Contacts of the strand formed by residues 1005 - 1012 (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 THR1005 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1003E ASN 3.8 7.4 + - - -
1004E PRO* 1.3 74.8 + - - +
1006E VAL* 1.3 62.3 - - - +
1021E SER* 4.4 4.5 - - - -
1022E PHE 3.2 15.7 + - - +
1023E GLU* 4.8 3.8 - - - +
1133E LYS* 3.4 36.8 - - - +
1163E GLN* 3.4 6.2 - - - +
1164E LEU* 2.8 42.4 + - + -
1165E GLU* 3.0 29.6 + - - +
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Residues in contact with VAL1006 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005E THR* 1.3 78.3 - - - +
1007E PHE* 1.3 65.1 + - - +
1008E PHE* 5.7 0.2 - - + -
1021E SER* 3.2 5.6 - - - -
1022E PHE* 2.8 36.4 + - + -
1024E LEU* 4.1 15.3 - - + -
1036E PHE* 3.6 33.7 - - + -
1037E ARG* 3.8 28.9 - - + +
1040E SER* 3.7 18.4 - - - +
1162E GLY 3.0 14.6 - - - +
1163E GLN* 4.2 8.3 - - + -
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Residues in contact with PHE1007 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006E VAL* 1.3 76.7 - - - +
1008E PHE* 1.3 71.5 + - - +
1009E ASP* 3.2 24.0 - - - -
1019E ARG* 3.2 42.0 - - + -
1020E VAL 3.0 16.2 - - - +
1021E SER* 3.7 12.1 - - - -
1022E PHE* 4.2 2.7 - - - -
1040E SER* 4.9 0.7 - - - -
1160E ASP* 3.9 11.0 - - + -
1161E CYS* 2.9 36.2 - - - +
1162E GLY* 3.0 44.2 + - - -
1163E GLN 5.2 0.2 - - - -
1164E LEU* 3.6 32.5 - - + -
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Residues in contact with PHE1008 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006E VAL* 5.7 0.2 - - + -
1007E PHE* 1.3 89.1 - - - +
1009E ASP* 1.3 59.9 + - - +
1010E ILE* 3.7 10.5 + - + -
1019E ARG* 3.3 1.7 - - - -
1020E VAL* 2.8 51.5 + - + +
1022E PHE* 3.6 23.8 - + - -
1036E PHE* 3.6 23.6 - + - -
1040E SER* 4.1 8.1 - - - -
1048E TYR* 3.7 24.5 - + - -
1053E PHE* 4.2 9.4 - + - -
1112E PHE* 3.5 29.6 - + - -
1114E ILE* 5.1 0.2 - - + -
1158E ILE* 3.6 26.7 - - + -
1160E ASP 3.3 4.3 - - - -
1161E CYS* 3.4 18.4 - - + -
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Residues in contact with ASP1009 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007E PHE* 3.2 23.6 - - - -
1008E PHE* 1.3 70.6 - - - +
1010E ILE* 1.3 60.1 + - - +
1018E GLY 3.6 5.4 - - - +
1019E ARG* 3.3 37.1 + - - +
1157E THR 3.5 0.7 - - - +
1158E ILE 3.5 0.7 - - - -
1159E ALA* 2.6 41.5 + - + +
1160E ASP* 2.5 33.9 + - + +
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Residues in contact with ILE1010 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008E PHE* 3.8 22.4 - - + -
1009E ASP* 1.3 73.3 - - - +
1011E ALA* 1.3 60.1 + - - +
1012E VAL* 5.1 0.4 - - + -
1016E PRO* 3.6 2.3 - - - +
1017E LEU* 2.7 48.1 + - + +
1018E GLY 2.7 17.1 + - - +
1020E VAL* 4.1 11.0 - - + -
1053E PHE* 4.2 13.2 - - + -
1138E ILE* 3.9 16.6 - - + -
1142E MET* 3.3 38.8 - - + -
1156E ILE* 3.6 19.3 - - + -
1157E THR 3.3 10.3 - - - +
1158E ILE* 4.3 2.7 - - + -
1159E ALA* 5.0 0.4 - - - -
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Residues in contact with ALA1011 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010E ILE* 1.3 76.9 - - - +
1012E VAL* 1.3 62.6 + - - +
1013E ASP 3.8 0.4 - - - -
1014E GLY* 3.6 31.6 - - - +
1015E GLU 3.3 6.7 - - - +
1016E PRO* 4.2 2.2 - - + -
1155E LYS 3.6 1.4 - - - +
1156E ILE* 3.3 7.1 - - - +
1157E THR* 2.9 40.9 + - - +
1159E ALA* 4.2 17.5 - - + -
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Residues in contact with VAL1012 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010E ILE* 5.1 1.6 - - + -
1011E ALA* 1.3 73.0 - - - +
1013E ASP* 1.3 72.5 + - - +
1015E GLU* 2.8 36.0 + - - +
1017E LEU* 3.9 33.4 - - + -
1142E MET* 6.3 0.4 - - - -
1145E PHE* 3.7 26.0 - - + -
1154E LYS* 3.2 42.0 - - + -
1155E LYS 4.0 2.0 - - - -
1156E ILE* 4.0 9.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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