Contacts of the helix formed by residues 605 - 614 (chain 1) in PDB entry 6AH0
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 GLY 605 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6011 ALA* 4.3 4.5 - - - +
6041 ALA* 1.3 75.7 - - - +
6061 LEU* 1.3 68.1 + - - -
6071 ALA 3.5 1.3 - - - -
6081 THR* 3.1 9.0 + - - +
6091 MET* 2.9 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 606 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6011 ALA 4.8 1.3 + - - -
6041 ALA 4.2 0.4 + - - -
6051 GLY* 1.3 69.1 - - - -
6071 ALA* 1.3 54.5 + - - +
6091 MET* 2.5 27.6 + - - +
6101 ILE 3.0 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 607 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2301 LEU 5.7 0.7 - - - -
2311 ARG* 4.7 23.0 - - - +
2341 GLU* 5.0 10.3 - - - +
6051 GLY 3.5 0.4 - - - -
6061 LEU* 1.3 72.4 - - - +
6081 THR* 1.3 60.4 + - - +
6101 ILE* 4.5 2.7 - - - +
6111 SER* 2.9 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 608 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6051 GLY* 3.1 13.9 + - - +
6061 LEU 2.8 2.0 + - - -
6071 ALA* 1.3 75.8 - - - +
6091 MET* 1.3 62.5 + - - +
6121 THR* 2.8 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 609 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6011 ALA* 6.3 2.5 - - - +
6051 GLY 2.9 8.3 + - - -
6061 LEU* 2.5 14.1 + - - +
6081 THR* 1.3 72.2 - - - +
6101 ILE* 1.3 63.6 + - - +
6121 THR* 3.4 1.6 + - - +
6131 MET* 2.9 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 610 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6061 LEU 3.0 11.2 + - - -
6071 ALA* 4.1 2.5 - - - +
6091 MET* 1.3 72.0 - - - +
6111 SER* 1.3 54.5 + - - +
6121 THR 3.0 0.2 - - - -
6131 MET* 2.3 32.2 + - - +
6141 ARG 3.4 7.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 611 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2341 GLU 5.0 2.5 - - - -
2351 THR* 4.4 24.5 - - - +
3011 ARG* 5.6 6.6 - - - -
6071 ALA* 2.9 19.6 + - - +
6081 THR* 5.4 0.2 - - - +
6101 ILE* 1.3 69.4 - - - +
6121 THR* 1.3 63.0 + - - +
6141 ARG 4.7 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 612 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5721 HIS* 6.0 6.3 - - - +
6081 THR 2.8 15.2 + - - -
6091 MET 3.5 4.7 - - - -
6101 ILE 2.7 3.2 + - - -
6111 SER* 1.3 78.1 - - - +
6131 MET* 1.3 58.8 + - - +
6141 ARG 3.4 1.7 + - - -
6151 PRO 4.3 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 613 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6091 MET 2.9 9.4 + - - -
6101 ILE* 2.3 19.5 + - - +
6121 THR* 1.3 68.6 - - - +
6141 ARG* 1.3 67.7 + - - +
6151 PRO 3.4 0.9 - - - -
6161 ASP* 3.8 6.3 + - - +
6171 ILE 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 614 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6101 ILE 3.4 7.3 + - - -
6111 SER 4.7 1.6 + - - -
6121 THR 3.4 2.4 + - - -
6131 MET* 1.3 77.4 - - - +
6151 PRO* 1.3 51.7 - - - +
6161 ASP 2.5 0.6 + - - -
6171 ILE* 2.5 35.3 + - - -
6181 ASP 4.5 0.2 + - - -
----------------------------------------------------------
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