Contacts of the helix formed by residues 698 - 716 (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 GLN 698 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6961 ASP* 3.2 12.4 - - - +
6971 GLU* 1.3 79.4 - - - +
6991 GLN* 1.3 65.6 + - - +
7001 LYS 3.8 0.4 - - - -
7011 VAL* 4.7 3.7 - - - -
7021 ARG* 4.1 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 699 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6971 GLU 3.6 1.7 + - - -
6981 GLN* 1.3 70.0 - - - +
7001 LYS* 1.3 71.1 + - - +
7011 VAL 3.0 2.5 - - - -
7021 ARG* 2.6 18.1 + - - +
7031 THR* 2.9 6.3 + - - -
159G U 4.9 15.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 700 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6621 HIS* 6.2 0.2 - - - -
6991 GLN* 1.3 70.6 - - - +
7011 VAL* 1.3 56.1 + - - +
7031 THR* 2.2 29.9 + - - +
7041 ILE* 2.8 13.6 + - - +
158G U 5.4 8.3 + - - -
159G U 5.5 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 701 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6611 ARG 5.9 0.9 - - - -
6621 HIS* 5.1 17.1 - - - +
6931 GLY* 5.0 10.0 - - - -
6981 GLN* 4.6 3.8 + - - +
6991 GLN 2.8 2.4 + - - +
7001 LYS* 1.3 73.4 - - - +
7021 ARG* 1.3 64.3 + - - +
7041 ILE* 4.9 0.9 - - - +
7051 SER* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 702 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6931 GLY 4.7 3.4 + - - -
6941 LEU* 4.4 26.8 - - - +
6961 ASP* 5.6 1.9 - - - +
6981 GLN 4.1 6.9 + - - -
6991 GLN 2.6 15.4 + - - -
7011 VAL* 1.3 72.7 - - - +
7031 THR* 1.3 65.5 + - - +
7051 SER* 3.5 0.5 - - - -
7061 ALA* 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 703 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6991 GLN 2.9 6.0 + - - -
7001 LYS* 2.2 19.6 + - - +
7021 ARG* 1.3 72.2 - - - +
7041 ILE* 1.3 64.2 + - - +
7061 ALA* 3.2 1.4 + - - -
7071 LEU* 3.0 16.8 + - - -
7421 GLY* 5.2 15.0 - - - -
7451 ALA* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 704 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6651 ILE* 6.0 4.8 - - - -
6661 LYS* 6.1 2.0 - - - +
7001 LYS* 2.8 12.3 + - - +
7011 VAL* 4.3 0.9 - - - +
7031 THR* 1.3 70.4 - - - +
7051 SER* 1.3 69.0 + - - +
7071 LEU* 2.9 5.3 + - - +
7081 ALA* 2.8 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 705 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6651 ILE* 5.9 6.5 - - - +
6901 ILE* 5.6 5.6 - - - +
6931 GLY* 6.2 1.6 - - - -
6941 LEU* 6.0 3.6 - - - +
7011 VAL 3.0 16.5 + - - -
7021 ARG 3.5 3.6 - - - -
7031 THR 3.0 0.2 + - - -
7041 ILE* 1.3 73.6 - - - +
7061 ALA* 1.3 66.8 + - - +
7081 ALA* 2.5 16.3 + - - -
7091 ILE 3.1 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 706 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6941 LEU* 5.9 2.6 - - - +
7021 ARG 3.0 11.4 + - - -
7031 THR 3.7 2.2 - - - -
7051 SER* 1.3 73.1 - - - +
7071 LEU* 1.3 65.4 + - - +
7091 ILE* 2.8 15.9 + - - +
7101 ALA* 3.0 9.0 + - - -
7451 ALA 5.8 4.3 - - - -
7461 PHE* 5.9 6.1 - - - +
7491 ALA* 5.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 707 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7031 THR 3.0 9.4 + - - -
