Contacts of the strand formed by residues 1042 - 1047 (chain E) in PDB entry 3T06
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 ALA1042 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975E ARG* 4.1 0.2 - - - +
1036E VAL* 3.8 23.1 + - + +
1039E ASP* 2.9 28.1 + - - +
1041E ARG* 1.3 77.3 - - - +
1043E PHE* 1.3 64.5 + - - +
1058E GLU* 3.9 17.0 - - + +
1059E LEU 3.1 15.0 - - - +
1060E VAL* 4.0 10.1 - - + +
1067E LYS* 3.5 17.8 + - - +
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Residues in contact with PHE1043 (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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972E LEU* 4.0 32.8 - - + -
1033E ILE* 4.9 2.0 - - + -
1034E ARG 3.8 10.5 - - - +
1035E SER* 4.4 1.3 - - - +
1036E VAL* 4.2 5.6 - - - -
1041E ARG 4.2 7.4 - - - -
1042E ALA* 1.3 80.6 - - - +
1044E PHE* 1.3 72.3 + - - +
1045E ILE* 3.7 15.5 - - + -
1057E TYR 3.8 1.4 - - - +
1058E GLU* 3.7 1.9 - - - -
1059E LEU* 3.0 43.1 + - + -
1061E ALA* 4.8 4.5 - - + -
1067E LYS* 4.5 9.6 - - + -
1070E TRP* 4.2 24.2 - + + -
1071E MET* 4.0 22.9 - - + -
1074E LEU* 3.5 31.4 - - + -
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Residues in contact with PHE1044 (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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1033E ILE* 3.6 5.2 - - - -
1034E ARG* 2.9 36.7 + - + +
1035E SER 4.3 4.3 - - - -
1036E VAL* 3.1 53.8 - - + -
1043E PHE* 1.3 73.2 - - - +
1045E ILE* 1.3 72.3 + - - +
1046E ILE* 3.8 18.2 - - + -
1056E ILE* 4.2 17.5 - - + -
1057E TYR 3.8 0.7 - - - -
1058E GLU* 3.5 43.1 - - + -
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Residues in contact with ILE1045 (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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993E LEU* 3.9 22.0 - - + -
1026E LEU* 4.1 20.2 - - + -
1031E VAL* 4.0 23.6 - - + -
1032E LEU 3.4 4.9 - - - +
1033E ILE* 3.9 11.9 - - + -
1043E PHE* 3.7 26.0 - - + -
1044E PHE* 1.3 84.0 - - - +
1046E ILE* 1.3 63.6 + - - +
1047E CYS 4.0 0.7 + - - -
1055E GLN 3.4 1.0 - - - +
1056E ILE* 3.3 6.4 - - - -
1057E TYR* 3.0 40.8 + - + +
1059E LEU* 3.7 17.0 - - + -
1074E LEU* 4.0 9.4 - - + -
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Residues in contact with ILE1046 (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 VAL* 3.3 16.6 - - - -
1032E LEU* 3.2 30.0 + - + +
1034E ARG* 4.5 17.9 - - + -
1044E PHE* 3.8 17.0 - - + +
1045E ILE* 1.3 90.4 - - - +
1047E CYS* 1.3 60.4 + - - +
1048E THR* 3.1 12.8 + - - +
1054E PRO* 4.8 12.1 - - + -
1055E GLN 3.2 7.0 - - - +
1056E ILE* 3.8 15.9 - - + -
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Residues in contact with CYS1047 (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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952E LEU* 4.7 14.4 - - - -
1026E LEU* 4.1 20.8 - - + +
1027E LYS 5.3 4.9 - - - -
1030E ALA* 3.5 18.2 - - - -
1031E VAL* 3.6 13.8 - - + +
1045E ILE 4.0 1.4 + - - -
1046E ILE* 1.3 70.8 - - - +
1048E THR* 1.3 52.2 + - - +
1049E SER* 2.6 31.7 + - - -
1054E PRO* 3.1 5.0 - - - +
1055E GLN* 2.8 46.1 + - + -
1057E TYR* 4.5 1.8 - - + -
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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