Contacts of the helix formed by residues 4152 - 4162 (chain D) 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 ASP4152 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D VAL* 5.4 9.4 - - + -
4149D VAL* 4.1 18.7 - - + +
4151D HIS* 1.3 75.9 - - - +
4153D PRO* 1.3 71.4 - - + +
4154D ARG* 4.5 2.2 - - + +
4155D LEU* 3.2 30.9 + - + +
4156D ARG* 3.3 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO4153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4151D HIS 4.4 3.6 - - - +
4152D ASP* 1.3 85.0 - - + +
4154D ARG* 1.3 61.6 + - - +
4156D ARG* 3.5 6.7 + - + +
4157D ASN* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D VAL* 5.1 6.3 - - + +
4043D LEU* 4.9 10.5 - - + +
4044D VAL* 4.4 23.3 - - + +
4047D SER* 6.1 0.2 - - - +
4152D ASP* 3.2 2.4 - - + -
4153D PRO* 1.3 78.7 - - - +
4155D LEU* 1.3 64.6 + - - +
4157D ASN* 3.4 6.8 + - - +
4158D PHE* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4040D VAL* 5.5 5.4 - - + -
4043D LEU* 5.4 5.8 - - - -
4145D LEU* 5.4 7.6 - - + +
4146D SER* 4.4 28.6 - - - +
4149D VAL* 4.6 4.3 - - + -
4152D ASP* 3.2 25.6 + - + +
4154D ARG* 1.3 80.7 - - - +
4156D ARG* 1.3 57.1 + - - +
4158D PHE* 3.5 4.3 + - - +
4159D LEU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4152D ASP 3.3 9.6 + - - +
4153D PRO* 3.5 8.5 + - + +
4155D LEU* 1.3 78.7 - - - +
4157D ASN* 1.3 58.0 + - - +
4159D LEU* 4.0 5.4 - - - +
4160D GLU* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4153D PRO 3.2 18.0 + - - +
4154D ARG* 3.7 7.9 - - - +
4155D LEU 3.2 0.2 - - - -
4156D ARG* 1.3 75.1 - - - +
4158D PHE* 1.3 64.9 + - - +
4160D GLU* 3.3 5.5 + - - +
4161D LEU* 3.1 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4043D LEU* 3.9 24.9 - - + -
4050D VAL* 5.5 11.0 - - + -
4154D ARG 3.1 17.1 + - - +
4155D LEU* 4.1 2.9 - - - +
4157D ASN* 1.3 76.9 - - - +
4159D LEU* 1.3 61.2 + - - +
4161D LEU* 3.6 8.9 + - - +
4162D ALA* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4142D LEU* 5.5 12.6 - - + +
4146D SER* 5.5 9.6 - - - +
4155D LEU 3.0 19.0 + - - +
4156D ARG* 4.0 6.3 - - - +
4158D PHE* 1.3 74.5 - - - +
4160D GLU* 1.3 64.5 + - - +
4162D ALA* 3.4 5.6 + - - -
4163D GLU* 3.2 20.3 + - - +
4166D LEU* 4.0 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4156D ARG 3.0 19.4 + - - +
4157D ASN* 3.3 6.7 + - - +
4159D LEU* 1.3 77.5 - - - +
4161D LEU* 1.3 64.8 + - + +
4163D GLU* 3.3 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4047D SER 6.0 0.4 - - - +
4050D VAL* 6.0 4.7 - - + -
4051D GLU* 4.9 19.3 - - + -
4054D LEU* 4.6 14.1 - - + +
4058D ASP* 3.0 19.2 - - - +
4157D ASN* 3.1 32.0 + - - +
4158D PHE* 4.1 7.0 - - - +
4160D GLU* 1.3 79.0 - - + +
4162D ALA* 1.3 56.4 + - - +
4163D GLU 3.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4054D LEU* 5.1 10.3 - - + -
4058D ASP* 4.1 5.8 - - - +
4138D VAL* 5.7 9.4 - - + -
4142D LEU* 5.7 8.5 - - + -
4158D PHE 3.2 17.2 + - - +
4159D LEU* 3.4 8.0 + - - +
4160D GLU 3.2 0.8 - - - -
4161D LEU* 1.3 76.4 - - - +
4163D GLU* 1.3 62.1 + - - +
4164D SER 3.2 2.5 - - - -
4165D ILE* 3.3 20.8 + - + +
4166D LEU* 3.4 16.4 + - + +
----------------------------------------------------------
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