Contacts of the helix formed by residues 4221 - 4239 (chain B) in PDB entry 6X34
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 GLY4221 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4219B GLU* 3.3 8.7 - - - +
4220B GLY* 1.3 75.9 - - - +
4222B GLU* 1.3 60.3 + - - -
4223B SER 3.4 2.5 - - - -
4224B GLU* 3.9 14.7 - - - +
4225B LYS* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4222 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4220B GLY 3.5 6.1 + - - +
4221B GLY* 1.3 69.9 - - - -
4223B SER* 1.3 65.1 + - - +
4225B LYS* 3.4 14.0 + - - +
4226B MET* 3.6 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER4223 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4221B GLY* 3.4 0.4 - - - -
4222B GLU* 1.3 75.6 - - - +
4224B GLU* 1.3 64.2 + - - +
4226B MET* 3.3 22.9 + - - +
4227B GLU* 4.0 3.8 + - - +
4971D HIS* 6.5 1.1 - - - -
4973D PHE* 5.1 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4224 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4221B GLY* 3.7 15.1 + - - +
4222B GLU 3.3 0.6 - - - -
4223B SER* 1.3 79.0 - - - +
4225B LYS* 1.3 61.8 + - - +
4226B MET 3.4 0.5 + - - -
4227B GLU* 3.4 16.3 + - - +
4228B LEU* 3.6 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS4225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4212B PHE* 5.3 1.4 - - - -
4216B VAL* 4.4 25.0 - - + +
4219B GLU* 4.8 7.6 - - + +
4221B GLY 3.1 18.6 + - - +
4222B GLU* 3.6 9.2 - - - +
4223B SER 3.2 0.4 - - - -
4224B GLU* 1.3 76.2 - - - +
4226B MET* 1.3 64.7 + - - +
4228B LEU* 3.3 23.8 + - + +
4229B PHE* 3.6 7.3 + - - +
4957B PHE* 5.0 14.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET4226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4222B GLU 3.6 15.9 - - - +
4223B SER* 3.5 12.6 - - - +
4224B GLU 3.2 0.8 - - - -
4225B LYS* 1.3 79.6 - - - +
4227B GLU* 1.3 61.3 + - - +
4229B PHE* 3.4 20.3 + - + +
4230B VAL* 3.9 8.8 - - - +
4957B PHE* 3.8 33.2 - - + +
4958B ILE* 5.3 4.0 - - - +
5017B TRP* 5.2 8.9 - - + +
5020B PHE* 3.7 48.4 - - + -
5022B ALA* 5.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4223B SER 4.0 3.8 + - - +
4224B GLU* 3.4 12.1 + - - +
4225B LYS 3.3 0.4 - - - -
4226B MET* 1.3 75.9 - - - +
4228B LEU* 1.3 63.7 + - - +
4229B PHE 3.2 0.2 - - - -
4230B VAL* 3.4 19.4 + - - +
4231B SER* 3.6 9.7 + - - -
5017B TRP* 5.1 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4212B PHE* 3.7 22.6 - - + -
4215B ASP 5.5 7.0 - - - +
4216B VAL* 5.7 7.4 - - + -
4224B GLU 3.6 10.1 + - - +
4225B LYS* 3.3 18.6 + - + +
4226B MET 3.2 1.0 - - - -
4227B GLU* 1.3 76.5 - - - +
4229B PHE* 1.3 63.6 + - - +
4230B VAL 3.3 0.2 - - - -
4231B SER* 3.5 13.3 + - - +
4232B PHE* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4212B PHE* 3.5 32.9 - + + -
4225B LYS 3.6 5.9 + - - +
4226B MET* 3.4 14.0 + - + +
4227B GLU 3.2 0.8 - - - -
4228B LEU* 1.3 77.5 - - - +
4230B VAL* 1.3 65.8 + - - +
4232B PHE* 3.2 16.8 + + - +
4233B CYS* 3.2 44.7 + - - -
4957B PHE* 4.6 15.0 - + + -
4958B ILE* 5.2 11.9 - - + -
4983B LEU 5.2 8.7 - - - -
4986B TYR* 4.4 26.0 - + + -
4987B MET 5.8 0.2 - - - -
4990B LEU* 6.2 1.8 - - + -
5020B PHE* 3.5 33.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4226B MET 3.9 15.0 - - - +
4227B GLU* 3.4 8.3 + - - +
4228B LEU 3.3 0.6 - - - -
4229B PHE* 1.3 75.6 - - - +
4231B SER* 1.3 62.1 + - - +
4233B CYS* 3.5 8.3 + - - +
