Contacts of the helix formed by residues 4831 - 4856 (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 ASN4831 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4829D THR 3.4 0.2 + - - -
4830D HIS* 1.3 94.8 + - + +
4832D GLY* 1.3 59.1 + - - +
4833D LYS* 3.3 3.6 - - - +
4834D GLN* 2.9 31.4 + - - +
4835D LEU* 3.9 7.3 + - - +
4933D LEU* 5.6 13.7 - - + +
4937D ALA* 5.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4832 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4829D THR* 3.0 19.6 + - - -
4830D HIS 4.2 0.7 - - - -
4831D ASN* 1.3 74.4 - - - +
4833D LYS* 1.3 63.5 + - - +
4834D GLN 3.2 2.5 - - - -
4835D LEU* 3.1 25.8 + - - +
4836D VAL* 3.3 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS4833 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4831D ASN* 3.3 1.2 - - - -
4832D GLY* 1.3 76.4 - - - +
4834D GLN* 1.3 66.3 + - - +
4836D VAL* 3.3 22.0 - - - +
4837D MET* 3.8 7.4 + - - +
4820F THR* 4.7 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN4834 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4831D ASN* 2.9 34.3 - - - +
4832D GLY 3.2 0.2 - - - -
4833D LYS* 1.3 82.4 + - + +
4835D LEU* 1.3 62.3 + - - +
4836D VAL 3.4 0.2 - - - -
4837D MET* 3.1 2.8 + - - +
4838D THR* 3.0 26.9 + - + +
4933D LEU* 4.9 22.7 - - + +
4820F THR* 3.8 29.3 + - + +
4938F PHE* 6.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4835 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4828D VAL* 3.6 28.7 - - + +
4830D HIS 6.0 0.4 - - - +
4831D ASN 3.9 4.7 + - - +
4832D GLY* 3.1 19.0 + - - +
4834D GLN* 1.3 78.0 - - - +
4836D VAL* 1.3 63.3 + - - +
4838D THR* 3.3 9.1 - - + +
4839D VAL* 3.1 47.4 + - + +
4930D ILE* 5.6 7.4 - - + -
4933D LEU* 6.2 3.8 - - + +
4934D ILE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4836 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4832D GLY 3.3 9.0 + - - +
4833D LYS* 3.3 22.4 - - - +
4835D LEU* 1.3 81.0 - - - +
4837D MET* 1.3 57.6 + - + +
4839D VAL* 4.1 5.7 - - + +
4840D GLY* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET4837 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4833D LYS 3.9 6.7 - - - +
4834D GLN 3.1 10.6 + - - +
4836D VAL* 1.3 80.0 - - + +
4838D THR* 1.3 53.1 + - - +
4840D GLY* 3.2 3.2 + - - -
4841D LEU* 2.7 40.0 + - + +
4818F VAL* 6.1 2.0 - - + -
4820F THR* 3.7 27.8 - - + -
4821F LEU* 5.0 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR4838 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4834D GLN* 3.0 19.6 + - + +
4835D LEU* 3.3 15.9 - - + +
4837D MET* 1.3 71.0 - - - +
4839D VAL* 1.3 54.9 + - - +
4841D LEU* 3.1 15.4 + - - +
4842D LEU* 2.6 35.2 + - - +
4926D LEU* 4.6 2.9 + - - +
4929D ILE* 4.1 29.0 - - + +
4930D ILE* 3.3 27.9 - - + +
4933D LEU* 5.9 3.6 - - + -
4824F ILE* 5.7 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4839 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920B PHE* 6.2 6.1 - - + -
4835D LEU* 3.1 37.8 + - + +
4836D VAL* 4.1 5.8 - - + +
4838D THR* 1.3 76.2 - - - +
4840D GLY* 1.3 56.8 + - - +
4842D LEU* 3.1 17.3 + - + +
4843D ALA* 2.9 28.5 + - + +
4885D MET* 6.5 0.4 - - + -
4930D ILE* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY4840 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4836D VAL 3.0 17.3 + - - -
4837D MET 3.2 4.0 + - - -
