Contacts of the helix formed by residues 4806 - 4815 (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 PHE4806 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4796B MET* 4.7 11.9 - - + +
4799B LEU* 4.1 49.6 + - + +
4800B GLY* 4.8 1.8 - - - +
4802B TYR* 6.0 2.5 - + - -
4804B ASN* 3.8 23.7 + - + -
4805B PHE* 1.3 83.1 - - - +
4807B PHE* 1.3 64.8 + - - +
4808B ALA* 3.1 7.9 - - - +
4809B ALA* 3.2 29.1 + - + +
4810B HIS* 4.0 8.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4807 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4571B ILE* 3.6 43.7 - - + -
4572B ASN* 5.8 5.7 - - + +
4575B LEU* 3.6 35.9 - - + -
4645B SER* 5.0 12.1 - - - -
4648B HIS* 5.6 4.0 - + + -
4797B SER 5.6 0.9 - - - -
4800B GLY* 3.4 40.6 - - - -
4805B PHE* 3.7 20.1 - - + +
4806B PHE* 1.3 76.4 - - - +
4808B ALA* 1.3 63.1 + - - +
4809B ALA 3.2 0.4 - - - -
4810B HIS* 3.1 40.0 + + + +
4811B LEU* 3.3 9.9 + - - +
4847H TYR* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4808 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4575B LEU* 5.8 1.0 - - - +
4805B PHE* 5.4 8.0 - - + +
4806B PHE* 3.1 2.3 - - - -
4807B PHE* 1.3 77.8 - - - +
4809B ALA* 1.3 61.9 + - - +
4811B LEU* 3.1 22.9 + - - +
4812B LEU* 3.7 2.3 + - - +
4847H TYR* 4.9 8.1 - - + -
4848H LEU* 3.3 22.1 - - + +
4851H VAL* 3.8 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4809 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4792B TRP* 4.1 31.3 - - + -
4793B TYR* 5.8 0.2 - - - -
4796B MET* 5.3 5.6 - - + -
4806B PHE* 3.2 24.0 + - + +
4808B ALA* 1.3 76.9 - - - +
4810B HIS* 1.3 67.5 + - + +
4812B LEU* 3.1 22.6 + - - +
4813B ASP* 3.8 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS4810 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4568B ALA* 5.2 11.7 - - + +
4571B ILE* 6.3 0.4 - - - +
4648B HIS* 3.3 29.4 + + - +
4792B TRP* 5.8 1.6 - + - -
4793B TYR* 3.4 41.1 + + + +
4796B MET* 3.8 40.3 - - + +
4797B SER* 4.0 7.6 + - - -
4800B GLY* 6.0 0.2 - - - -
4806B PHE 4.6 3.3 + - - -
4807B PHE* 3.1 42.2 + + + +
4809B ALA* 1.3 79.3 - - + +
4811B LEU* 1.3 60.4 + - - +
4813B ASP* 3.2 14.3 + - - +
4814B ILE* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4811 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4568B ALA* 5.9 1.8 - - - +
4572B ASN* 5.1 11.7 - - - +
4807B PHE 3.3 6.9 + - - +
4808B ALA* 3.1 18.4 + - - +
4810B HIS* 1.3 76.7 - - - +
4812B LEU* 1.3 57.1 + - - +
4814B ILE* 3.2 26.9 - - + +
4815B ALA* 3.8 8.0 + - - +
4844H VAL* 4.9 17.0 - - + +
4847H TYR* 4.9 10.8 - - + -
4848H LEU* 4.1 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4812 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4792B TRP* 6.0 3.8 - - + -
4808B ALA 3.7 4.0 + - - +
4809B ALA* 3.1 14.3 + - - +
4810B HIS 3.1 1.0 - - - -
4811B LEU* 1.3 77.7 - - - +
4813B ASP* 1.3 63.2 + - - +
4814B ILE 3.5 0.2 - - - -
4815B ALA* 3.8 14.7 + - - +
4816B MET* 4.1 5.4 + - - +
4825B LEU* 5.6 4.5 - - - +
4848H LEU* 4.7 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP4813 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4561B ARG* 3.4 27.9 + - - -
4789B TYR* 2.7 35.5 + - + +
4792B TRP* 5.9 4.2 - - + -
4793B TYR* 3.2 39.7 - - + +
4809B ALA 3.8 2.6 + - - +
4810B HIS* 3.2 12.1 + - - +
4812B LEU* 1.3 76.7 - - - +
4814B ILE* 1.3 65.1 + - - +
4815B ALA 3.1 1.8 - - - -
4816B MET* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4814 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4564B ALA 5.2 2.0 - - - +
4565B LEU* 3.2 48.0 - - + +
4568B ALA* 4.5 10.5 - - + -
4569B PHE* 3.5 36.8 - - + -
4810B HIS 3.4 4.3 + - - +
4811B LEU* 3.2 32.5 - - + +
4813B ASP* 1.3 77.6 - - - +
4815B ALA* 1.3 63.0 + - - +
4816B MET 3.0 9.6 - - - +
4818B VAL* 5.8 0.9 - - - +
4844H VAL* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4815 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4811B LEU 3.8 8.0 + - - +
4812B LEU* 3.9 13.0 - - - +
4813B ASP 3.1 0.6 - - - -
4814B ILE* 1.3 83.3 - - - +
4816B MET* 1.3 59.4 + - - +
4818B VAL* 4.0 6.6 - - - +
4821B LEU* 3.8 23.0 - - - +
4825B LEU* 5.9 6.7 - - + -
4841H LEU* 4.1 22.4 - - + +
4844H VAL* 4.9 10.5 - - + -
----------------------------------------------------------
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