Contacts of the strand formed by residues 1015 - 1024 (chain D) in PDB entry 1AWV
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 GLU1015 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011D ALA* 2.9 4.6 - - - -
1012D VAL* 2.7 54.6 + - - +
1013D ASP 2.6 10.8 + - - +
1014D GLY* 1.3 71.8 - - - +
1016D PRO* 1.3 91.0 - - + +
1017D LEU* 3.9 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1016 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010D ILE 3.8 6.5 - - - +
1011D ALA* 4.4 3.4 - - + -
1014D GLY 3.7 6.5 - - - +
1015D GLU* 1.3 100.2 - - + +
1017D LEU* 1.3 63.0 + - - +
1018D GLY 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1017 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010D ILE* 2.9 19.0 + - + +
1012D VAL* 3.6 35.0 - - + -
1015D GLU* 3.5 11.0 + - - +
1016D PRO* 1.3 73.4 - - - +
1018D GLY* 1.3 59.7 + - - +
1138D ILE* 3.6 38.5 - - + +
1141D ALA* 3.8 22.7 - - + -
1142D MET* 3.8 14.8 - - + +
1145D PHE* 4.6 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1018 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009D ASP* 4.7 2.7 - - - -
1010D ILE* 2.8 32.6 + - - +
1016D PRO* 3.8 1.0 - - - +
1017D LEU* 1.3 82.9 - - - +
1019D ARG* 1.3 59.3 + - - -
1138D ILE* 3.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1019 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007D PHE* 3.6 32.1 - - + -
1008D PHE 3.3 12.6 - - - +
1009D ASP* 3.2 31.1 + - - +
1018D GLY* 1.3 73.6 - - - -
1020D VAL* 1.3 80.7 + - - +
1021D SER* 4.5 4.7 - - - +
1134D GLU 3.8 1.0 - - - +
1135D GLY* 3.4 9.5 - - - -
1138D ILE* 3.4 20.4 - - - +
1164D LEU* 3.8 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1020 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007D PHE* 3.2 1.4 - - - -
1008D PHE* 2.8 57.4 + - + +
1010D ILE* 4.0 16.6 - - + -
1019D ARG* 1.3 81.5 - - - +
1021D SER* 1.3 61.6 + - - +
1022D PHE* 3.5 20.8 - - + -
1114D ILE* 5.3 2.5 - - + -
1132D VAL* 3.5 34.3 - - + -
1134D GLU 3.3 8.5 - - - +
1135D GLY 4.6 2.2 - - - +
1138D ILE* 5.1 1.3 - - + -
1139D VAL* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1021 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005D THR* 4.5 11.9 - - - -
1006D VAL 3.2 12.8 - - - -
1007D PHE* 3.9 7.9 - - - -
1019D ARG* 4.5 5.5 - - - +
1020D VAL* 1.3 76.0 - - - +
1022D PHE* 1.3 58.6 + - - +
1132D VAL* 3.4 7.4 - - - -
1133D LYS* 2.8 48.4 + - - +
1134D GLU* 3.2 19.0 + - - +
1164D LEU* 5.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1022 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004D PRO 3.9 0.2 - - - +
1005D THR* 3.3 9.2 - - - +
1006D VAL* 2.8 45.1 + - + +
1007D PHE* 4.3 0.7 - - - -
1008D PHE* 3.5 43.7 - + - -
1020D VAL* 3.5 32.3 - - + -
1021D SER* 1.3 77.8 - - - +
1023D GLU* 1.3 61.2 + - - +
1024D LEU* 4.0 3.1 + - + -
1036D PHE* 3.9 11.4 - + - -
1098D LEU* 3.5 33.4 - - + -
1114D ILE* 3.8 29.6 - - + -
1131D LYS 3.5 5.6 - - - +
1132D VAL* 4.0 16.4 - - + -
1133D LYS* 3.9 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1023 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003D ASN* 2.8 45.2 + - + +
1004D PRO 3.7 2.2 - - - -
1022D PHE* 1.3 72.8 - - - +
1024D LEU* 1.3 60.8 + - - +
1025D PHE* 3.2 25.0 + - + -
1130D GLY* 3.0 27.4 - - - -
1131D LYS* 3.3 26.5 + - + +
1133D LYS* 3.2 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1024 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003D ASN* 2.8 25.8 - - - +
1004D PRO* 2.9 23.9 + - + +
1006D VAL* 3.9 20.0 - - + -
1022D PHE* 4.4 1.1 - - + -
1023D GLU* 1.3 76.0 - - - +
1025D PHE* 1.3 61.6 + - - +
1026D ALA 3.0 3.3 + - - -
1033D ALA* 3.4 28.3 - - + +
1036D PHE* 3.4 31.4 - - + -
1037D ARG* 3.3 41.3 - - + +
1098D LEU* 4.3 10.5 - - + -
1129D PHE* 3.6 7.6 - - + +
----------------------------------------------------------
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