Contacts of the helix formed by residues 1030 - 1041 (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 PRO1030 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026E ALA* 3.4 26.0 - - + +
1027E ASP 4.5 2.5 - - - +
1028E LYS* 3.4 7.4 - - - +
1029E VAL* 1.3 85.7 - - - +
1031E LYS* 1.3 54.4 + - + +
1033E ALA* 3.7 0.3 - - - +
1034E GLU* 2.7 40.2 + - - +
1086E GLU* 3.3 16.8 - - - +
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Residues in contact with LYS1031 (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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1029E VAL 3.3 0.4 - - - -
1030E PRO* 1.3 79.3 - - + +
1032E THR* 1.3 62.7 + - - +
1034E GLU* 4.6 1.6 - - - -
1035E ASN* 3.2 12.0 + - - +
1079E TYR* 2.5 54.1 + - + +
1083E PHE* 3.5 30.7 - - + +
1084E GLU* 2.8 30.8 + - + +
1086E GLU* 3.6 22.4 + - + +
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Residues in contact with THR1032 (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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1029E VAL* 3.1 10.6 + - - -
1031E LYS* 1.3 74.0 - - - +
1033E ALA* 1.3 63.9 + - - +
1035E ASN* 3.6 5.2 + - - +
1036E PHE* 3.4 20.4 + - - +
1083E PHE* 3.9 19.9 - - + -
1086E GLU* 3.0 28.7 + - - +
1100E MET* 3.8 18.6 - - + +
1108E ASN* 6.1 0.7 - - - -
1127E VAL* 4.0 15.3 - - + +
1129E PHE* 3.5 33.3 - - + -
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Residues in contact with ALA1033 (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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1004E PRO* 5.7 1.6 - - + -
1024E LEU* 3.7 19.3 - - + +
1026E ALA* 3.8 30.3 - - + +
1029E VAL* 2.7 28.0 + - + +
1030E PRO 3.7 2.2 - - - +
1032E THR* 1.3 71.1 - - - +
1034E GLU* 1.3 67.1 + - - +
1036E PHE 3.1 2.8 + - - -
1037E ARG* 3.0 24.2 + - - +
1129E PHE* 4.3 11.0 - - - +
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Residues in contact with GLU1034 (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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1030E PRO 2.7 22.8 + - - +
1031E LYS* 3.9 4.7 - - - +
1033E ALA* 1.3 72.8 - - - +
1035E ASN* 1.3 58.2 + - - +
1037E ARG* 2.9 41.2 + - - +
1038E ALA* 2.9 38.7 + - - +
1043E GLU* 3.9 2.6 - - - +
1044E LYS* 4.9 1.7 + - - -
1078E ILE* 4.4 10.8 - - + +
1079E TYR* 4.1 9.2 - - + +
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Residues in contact with ASN1035 (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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1031E LYS 3.2 16.1 + - - +
1032E THR 3.6 6.7 + - - +
1033E ALA 3.2 0.4 - - - -
1034E GLU* 1.3 78.9 - - - +
1036E PHE* 1.3 60.5 + - - +
1038E ALA* 3.6 2.4 + - - +
1039E LEU* 3.2 44.3 + - - +
1048E TYR* 5.4 0.6 + - - -
1077E SER* 3.5 4.9 - - - -
1078E ILE* 3.5 28.2 + - - +
1079E TYR* 3.8 11.4 + - + +
1083E PHE* 3.0 31.8 - - + -
1100E MET* 4.2 8.5 - - - +
1109E GLY 3.3 14.8 + - - -
1110E SER* 5.1 0.2 - - - +
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Residues in contact with PHE1036 (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* 3.6 16.8 - - + -
1008E PHE* 3.6 26.0 - + - -
1022E PHE* 4.7 3.4 - + - -
1024E LEU* 3.7 17.7 - - + -
1032E THR 3.4 4.1 + - - +
1033E ALA 3.1 7.6 + - - +
1035E ASN* 1.3 80.2 - - - +
1037E ARG* 1.3 54.1 + - - +
1039E LEU* 3.5 2.2 + - - +
1040E SER* 2.7 51.2 + - - -
1048E TYR* 3.4 30.0 - + - -
1098E LEU* 3.7 25.4 - - + -
1100E MET* 5.4 2.7 - - - -
1112E PHE* 3.7 24.9 - + + -
1129E PHE* 3.3 33.4 - + + -
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Residues in contact with ARG1037 (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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1004E PRO* 3.8 28.8 - - + +
1006E VAL* 3.8 9.4 - - + -
1024E LEU* 3.8 10.9 - - + +
1033E ALA 3.0 13.2 + - - +
1034E GLU* 2.9 46.2 + - - +
1036E PHE* 1.3 73.8 - - - +
1038E ALA* 1.3 59.5 + - - +
1039E LEU 3.0 8.1 + - - -
1040E SER* 3.1 11.3 + - - -
1041E THR* 3.2 24.5 + - - +
1043E GLU* 2.8 37.7 + - - -
1163E GLN* 3.2 39.4 + - - +
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Residues in contact with ALA1038 (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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1034E GLU* 2.9 24.3 + - - +
1035E ASN 4.0 2.0 - - - +
1037E ARG* 1.3 72.5 - - - +
1039E LEU* 1.3 58.0 + - - +
1041E THR* 3.8 8.7 - - - -
1042E GLY* 3.3 17.2 + - - -
1043E GLU* 3.5 33.6 + - + +
1044E LYS* 3.7 24.8 + - - +
1046E PHE 4.7 1.9 - - - +
1078E ILE* 4.1 13.7 - - + +
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Residues in contact with LEU1039 (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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1035E ASN* 3.2 40.3 + - - +
1036E PHE 3.7 0.7 - - - +
1037E ARG 3.0 0.6 - - - -
1038E ALA* 1.3 78.6 - - - +
1040E SER* 1.3 63.1 + - - +
1041E THR 3.2 1.7 + - - -
1042E GLY 3.7 4.5 + - - -
1046E PHE* 3.8 8.5 - - + +
1047E GLY* 3.3 39.7 - - - -
1048E TYR* 3.3 41.7 + - + +
1067E PHE* 3.4 33.7 - - + -
1076E LYS 4.0 13.0 - - - +
1077E SER* 4.7 0.7 - - - -
1078E ILE* 4.7 8.7 - - + -
1110E SER* 4.0 5.6 - - - -
1161E CYS* 4.8 0.3 - - - -
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Residues in contact with SER1040 (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* 3.7 23.8 - - - +
1008E PHE* 4.1 3.0 - - - -
1036E PHE* 2.7 43.2 + - - -
1037E ARG 3.1 5.3 + - - -
1039E LEU* 1.3 78.1 - - - +
1041E THR* 1.3 57.2 + - - +
1048E TYR* 3.9 11.2 - - - -
1161E CYS* 2.8 42.2 - - - +
1162E GLY 4.2 7.0 - - - -
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Residues in contact with THR1041 (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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1037E ARG* 3.2 26.4 + - - +
1038E ALA 3.5 2.8 + - - -
1039E LEU 4.2 0.2 - - - -
1040E SER* 1.3 80.0 - - - +
1042E GLY* 1.3 69.0 + - - +
1043E GLU* 3.0 30.3 + - - +
1049E LYS* 5.4 8.5 - - - +
1161E CYS* 4.7 3.8 - - - +
1162E GLY* 4.3 7.4 - - - -
1163E GLN* 3.8 33.7 - - + +
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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