Contacts of the strand formed by residues 1015 - 1024 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011E ALA* 4.0 0.4 - - - -
1012E VAL* 2.8 44.1 + - - +
1013E ASP 3.3 4.5 + - - +
1014E GLY* 1.3 74.7 - - - +
1016E PRO* 1.3 84.7 - - + +
1017E LEU* 3.3 3.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1016 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010E ILE 3.7 6.5 - - - +
1011E ALA* 4.1 4.7 - - + -
1014E GLY 3.2 9.9 - - - +
1015E GLU* 1.3 96.0 - - + +
1017E LEU* 1.3 62.1 + - - +
1018E GLY 5.1 0.9 - - - +
1159E ALA* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1017 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010E ILE* 2.7 27.5 + - + +
1012E VAL* 3.9 32.1 - - + -
1015E GLU* 3.3 3.3 + - + +
1016E PRO* 1.3 76.5 - - - +
1018E GLY* 1.3 57.4 + - - +
1138E ILE* 3.9 39.4 - - + +
1141E ALA* 4.3 22.2 - - + -
1142E MET* 4.8 2.0 - - - +
1145E PHE* 5.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1018 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009E ASP* 3.6 5.2 - - - -
1010E ILE* 2.7 37.4 + - - +
1016E PRO* 3.8 1.2 - - - +
1017E LEU* 1.3 82.8 - - - +
1019E ARG* 1.3 57.5 + - - -
1138E ILE* 3.7 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1019 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007E PHE* 3.2 53.9 - - + -
1008E PHE 3.3 10.5 - - - +
1009E ASP* 3.3 29.9 + - - +
1018E GLY* 1.3 74.9 - - - -
1020E VAL* 1.3 68.8 + - - +
1021E SER* 4.3 3.8 - - - +
1134E GLU 4.4 0.2 - - - +
1135E GLY* 3.8 10.0 - - - -
1138E ILE* 3.7 14.6 - - - +
1164E LEU* 4.0 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1020 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007E PHE* 3.0 4.3 - - - -
1008E PHE* 2.8 61.9 + - + +
1010E ILE* 4.1 15.0 - - + -
1019E ARG* 1.3 77.2 - - - +
1021E SER* 1.3 62.9 + - - +
1022E PHE* 3.6 30.8 - - + -
1114E ILE* 5.5 0.9 - - + -
1132E VAL* 4.1 8.5 - - + -
1134E GLU 3.6 10.8 - - - +
1135E GLY 4.1 8.1 - - - +
1138E ILE* 4.7 2.2 - - + -
1139E VAL* 4.0 23.3 - - + -
1142E MET* 5.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1021 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005E THR* 4.4 4.7 - - - -
1006E VAL 3.2 11.7 - - - -
1007E PHE* 3.7 9.2 - - - -
1019E ARG* 4.3 5.2 - - - +
1020E VAL* 1.3 74.9 - - - +
1022E PHE* 1.3 62.8 + - - +
1132E VAL* 3.6 6.6 - - - +
1133E LYS* 2.9 46.7 + - - -
1134E GLU* 3.0 24.3 + - - +
1164E LEU* 5.2 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1022 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005E THR* 3.2 10.4 - - - +
1006E VAL* 2.8 53.4 + - + +
1007E PHE* 4.2 0.9 - - - -
1008E PHE* 3.6 35.7 - + - -
1020E VAL* 3.6 27.4 - - + -
1021E SER* 1.3 74.7 - - - +
1023E GLU* 1.3 61.6 + - - +
1024E LEU* 4.0 10.1 - - + -
1036E PHE* 4.7 2.5 - + - -
1098E LEU* 4.3 19.7 - - + -
1114E ILE* 3.7 36.6 - - + -
1131E LYS 3.3 10.3 - - - +
1132E VAL* 3.7 31.2 - - + -
1133E LYS* 3.8 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1023 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003E ASN* 2.9 37.9 + - + +
1004E PRO 3.7 4.0 - - - +
1005E THR* 4.7 3.1 - - - +
1022E PHE* 1.3 73.4 - - - +
1024E LEU* 1.3 62.8 + - - +
1025E PHE* 3.7 21.2 - - + -
1130E GLY* 3.2 2.9 - - - -
1131E LYS* 2.8 48.2 + - - +
1133E LYS* 3.7 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1024 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003E ASN* 3.2 20.1 + - - +
1004E PRO* 2.9 26.1 + - + +
1006E VAL* 4.1 17.9 - - + -
1022E PHE* 4.5 2.2 - - + -
1023E GLU* 1.3 77.2 - - - +
1025E PHE* 1.3 62.6 + - - +
1026E ALA 3.0 7.1 + - - -
1033E ALA* 3.7 32.5 - - + +
1036E PHE* 3.7 19.7 - - + -
1037E ARG* 3.8 26.7 - - + +
1098E LEU* 3.7 30.5 - - + -
1129E PHE* 3.5 12.1 - - + +
----------------------------------------------------------
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