4839D VAL* 1.3 77.9 - - - +
4841D LEU* 1.3 59.6 + - - +
4843D ALA* 3.2 7.9 + - - +
4844D VAL* 3.2 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4841 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4837D MET* 2.7 21.0 + - + +
4838D THR* 3.1 15.0 + - - +
4840D GLY* 1.3 74.2 - - - +
4842D LEU* 1.3 61.1 + - - +
4844D VAL* 3.2 17.8 - - + +
4845D VAL* 3.2 22.0 - - + +
4815F ALA* 4.1 26.5 - - + +
4821F LEU* 3.6 37.2 - - + +
4824F ILE* 3.7 35.2 - - + -
4825F LEU* 6.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4842 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920B PHE* 5.3 8.3 - - + -
4838D THR* 2.6 20.0 + - - +
4839D VAL* 3.1 17.7 + - + +
4841D LEU* 1.3 73.6 - - - +
4843D ALA* 1.3 62.4 + - + +
4845D VAL* 3.3 16.1 - - + +
4846D VAL* 3.2 22.6 - - + +
4885D MET* 3.7 34.5 - - + -
4889D VAL* 5.0 13.2 - - + -
4922D VAL* 5.4 3.6 - - + +
4926D LEU* 4.6 22.2 - - + -
4927D LEU* 4.7 15.5 - - + -
4930D ILE* 4.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4843 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4839D VAL* 2.9 15.8 + - + +
4840D GLY* 3.2 8.9 + - - +
4842D LEU* 1.3 82.1 - - + +
4844D VAL* 1.3 62.8 + - + +
4846D VAL* 3.3 16.1 - - - +
4847D TYR* 3.4 9.4 + - - +
4881D TYR* 3.2 25.6 + - - +
4885D MET* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4844 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4840D GLY 3.2 14.5 + - - +
4841D LEU* 3.2 31.2 - - + +
4843D ALA* 1.3 80.2 - - + +
4845D VAL* 1.3 67.8 + - + +
4847D TYR* 3.1 9.2 + - + +
4848D LEU* 3.0 30.9 + - + +
4569F PHE* 6.2 4.5 - - + -
4811F LEU* 4.9 20.4 - - + +
4814F ILE* 5.7 4.7 - - + -
4815F ALA* 4.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4845 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4841D LEU* 3.2 22.7 - - + +
4842D LEU* 3.3 17.0 - - + +
4844D VAL* 1.3 82.3 - - + +
4846D VAL* 1.3 62.9 + - + +
4848D LEU* 3.4 13.8 + - + +
4849D TYR* 3.1 34.9 + - + -
4921D PHE* 6.6 0.2 - - + -
4922D VAL* 4.0 23.3 - - + -
4926D LEU* 5.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4846 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4842D LEU* 3.2 22.7 - - + +
4843D ALA* 3.3 16.8 - - - +
4845D VAL* 1.3 75.5 - - - +
4847D TYR* 1.3 54.3 + - - +
4849D TYR* 3.4 8.8 + - - +
4850D THR* 2.3 38.6 + - - +
4881D TYR* 4.1 14.1 - - + +
4884D HIS* 5.2 13.6 + - + +
4885D MET* 4.8 20.0 - - + -
4889D VAL* 5.4 9.2 - - + -
4918D PHE* 4.5 15.0 - - + -
4922D VAL* 4.4 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4847 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4843D ALA 3.5 12.1 - - - +
4844D VAL* 3.1 14.6 + - + +
4846D VAL* 1.3 80.0 - - - +
4848D LEU* 1.3 75.8 + - + +
4850D THR* 3.2 17.3 + - + -
4851D VAL* 3.3 32.6 + - + +
4881D TYR* 4.1 23.6 - + + -
4572F ASN* 3.1 49.1 + - + +
4575F LEU* 4.4 11.8 - - - +
4576F LEU* 4.8 11.7 + - + -
4808F ALA* 4.9 11.4 - - + -
4811F LEU* 4.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU4848 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4844D VAL* 3.0 17.6 + - + +
4845D VAL* 3.8 14.1 - - + +
4846D VAL 3.3 0.2 - - - -
4847D TYR* 1.3 80.7 - - + +
4849D TYR* 1.3 63.0 + - + +
4851D VAL* 3.2 11.4 - - - +
4852D VAL* 3.2 24.3 - - - +
4808F ALA* 3.3 34.8 - - + +
4811F LEU* 4.1 15.0 - - + -
