4 + - - -
408A GLY* 3.2 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 3.3 10.8 - - - +
395A GLY 5.3 0.2 - - - +
399A ALA* 3.7 26.0 - - + -
403A ARG* 3.5 8.7 - - - +
404A ALA* 1.3 86.4 - - - +
406A LEU* 1.3 60.8 + - - +
408A GLY* 3.2 1.9 + - - +
409A ILE* 2.8 42.5 + - + +
429A GLY 4.3 8.7 - - - +
430A LEU* 4.6 13.9 - - + -
433A THR* 3.9 23.1 - - + +
215B ILE* 6.0 1.3 - - + -
216B LYS* 6.0 6.5 - - + -
219B PHE* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.6 28.9 - - + +
202A GLU* 3.1 23.8 + - + +
405A PRO* 1.3 79.8 - - - +
407A THR* 1.3 61.3 + - - +
409A ILE* 3.9 1.5 - - + +
410A ILE* 3.2 37.0 + - + +
194B LEU* 4.3 9.9 - - + -
197B ILE* 4.4 8.7 - - + -
198B LEU* 3.8 22.9 - - + -
201B ILE* 3.9 15.5 - - + -
215B ILE* 4.9 4.9 - - + -
219B PHE* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 4.8 2.7 - - + -
195A ALA* 3.8 19.7 - - + +
198A LEU* 3.6 12.0 + - - +
199A PHE* 3.4 44.9 + - + -
202A GLU* 2.8 23.3 + - - -
357A PHE* 4.4 17.9 - - + -
404A ALA* 3.7 6.7 - - + -
405A PRO 3.2 0.2 - - - -
406A LEU* 1.3 74.8 - - - +
408A GLY* 1.3 54.8 + - - +
410A ILE* 3.2 2.8 + - - +
411A LEU* 2.7 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 4.6 11.4 - - - -
398A LEU* 4.0 26.7 - - - -
404A ALA 3.2 8.4 + - - -
405A PRO 3.2 6.1 + - - -
407A THR* 1.3 78.1 - - - +
409A ILE* 1.3 61.8 + - - +
411A LEU* 3.7 2.4 - - - +
412A VAL* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY* 5.0 4.5 + - - +
405A PRO* 2.8 31.6 + - + +
406A LEU* 3.9 4.3 - - - +
408A GLY* 1.3 73.3 - - - +
410A ILE* 1.3 58.6 + - - +
412A VAL* 3.9 4.7 - - - +
413A LEU* 3.0 26.7 + - - +
422A ILE* 4.0 26.5 - - + -
425A MET* 4.0 25.5 - - + +
426A ILE* 3.6 33.2 - - + +
429A GLY* 4.9 4.9 - - - -
430A LEU* 5.4 0.2 - - + -
194B LEU* 4.2 9.6 - - + -
219B PHE* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.9 30.5 - - + -
195A ALA* 4.1 9.4 - - - +
198A LEU* 4.0 18.6 - - + -
406A LEU* 3.2 30.6 + - + +
407A THR* 3.9 3.4 - - - +
409A ILE* 1.3 73.9 - - - +
411A LEU* 1.3 60.3 + - - +
413A LEU* 3.5 10.9 + - + +
414A GLU* 3.0 29.9 + - + +
194B LEU* 3.9 25.8 - - + -
198B LEU* 4.4 2.9 - - + -
410B ILE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 5.8 1.6 - - + -
190A PHE* 3.8 26.7 - - + -
192A ALA* 3.7 24.9 - - + -
195A ALA* 3.7 15.8 - - + +
357A PHE* 3.5 33.9 - - + -
361A LEU* 4.1 21.8 - - + -
398A LEU* 4.2 3.8 - - + -
407A THR* 2.7 23.2 + - + +
408A GLY 3.7 3.6 - - - +
410A ILE* 1.3 70.5 - - - +
412A VAL* 1.3 66.9 + - - +
414A GLU* 3.0 5.2 + - - +
415A MET* 3.0 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 4.5 6.7 - - + -
391A ILE* 3.7 24.0 - - + +
394A MET* 3.8 25.1 - - + -
395A GLY* 3.5 28.9 - - - +
408A GLY 3.0 18.2 + - - +
409A ILE* 3.9 3.8 - - - +
411A LEU* 1.3 75.9 - - + +
413A LEU* 1.3 52.0 + - - +
416A THR* 2.6 59.1 + - + +
425A MET* 3.8 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 6.3 0.2 - - + -
409A ILE 3.0 19.0 + - - +
410A ILE* 3.5 12.1 - - + +
412A VAL* 1.3 77.7 - - - +
414A GLU* 1.3 60.5 + - + +
416A THR* 4.2 3.6 - - - -
417A ASP* 3.0 30.4 + - - +
418A ASN 4.6 2.7 - - - +
419A TYR* 3.7 49.8 - - + +
422A ILE* 4.5 1.8 - - + -
425A MET* 4.4 15.4 - - + -
194B LEU* 3.9 27.1 - - + -
413B LEU* 4.6 21.5 - - + -
414B GLU* 6.1 0.2 - - + -
419B TYR* 5.2 5.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ASN 5.1 3.2 - - - +
192A ALA* 3.3 17.0 - - + +
193A PRO* 3.2 16.6 - - - +
194A LEU* 3.1 19.1 + - + +
195A ALA* 2.6 38.3 + - - +
410A ILE* 3.0 21.4 + - + +
411A LEU 3.0 7.2 + - - +
413A LEU* 1.3 78.9 - - + +
415A MET* 1.3 61.3 + - - +
417A ASP* 4.7 2.1 + - - +
419B TYR* 2.3 63.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.6 40.2 - - + +
192A ALA* 5.1 0.4 - - + -
237A ALA* 5.7 0.5 - - - +
238A LEU* 4.8 9.6 - - + -
239A ILE* 3.1 42.8 + - + +
317A PHE* 4.9 2.7 - - + -
361A LEU* 3.7 26.2 - - + -
394A MET* 3.6 27.8 - - + -
411A LEU* 3.0 36.6 + - + +
412A VAL 3.9 2.9 - - - +
414A GLU* 1.3 82.5 - - + +
416A THR* 1.3 62.2 + - - +
417A ASP* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 4.6 7.2 - - + -
241A VAL* 3.9 21.3 + - + +
242A GLY 4.4 1.4 + - - +
391A ILE* 3.6 36.3 - - + +
394A MET* 3.7 24.7 - - + -
412A VAL* 2.6 37.3 + - + +
413A LEU* 4.2 1.6 - - - -
415A MET* 1.3 77.8 - - - +
417A ASP* 1.3 70.2 + - - +
418A ASN* 3.1 19.9 + - - +
425A MET* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LYS* 3.7 13.9 + - - -
413A LEU* 3.0 21.6 + - - +
414A GLU 5.3 2.0 - - - +
415A MET 3.7 0.6 - - - -
416A THR* 1.3 81.2 + - - +
418A ASN* 1.3 61.4 + - - +
419A TYR* 3.7 3.9 + - - +
243B LYS* 4.6 11.9 + - - -
417B ASP* 4.2 13.3 - - - +
419B TYR* 4.1 32.9 + - + +
420B GLN* 5.1 2.9 + - - +
----------------------------------------------------------
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