Contacts of the helix formed by residues 1024 - 1032 (chain E) in PDB entry 2FO1
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 ILE1024 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661A LEU* 5.9 2.8 - - + +
1022E SER* 2.9 19.5 + - - +
1023E PRO* 1.3 66.3 - - - +
1025E LYS* 1.3 65.0 + - - +
1026E LEU* 3.7 12.6 - - + +
1027E HIS* 2.9 50.6 + - + +
1028E THR* 2.9 14.1 + - - +
1048E ILE* 3.7 33.0 - - + -
1049E ASP 5.8 0.2 - - - -
1050E PRO* 5.3 9.9 - - + -
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Residues in contact with LYS1025 (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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1023E PRO 2.9 9.1 + - - +
1024E ILE* 1.3 70.3 - - - +
1026E LEU* 1.3 66.0 + - - +
1028E THR* 2.8 28.6 - - + +
1029E GLU* 3.0 27.1 + - + +
1037E THR* 5.8 3.9 - - - +
1038E GLU* 3.0 30.2 + - + +
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Residues in contact with LEU1026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024E ILE* 3.2 10.0 - - + +
1025E LYS* 1.3 79.3 - - - +
1027E HIS* 1.3 65.5 + - + +
1029E GLU* 3.0 6.6 + - + +
1030E ALA* 2.8 31.6 + - + +
1037E THR 4.6 13.2 - - - +
1038E GLU* 4.1 20.5 - - + +
1039E PRO 4.3 5.6 - - - +
1040E ILE* 5.2 9.4 - - + -
1044E SER* 3.8 32.1 - - - +
1045E VAL* 4.8 1.6 - - + -
1048E ILE* 6.2 0.2 - - + -
1056E VAL* 3.7 41.3 - - + -
1076E GLU* 5.9 1.6 - - - +
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Residues in contact with HIS1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 5.3 7.2 - - + -
1024E ILE* 2.9 27.6 + - + +
1026E LEU* 1.3 77.4 - - + +
1028E THR* 1.3 55.7 - - - +
1029E GLU 3.0 0.3 + - - -
1030E ALA* 3.0 5.7 + - - +
1031E ALA* 2.6 37.9 + - - +
1048E ILE* 3.1 33.0 + - + +
1050E PRO* 4.0 10.2 - - + +
1054E ARG 3.7 20.0 - - - -
1055E THR 3.9 0.2 - - - -
1056E VAL* 3.5 43.6 + - + +
1059E TRP* 3.6 30.6 + + + +
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Residues in contact with THR1028 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A LEU* 4.8 18.6 + - - +
1023E PRO 5.2 2.7 - - - +
1024E ILE 2.9 11.8 + - - +
1025E LYS* 2.8 41.5 - - + +
1027E HIS* 1.3 71.9 - - - +
1029E GLU* 1.3 58.8 + - + +
1031E ALA* 3.1 7.5 - - - +
1032E GLY* 2.4 38.6 + - - -
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Residues in contact with GLU1029 (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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1025E LYS* 3.0 31.6 + - + +
1026E LEU* 3.0 8.7 - - + +
1027E HIS 3.0 0.4 + - - -
1028E THR* 1.3 87.6 - - + +
1030E ALA* 1.3 68.8 + - - +
1031E ALA 2.7 3.1 + - - -
1032E GLY* 2.7 13.4 + - - -
1033E SER 3.8 5.4 + - - -
1034E TYR 5.3 0.5 + - - -
1035E ALA* 3.4 36.0 + - + +
1037E THR* 3.0 55.5 + - - +
1038E GLU* 3.5 10.2 - - - +
1076E GLU* 5.8 0.2 - - - +
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Residues in contact with ALA1030 (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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1026E LEU* 2.8 18.5 + - + +
1027E HIS* 3.3 12.1 - - - +
1029E GLU* 1.3 73.6 - - - +
1031E ALA* 1.3 65.4 + - - +
1033E SER 4.9 2.1 + - - +
1035E ALA 4.4 0.6 + - - -
1056E VAL* 4.3 7.6 - - + -
1059E TRP* 4.6 8.4 - - + +
1060E ILE* 3.2 36.9 - - + +
1065E SER* 3.2 12.1 + - - -
1076E GLU* 4.2 17.8 + - - +
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Residues in contact with ALA1031 (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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661A LEU* 4.1 20.2 - - + -
1027E HIS 2.6 16.5 + - - +
1028E THR* 3.1 13.0 - - - +
1029E GLU 2.7 1.4 + - - -
1030E ALA* 1.3 70.3 - - - +
1032E GLY* 1.3 71.8 + - - +
1059E TRP* 4.5 21.5 - - + +
1064E SER 5.0 0.7 - - - +
1065E SER* 2.9 23.5 + - - -
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Residues in contact with GLY1032 (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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1028E THR* 2.4 26.4 + - - -
1029E GLU* 2.7 4.2 + - - -
1031E ALA* 1.3 72.0 - - - +
1033E SER* 1.3 62.8 + - - -
1064E SER 4.8 1.0 - - - +
1065E SER* 3.8 8.8 - - - -
1066E ALA 4.0 3.5 + - - +
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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
------------------------------------------------------------
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