Contacts of the helix formed by residues 4127 - 4149 (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 PHE4127 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3999D ALA* 6.0 6.7 - - + -
4005D ILE* 4.8 20.4 - - + -
4060D PHE* 3.5 57.7 - + + -
4063D LEU* 5.4 4.7 - - + -
4123D PHE 5.2 8.1 - - - -
4124D ALA 5.2 7.6 - - - -
4126D ARG* 1.3 91.1 - - + +
4128D GLN* 1.3 63.3 + - - +
4129D GLU* 3.3 7.4 - - - -
4130D PRO* 3.4 17.9 - - + +
4131D ALA* 3.7 17.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4064D LYS* 6.1 4.7 - - + +
4125D ASN* 5.2 19.3 - - + +
4126D ARG 3.7 1.8 - - - -
4127D PHE* 1.3 76.3 - - - +
4129D GLU* 1.3 68.9 + - + +
4131D ALA* 4.1 5.2 - - - +
4132D ARG* 3.3 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4126D ARG 3.9 14.4 - - - +
4128D GLN* 1.3 85.5 + - + +
4130D PRO* 1.3 75.2 - - + +
4132D ARG* 3.3 18.1 + - - +
4133D ASP* 4.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO4130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4009D LYS* 4.8 23.1 - - + +
4012D LEU* 3.5 28.4 - - + +
4013D ASP* 5.2 5.8 - - - +
4016D LYS* 6.0 0.9 - - - +
4127D PHE* 3.4 21.5 - - + +
4129D GLU* 1.3 104.5 - - + +
4131D ALA* 1.3 58.0 + - - +
4132D ARG 3.3 0.5 + - - -
4133D ASP* 3.6 10.5 + - + +
4134D ILE* 3.4 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4012D LEU* 4.0 4.0 - - + +
4057D PHE* 4.9 16.3 - - + -
4060D PHE* 6.4 2.5 - - + -
4127D PHE* 3.7 20.1 + - + +
4128D GLN* 4.3 5.4 - - - +
4129D GLU 3.3 1.2 - - - -
4130D PRO* 1.3 78.9 - - - +
4132D ARG* 1.3 59.6 + - - +
4134D ILE* 3.7 10.4 - - + +
4135D GLY* 2.8 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG4132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4128D GLN 3.3 17.7 + - - +
4129D GLU* 3.3 9.6 + - - +
4130D PRO 3.2 1.2 - - - -
4131D ALA* 1.3 75.8 - - - +
4133D ASP* 1.3 65.4 + - - +
4135D GLY* 5.0 0.4 - - - -
4136D PHE* 3.4 21.5 + - - +
4168D TYR* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP4133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4016D LYS* 3.7 39.2 + - + +
4129D GLU 4.0 4.9 + - - +
4130D PRO* 3.6 7.9 + - + +
4132D ARG* 1.3 77.3 - - - +
4134D ILE* 1.3 64.2 + - - +
4136D PHE* 3.4 6.3 + - - +
4137D ASN* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE4134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4012D LEU* 3.7 19.5 - - + -
4015D GLN* 4.7 8.7 - - + +
4016D LYS* 4.5 23.5 - - + +
4019D VAL* 4.6 9.9 - - + -
4057D PHE* 3.6 37.0 - - + -
4130D PRO 3.4 18.8 + - - +
4131D ALA* 3.7 7.0 - - - -
4133D ASP* 1.3 77.7 - - - +
4135D GLY* 1.3 69.0 + - - +
4137D ASN* 3.0 22.8 + - + -
4138D VAL* 3.0 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4057D PHE* 5.0 9.6 - - - -
4131D ALA 2.8 22.6 + - - -
4132D ARG* 4.1 1.1 - - - -
4133D ASP 3.3 0.2 - - - -
4134D ILE* 1.3 79.5 - - - +
4136D PHE* 1.3 58.8 + - - +
4138D VAL* 4.0 3.6 + - - +
4139D ALA* 3.6 18.0 + - - +
4165D ILE* 4.9 10.6 - - - +
4168D TYR* 6.6 0.2 - - - -
4169D PHE* 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4132D ARG 3.4 16.8 + - - +
4133D ASP* 4.0 4.0 - - - +
4134D ILE 3.2 0.2 - - - -
4135D GLY* 1.3 75.0 - - - +
4137D ASN* 1.3 63.2 + - - +
4139D ALA* 3.5 7.5 + - - +
4140D VAL* 3.2 30.3 + - + +
4169D PHE* 4.5 12.1 - - + -
4172D TYR* 5.8 6.5 - - + +
4191D GLU* 5.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4016D LYS* 3.3 29.7 + - - +
4019D VAL* 4.1 15.4 - - + +
4020D VAL* 4.3 6.9 - - - +
4023D LEU* 3.3 29.5 - - - +
4133D ASP* 3.2 21.2 + - - +
4134D ILE* 3.0 19.5 + - + +
4136D PHE* 1.3 75.3 - - - +
4138D VAL* 1.3 64.1 + - - +
4140D VAL* 3.2 19.2 - - - +
4141D LEU* 3.2 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4138 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4019D VAL* 6.0 0.4 - - + -
4057D PHE* 5.0 9.4 - - + -
4134D ILE* 3.0 34.9 + - + +
4135D GLY* 4.5 4.9 - - - +
4137D ASN* 1.3 76.2 - - - +
4139D ALA* 1.3 62.9 + - - +
4141D LEU* 3.4 21.3 - - + +
4142D LEU* 3.1 25.9 + - + +
4162D ALA* 5.7 9.4 - - + -
4165D ILE* 5.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4139 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4135D GLY 3.6 13.4 + - - +