7041 ILE* 2.9 9.8 + - - +
7061 ALA* 1.3 74.5 - - - +
7081 ALA* 1.3 67.1 + - - +
7101 ALA* 3.0 5.4 + - - +
7111 ALA* 3.0 14.2 + - - -
7451 ALA* 5.7 8.9 + - - +
7491 ALA 6.1 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 708 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6651 ILE 6.0 0.9 - - - -
6691 GLN* 4.8 20.3 - - - +
7041 ILE 2.8 8.1 + - - -
7051 SER 2.5 14.2 + - - -
7071 LEU* 1.3 69.5 - - - +
7091 ILE* 1.3 54.0 + - - +
7111 ALA* 2.5 28.2 + - - +
7121 LEU* 2.9 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 709 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7051 SER 3.1 6.1 + - - -
7061 ALA* 2.8 12.6 + - - +
7081 ALA* 1.3 68.0 - - - +
7101 ALA* 1.3 67.8 + - - +
7121 LEU* 3.2 2.6 + - - +
7131 ALA* 2.9 16.6 + - - -
7491 ALA* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 710 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7061 ALA 3.0 6.6 + - - -
7071 LEU* 3.0 7.5 + - - +
7081 ALA 2.8 1.4 + - - -
7091 ILE* 1.3 79.3 - - - +
7111 ALA* 1.3 65.3 + - - +
7131 ALA* 2.7 10.4 + - - -
7141 GLU* 2.9 9.0 + - - -
7481 LYS 4.8 3.4 - - - -
7491 ALA* 4.0 26.8 - - - +
7521 TYR* 5.8 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 711 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6691 GLN* 6.4 1.6 - - - +
6721 ALA* 5.5 10.0 - - - +
6731 ILE* 6.1 1.3 - - - +
7071 LEU 3.0 7.8 + - - -
7081 ALA* 2.5 12.8 + - - +
7101 ALA* 1.3 69.2 - - - +
7121 LEU* 1.3 65.3 + - - +
7141 GLU* 2.8 12.5 + - - +
7151 ALA* 2.9 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 712 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6721 ALA* 5.4 9.6 - - - +
7081 ALA 2.9 11.0 + - - -
7091 ILE* 3.6 3.8 - - - +
7111 ALA* 1.3 72.6 - - - +
7131 ALA* 1.3 54.6 + - - +
7151 ALA* 2.5 27.7 + - - -
7161 ALA* 2.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 713 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7091 ILE 2.9 9.1 + - - -
7101 ALA 2.7 11.8 + - - -
7121 LEU* 1.3 70.2 - - - +
7141 GLU* 1.3 54.8 + - - +
7161 ALA* 2.6 29.0 + - - +
7171 THR* 3.4 7.1 + - - -
7521 TYR 5.1 13.0 - - - -
7531 LEU* 6.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 714 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7101 ALA 2.9 7.7 + - - -
7111 ALA* 2.8 11.7 + - - +
7131 ALA* 1.3 76.0 - - - +
7151 ALA* 1.3 58.6 + - - +
7171 THR* 4.4 4.0 + - - -
7521 TYR* 5.9 4.7 - - - +
153G C 5.8 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 715 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6721 ALA 5.9 1.1 - - - -
6761 GLY* 4.6 19.0 - - - +
6771 CYS* 3.9 20.9 - - - +
7111 ALA 2.9 6.6 + - - -
7121 LEU 2.5 16.0 + - - -
7141 GLU* 1.3 71.4 - - - +
7161 ALA* 1.3 54.6 + - - -
7171 THR 3.1 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 716 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6801 LEU* 6.5 0.9 - - - +
7121 LEU 2.9 7.1 + - - -
7131 ALA* 2.6 22.0 + - - +
7151 ALA* 1.3 71.9 - - - +
7171 THR* 1.3 50.3 + - - +
7181 PRO 3.0 0.9 - - - -
7191 TYR* 2.4 42.4 + - - +
----------------------------------------------------------
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