Contacts of the helix formed by residues 1070 - 1089 (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 LYS1070 (chain 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10681 ALA* 3.1 11.4 - - - +
10691 HIS* 1.3 77.8 - - - +
10711 LYS* 1.3 66.3 + - - +
10721 ALA 3.7 0.9 - - - +
10731 ILE* 4.6 3.3 + - - +
10741 ARG* 4.4 7.1 + - - -
147G C 6.4 0.2 - - - -
148G U 4.8 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1071 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10701 LYS* 1.3 74.2 - - - +
10721 ALA* 1.3 66.2 + - - +
10741 ARG* 3.0 6.6 + - - -
10751 ARG* 2.9 18.1 + - - -
144G A 4.7 10.2 - - - -
148G U 5.0 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1072 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10701 LYS* 3.7 0.6 - - - +
10711 LYS* 1.3 74.3 - - - +
10731 ILE* 1.3 66.3 + - - +
10751 ARG* 3.0 3.2 + - - +
10761 ALA* 2.9 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1073 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10321 GLN 5.9 2.0 - - - -
10331 GLU* 5.7 9.0 - - - +
10651 LEU 5.9 0.7 - - - -
10701 LYS* 4.6 3.4 + - - +
10711 LYS 3.2 1.2 - - - -
10721 ALA* 1.3 76.4 - - - +
10741 ARG* 1.3 63.9 + - - +
10761 ALA* 3.3 0.5 + - - -
10771 THR* 2.7 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1074 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10651 LEU 5.4 7.8 + - - -
10661 LEU* 6.0 3.8 - - - +
10681 ALA* 6.0 2.6 - - - +
10701 LYS 4.4 5.9 + - - -
10711 LYS 3.0 7.7 + - - -
10731 ILE* 1.3 73.4 - - - +
10751 ARG* 1.3 66.1 + - - +
10771 THR* 4.3 2.5 - - - +
10781 VAL* 2.9 17.7 + - - -
144G A 4.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1075 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10711 LYS 2.9 13.1 + - - -
10721 ALA* 3.0 6.4 + - - +
10731 ILE 3.0 1.2 + - - -
10741 ARG* 1.3 79.1 - - - +
10761 ALA* 1.3 64.0 + - - +
10771 THR 3.0 0.2 + - - -
10781 VAL* 3.0 7.6 + - - -
10791 ASN* 3.2 8.8 + - - -
144G A 3.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1076 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10361 ILE 5.5 8.6 - - - +
10371 ASP* 6.5 1.1 - - - +
10401 GLY* 6.1 0.3 - - - -
10721 ALA 2.9 13.4 + - - -
10731 ILE 3.9 0.4 - - - -
10751 ARG* 1.3 72.3 - - - +
10771 THR* 1.3 63.3 + - - +
10791 ASN* 3.1 3.0 + - - +
10801 THR* 2.8 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1077 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10361 ILE* 6.2 3.1 - - - +
10731 ILE 2.7 18.4 + - - -
10741 ARG* 3.5 3.4 - - - +
10751 ARG 3.0 0.4 - - - -
10761 ALA* 1.3 77.0 - - - +
10781 VAL* 1.3 63.2 + - - +
10801 THR* 3.2 2.3 + - - +
10811 PHE* 2.9 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1078 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10741 ARG 2.9 13.6 + - - -
10751 ARG 3.6 2.7 - - - -
10771 THR* 1.3 74.6 - - - +
10791 ASN* 1.3 54.7 + - - +
10811 PHE* 2.5 27.7 + - - +
10821 GLY 3.0 8.3 + - - -
11111 CYS 6.0 1.3 - - - -
11141 VAL 6.4 0.2 - - - -
11151 ALA* 5.9 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1079 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10751 ARG 3.2 9.3 + - - -
10761 ALA* 3.1 7.4 + - - +
10781 VAL* 1.3 74.2 - - - +
10801 THR* 1.3 60.8 + - - +
10821 GLY* 3.4 3.7 + - - +
10831 TYR* 3.0 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1080 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10401 GLY* 5.0 16.8 - - - -
10761 ALA 2.8 13.3 + - - -
10771 THR 3.5 3.8 - - - -
10781 VAL 2.8 0.6 + - - -
10791 ASN* 1.3 73.2 - - - +
10811 PHE* 1.3 57.7 + - - +
10831 TYR* 2.4 26.9 + - - +
10841 ILE 3.0 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1081 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10771 THR 2.9 9.0 + - - -
10781 VAL* 2.5 16.7 + - - +
10801 THR* 1.3 68.9 - - - +
10821 GLY* 1.3 59.2 + - - +
10841 ILE* 3.6 1.4 + - - +
10851 ALA* 3.0 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1082 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10781 VAL 3.0 8.5 + - - -
10791 ASN* 3.6 4.9 - - - -
10801 THR 2.8 1.4 + - - -
10811 PHE* 1.3 73.6 - - - +
10831 TYR* 1.3 66.0 + - - -
10851 ALA* 2.7 13.3 + - - -
10861 LYS 2.8 11.3 + - - -
11181 ILE* 5.5 2.5 - - - -
11191 VAL* 5.2 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1083 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10431 ALA 4.3 17.2 - - - +
10441 ASP* 5.3 6.3 - - - +
10791 ASN 3.0 9.5 + - - -
10801 THR* 2.4 14.7 + - - +
10821 GLY* 1.3 71.9 - - - +
10841 ILE* 1.3 61.6 + - - +
10861 LYS* 3.1 3.6 + - - -
10871 ALA* 3.1 14.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1084 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10431 ALA* 4.8 5.2 + - - +
10801 THR 3.0 9.5 + - - -
10811 PHE 4.1 1.1 - - - -
10831 TYR* 1.3 73.4 - - - +
10851 ALA* 1.3 59.7 + - - +
10871 ALA* 2.6 24.6 + - - +
10881 ILE* 2.9 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1085 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10811 PHE 3.0 13.5 + - - -
10821 GLY* 2.7 14.5 + - - -
10841 ILE* 1.3 70.9 - - - +
10861 LYS* 1.3 54.1 + - - +
10881 ILE* 4.7 0.7 - - - +
10891 GLY* 2.9 36.5 + - - +
10901 PRO* 4.4 3.1 - - - +
10931 VAL* 6.3 3.4 - - - +
11191 VAL* 6.4 2.0 - - - +
11221 THR 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1086 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10821 GLY 2.8 12.1 + - - -
10831 TYR* 3.5 5.2 - - - +
10851 ALA* 1.3 78.5 - - - +
10871 ALA* 1.3 64.8 + - - +
10881 ILE 3.0 1.4 + - - -
10891 GLY* 3.5 5.7 + - - -
11221 THR* 5.0 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1087 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10471 ALA 5.8 4.3 - - - -
10831 TYR 3.1 8.9 + - - -
10841 ILE* 2.6 15.2 + - - +
10861 LYS* 1.3 72.2 - - - +
10881 ILE* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1088 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10841 ILE 2.9 11.0 + - - -
10851 ALA* 4.2 0.7 - - - +
10861 LYS 3.7 1.3 - - - -
10871 ALA* 1.3 80.4 - - - +
10891 GLY* 1.3 60.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1089 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10851 ALA* 2.9 23.5 + - - +
10861 LYS 3.5 3.3 + - - -
10881 ILE* 1.3 75.9 - - - +
10901 PRO* 1.3 65.4 - - - +
10911 HIS 3.7 1.6 + - - -
10921 ASP* 4.6 1.7 + - - -
10931 VAL* 4.4 5.9 + - - -
----------------------------------------------------------
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