4812F LEU* 4.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR4849 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4845D VAL* 3.1 29.3 + - + +
4846D VAL* 3.7 6.1 - - - +
4847D TYR 3.3 0.2 - - - -
4848D LEU* 1.3 78.8 - - + +
4850D THR* 1.3 60.1 + - - +
4852D VAL* 3.3 21.9 - - + +
4853D ALA* 3.5 11.4 + - - +
4884D HIS* 4.5 5.3 + - - +
4914D PHE* 3.5 36.6 - + + -
4917D THR* 3.6 31.3 + - + +
4918D PHE* 3.8 38.8 - + + -
4921D PHE* 4.3 12.5 - + + -
4922D VAL* 4.9 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR4850 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4846D VAL* 2.3 28.6 + - - +
4847D TYR* 3.5 13.3 - - + -
4848D LEU 3.2 0.4 - - - -
4849D TYR* 1.3 77.4 - - - +
4851D VAL* 1.3 62.4 + - + +
4852D VAL 3.2 0.2 - - - -
4853D ALA* 3.2 3.5 + - - +
4854D PHE* 3.0 28.0 + - + +
4877D MET 4.6 5.4 - - - +
4880D CYS* 3.9 27.9 - - + +
4881D TYR* 3.9 27.9 - - + +
4884D HIS* 4.0 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4851 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4847D TYR* 3.3 37.2 + - + +
4848D LEU* 3.2 17.9 - - - +
4850D THR* 1.3 78.5 - - + +
4852D VAL* 1.3 64.1 + - + +
4854D PHE* 3.5 6.8 + - - +
4855D ASN* 3.2 33.8 + - - +
4575F LEU* 6.6 0.2 - - + -
4805F PHE* 3.7 25.6 - - + -
4808F ALA* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4852 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4848D LEU 3.2 13.9 - - - +
4849D TYR* 3.3 26.9 - - + +
4851D VAL* 1.3 82.6 - - + +
4853D ALA* 1.3 64.5 + - - +
4855D ASN* 4.5 2.0 - - - +
4856D PHE* 3.2 45.2 + - + +
4857D PHE* 3.9 7.5 + - + -
4910D TYR* 5.9 1.8 - - - +
4914D PHE* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4853 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4849D TYR 3.5 14.1 + - - +
4850D THR 3.2 5.5 + - - +
4852D VAL* 1.3 80.3 - - + +
4854D PHE* 1.3 61.3 + - - +
4855D ASN 3.2 0.4 - - - -
4857D PHE* 2.9 47.6 + - + +
4858D ARG* 4.3 0.7 - - - -
4861D TYR* 3.8 19.3 - - + +
4874D CYS* 5.9 0.2 - - - +
4880D CYS* 6.0 3.1 - - - -
4884D HIS* 3.7 22.2 - - + -
4914D PHE* 5.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4854 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4850D THR* 3.0 16.3 + - + +
4851D VAL* 4.0 6.1 - - - +
4853D ALA* 1.3 76.7 - - - +
4855D ASN* 1.3 71.6 + - - +
4858D ARG* 4.8 14.7 - - + +
4874D CYS* 3.6 30.1 - - + -
4875D ASP 4.7 2.5 - - - -
4877D MET* 4.5 29.4 - - + -
4880D CYS* 4.9 13.4 - - + -
4578F TYR* 4.6 12.8 - - + -
4579F LYS* 4.4 13.7 - - - -
4580F VAL* 3.6 30.3 - - + +
4805F PHE* 4.3 18.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN4855 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4851D VAL* 3.2 21.3 + - - +
4852D VAL* 3.7 0.8 + - - +
4853D ALA 3.2 0.2 - - - -
4854D PHE* 1.3 85.4 - - - +
4856D PHE* 1.3 89.1 + - + +
4858D ARG* 5.5 2.6 - - - +
4804F ASN* 5.6 6.5 - - - +
4805F PHE* 3.2 41.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE4856 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4852D VAL* 3.2 33.8 + - + +
4855D ASN* 1.3 100.9 - - + +
4857D PHE* 1.3 73.8 + + + +
4858D ARG* 2.8 15.6 + - - +
4859D LYS* 4.6 5.7 + - - +
4860D PHE* 5.8 0.3 - - - -
4907D TYR* 4.7 31.4 - + + -
4910D TYR* 4.9 22.7 - + + -
----------------------------------------------------------
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