4234B GLU* 3.4 20.3 + - - +
4990B LEU* 4.5 10.5 - - + +
5012B TYR* 3.6 34.2 + - + +
5017B TRP* 3.5 33.9 - - + +
5019B PHE* 4.1 15.9 - - + -
5020B PHE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER4231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4227B GLU 3.6 8.4 + - - -
4228B LEU* 3.5 19.4 + - - -
4229B PHE 3.3 0.6 - - - -
4230B VAL* 1.3 77.4 - - - +
4232B PHE* 1.3 62.4 + - - +
4234B GLU* 3.7 7.5 + - - +
4235B ASP* 3.5 19.6 + - - +
4669B PHE* 5.6 0.9 - - - -
4673B LYS* 5.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4200B TRP* 5.9 7.6 - + - -
4205B VAL 5.2 1.8 - - - -
4208B SER* 3.2 43.5 - - - -
4209B LYS* 3.7 20.4 - - + -
4212B PHE* 3.6 50.7 - + + -
4228B LEU 3.2 4.4 + - - +
4229B PHE* 3.2 16.5 + + - +
4230B VAL 3.2 0.8 - - - -
4231B SER* 1.3 76.1 - - - +
4233B CYS* 1.3 74.0 + - - +
4235B ASP* 3.3 14.2 + - + +
4236B THR* 3.3 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS4233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4229B PHE* 3.2 45.9 + - - -
4230B VAL* 3.5 7.2 + - - +
4231B SER 3.4 0.2 - - - -
4232B PHE* 1.3 81.6 - - - +
4234B GLU* 1.3 61.8 + - - +
4236B THR* 2.7 26.1 + - - -
4237B ILE* 3.2 15.0 - - + +
4714B TRP* 5.3 0.2 - - - -
4986B TYR 5.3 0.2 - - - -
4987B MET* 4.3 26.9 - - + -
4990B LEU* 4.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4230B VAL 3.4 13.7 + - - +
4231B SER* 4.0 9.2 - - - +
4232B PHE 3.3 1.0 - - - -
4233B CYS* 1.3 78.2 - - - +
4235B ASP* 1.3 60.6 + - - +
4238B PHE 3.5 7.8 + - - -
4669B PHE* 3.5 23.2 - - + -
4714B TRP* 3.5 41.6 - - + -
4990B LEU* 5.7 1.9 - - + +
5012B TYR* 5.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP4235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4231B SER 3.5 10.9 + - - +
4232B PHE* 3.3 12.5 + - + +
4233B CYS 3.2 0.6 - - - -
4234B GLU* 1.3 77.4 - - - +
4236B THR* 1.3 64.7 + - + +
4238B PHE* 3.5 8.5 + - - +
4239B GLU* 3.3 19.3 + - - +
4666B LEU* 3.9 26.6 - - + +
4669B PHE* 4.1 13.4 - - + -
4670B LYS* 6.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4200B TRP* 6.1 5.2 - - + -
4205B VAL* 4.8 15.4 - - + +
4208B SER* 5.5 2.7 - - - +
4232B PHE* 3.3 38.4 - - + +
4233B CYS* 2.7 22.3 + - - -
4235B ASP* 1.3 77.0 - - + +
4237B ILE* 1.3 68.8 + - - +
4239B GLU* 3.0 42.4 + - - +
4987B MET* 4.4 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4196B ASN* 4.8 4.7 - - - +
4233B CYS* 3.2 15.8 + - + +
4235B ASP 3.4 0.2 - - - -
4236B THR* 1.3 87.3 - - - +
4238B PHE* 1.3 61.9 + - - +
4239B GLU 3.4 5.9 + - - +
4714B TRP* 3.6 31.9 - - + +
4987B MET* 4.5 20.9 - - + +
4990B LEU* 6.2 3.1 - - + -
4991B MET* 3.7 39.3 - - + +
4994B ILE* 5.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4234B GLU 3.5 11.5 + - - +
4235B ASP 3.5 9.8 + - - +
4236B THR 3.2 0.8 - - - -
4237B ILE* 1.3 78.8 - - - +
4239B GLU* 1.3 62.2 + - + +
4665B PRO* 3.2 40.8 - - + -
4666B LEU* 4.9 5.8 - - + -
4669B PHE* 4.1 22.0 - + + -
4712B ASN* 3.2 57.2 - - + -
4714B TRP* 4.7 10.0 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4204B GLN* 4.3 15.2 - - - +
4205B VAL* 3.3 30.6 - - - +
4235B ASP 3.3 14.4 - - - +
4236B THR* 3.0 29.3 - - - +
4237B ILE 3.2 7.8 - - - +
4238B PHE* 1.3 80.9 - - + +
4662B LEU 5.7 4.9 - - - +
4666B LEU* 5.6 13.5 - - + -
----------------------------------------------------------
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