4136D PHE 3.5 8.3 + - - +
4137D ASN 3.2 0.6 - - - -
4138D VAL* 1.3 81.2 - - - +
4140D VAL* 1.3 62.0 + - + +
4142D LEU* 3.5 4.9 + - - +
4143D THR* 3.3 24.1 + - - +
4165D ILE* 4.5 10.0 - - + +
4166D LEU* 4.6 14.6 - - + +
4169D PHE* 3.8 23.8 - - + -
4173D LEU* 4.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4140 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4023D LEU* 4.3 15.6 - - + +
4136D PHE* 3.2 15.9 + - + +
4137D ASN* 3.2 27.1 - - - +
4139D ALA* 1.3 78.4 - - + +
4141D LEU* 1.3 59.9 + - - +
4143D THR* 3.3 18.6 - - - +
4144D ASN* 3.4 12.5 - - - +
4173D LEU* 4.2 19.3 - - + -
4189D TYR* 4.0 37.8 - - + +
4190D PHE 4.7 8.1 - - - +
4191D GLU* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4141 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4019D VAL* 4.3 28.0 - - + +
4022D LEU* 5.6 6.5 - - + -
4023D LEU* 3.7 21.1 - - + -
4137D ASN* 3.2 21.1 + - - +
4138D VAL* 3.4 26.9 - - + +
4140D VAL* 1.3 79.4 - - - +
4142D LEU* 1.3 71.7 + - + +
4144D ASN* 3.2 11.7 + - - +
4145D LEU* 3.1 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4138D VAL* 3.1 23.3 + - + +
4139D ALA* 4.0 5.2 - - - +
4140D VAL 3.4 0.4 - - - -
4141D LEU* 1.3 83.0 - - + +
4143D THR* 1.3 50.2 + - - +
4145D LEU* 3.3 17.3 - - - +
4146D SER* 2.5 27.9 + - - -
4159D LEU* 5.5 14.4 - - + +
4162D ALA* 5.7 8.1 - - + -
4166D LEU* 6.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4139D ALA 3.3 18.5 + - - +
4140D VAL* 3.3 16.2 - - - +
4142D LEU* 1.3 77.8 - - - +
4144D ASN* 1.3 61.5 + - - +
4146D SER* 3.5 6.4 + - - -
4147D GLU* 3.4 31.2 + - - +
4173D LEU* 4.4 15.7 - - + -
4189D TYR* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4022D LEU 5.9 0.4 + - - -
4023D LEU* 5.7 7.5 - - + +
4026D LEU* 4.1 21.9 + - - +
4140D VAL 3.4 17.8 + - - +
4141D LEU* 3.2 9.3 + - - +
4143D THR* 1.3 78.6 - - + +
4145D LEU* 1.3 65.7 + - - +
4147D GLU* 3.7 1.2 + - - +
4148D HIS* 3.1 63.2 + - - -
4187D ARG* 4.8 11.8 - - - +
4189D TYR* 5.6 6.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4026D LEU* 5.5 5.6 - - + -
4036D ALA 5.8 2.0 - - - +
4039D MET* 4.2 26.2 - - + +
4040D VAL* 4.2 22.3 - - + +
4043D LEU* 4.3 26.9 - - + -
4141D LEU* 3.1 29.1 + - + +
4142D LEU* 3.3 23.1 - - - +
4144D ASN* 1.3 82.1 - - - +
4146D SER* 1.3 68.2 + - - +
4148D HIS* 3.7 5.3 + - - +
4149D VAL* 3.2 28.4 + - - +
4155D LEU* 5.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER4146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4142D LEU 2.5 26.1 + - - -
4143D THR* 3.5 8.8 + - - -
4145D LEU* 1.3 83.2 - - - +
4147D GLU* 1.3 62.4 + - - +
4149D VAL* 3.3 24.6 - - - +
4155D LEU* 4.4 22.0 - - - -
4159D LEU* 5.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU4147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4031D VAL* 5.3 1.0 - - - +
4143D THR* 3.4 25.3 + - - +
4144D ASN* 4.2 3.3 - - - +
4145D LEU 3.4 0.2 - - - -
4146D SER* 1.3 78.0 + - - +
4148D HIS* 1.3 72.7 + - + +
4149D VAL 3.7 4.9 - - - +
4187D ARG* 2.6 50.0 + - - -
5026D PHE* 4.7 7.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS4148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4026D LEU* 3.5 35.7 - - + +
4027D GLU 5.9 0.9 - - - -
4029D ASN 5.9 2.7 - - - -
4030D VAL 5.6 0.4 + - - -
4031D VAL* 3.0 60.0 - - + +
4036D ALA* 5.2 3.3 - - + +
4144D ASN* 3.1 48.9 + - - +
4145D LEU* 4.1 4.9 - - - +
4146D SER 3.4 0.4 - - - -
4147D GLU* 1.3 87.6 - - + +
4149D VAL* 1.3 65.3 + - + +
4150D PRO* 3.6 2.9 - - - +
4186D GLU* 6.1 2.6 - - + +
4187D ARG* 5.8 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4031D VAL 4.3 5.8 - - - +
4036D ALA* 5.0 8.1 - - + +
4037D ARG* 5.4 8.7 - - + -
4040D VAL* 3.8 26.0 - - + -
4145D LEU 3.2 21.3 + - - +
4146D SER* 3.3 22.9 - - - +
4147D GLU 3.7 4.6 - - - +
4148D HIS* 1.3 78.9 - - + +
4150D PRO* 1.3 74.0 - - + +
4151D HIS 4.6 1.3 - - - +
4152D ASP* 4.1 27.8 - - + +
4155D LEU* 4.6 4.9 - - + -
----------------------------------------------------------
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