Contacts of the helix formed by residues 94 - 102 (chain F) in PDB entry 1F33
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 THR 94 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E LEU* 5.0 4.3 - - - -
46E ILE* 5.3 5.8 - - + -
49E GLN* 3.2 25.6 - - + -
107E TYR* 4.0 21.1 - - + +
109E LEU* 3.6 19.7 - - + +
92F LEU 3.9 0.6 - - - -
93F GLY* 1.3 78.9 - - - +
95F THR* 1.3 66.1 + - - +
96F GLN* 3.7 17.2 - - - +
97F VAL* 3.1 30.5 + - - +
98F ILE* 3.0 22.8 + - - +
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Residues in contact with THR 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ASP* 3.0 32.4 + - - +
45E LEU* 4.1 17.3 - - - +
46E ILE* 6.2 0.2 - - - +
95E THR* 3.8 7.1 + - - -
98E ILE* 3.6 13.9 - - + +
99E ASN* 3.5 28.7 + - - +
102E THR* 4.6 2.7 - - + -
93F GLY 3.8 1.4 + - - -
94F THR* 1.3 71.6 - - - +
96F GLN* 1.3 83.2 + - - +
98F ILE* 3.2 6.0 + - - +
99F ASN* 2.8 31.4 + - - +
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Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ASP* 4.9 1.6 - - - +
46E ILE* 5.9 3.1 - - - +
99E ASN* 3.5 24.6 + - - +
102E THR* 5.0 6.7 - - - +
104E LEU 5.1 2.4 + - - +
106E SER* 3.3 45.1 + - - +
107E TYR 3.9 4.2 + - - -
109E LEU* 6.5 0.4 - - + -
94F THR* 3.7 16.1 - - - +
95F THR* 1.3 93.4 - - - +
97F VAL* 1.3 63.9 + - + +
99F ASN* 3.5 1.6 + - - +
100F SER* 3.1 26.7 + - - -
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E LEU* 3.8 25.4 - - + -
38F ILE* 3.6 27.1 - - + -
92F LEU* 4.1 23.1 - - + +
94F THR* 3.1 27.0 + - - +
96F GLN* 1.3 75.9 - - + +
98F ILE* 1.3 67.5 + - + +
100F SER* 3.5 6.3 + - - -
101F LYS* 3.0 35.2 + - + +
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 5.3 2.0 - - + -
95E THR* 3.5 18.8 - - - +
38F ILE* 3.5 41.5 - - + +
41F ILE* 3.9 27.4 - - + -
42F ASP* 3.7 32.5 - - + +
45F LEU* 5.2 1.3 - - + -
93F GLY* 4.1 9.6 - - - +
94F THR 3.0 19.8 + - - +
95F THR* 3.5 7.9 - - - +
97F VAL* 1.3 76.6 - - + +
99F ASN* 1.3 58.3 + - - +
102F THR* 2.7 37.3 + - - +
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Residues in contact with ASN 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E THR* 3.5 12.1 + - - +
96E GLN* 3.5 38.9 + - - +
99E ASN* 3.8 29.2 + - + +
95F THR 2.8 20.4 + - - +
96F GLN 3.9 3.3 - - - +
98F ILE* 1.3 76.1 - - - +
100F SER* 1.3 65.3 + - - +
102F THR* 3.7 13.9 - - - +
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Residues in contact with SER 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F GLN 3.1 15.8 + - - -
97F VAL* 3.5 9.2 + - - -
99F ASN* 1.3 81.7 - - - +
101F LYS* 1.3 72.8 + - - +
102F THR 3.7 0.6 - - - +
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Residues in contact with LYS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F GLU* 6.2 1.8 - - - +
34F ASN* 6.0 2.4 - - - +
35F ARG* 6.3 0.8 - - - +
38F ILE* 3.8 30.9 - - + +
92F LEU* 5.0 11.0 - - - +
97F VAL* 3.0 23.3 + - + +
100F SER* 1.3 90.2 - - - +
102F THR* 1.3 67.7 + - - +
103F PRO* 3.4 7.4 - - - +
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Residues in contact with THR 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E THR* 4.6 6.5 - - + -
96E GLN* 5.0 4.3 - - - +
38F ILE* 4.0 5.8 - - - +
42F ASP* 2.6 41.0 + - - +
98F ILE* 2.7 28.8 + - - +
99F ASN* 3.7 15.7 - - - +
100F SER 3.7 0.9 - - - +
101F LYS* 1.3 73.8 - - - +
103F PRO* 1.3 69.7 - - - +
104F LEU* 3.1 18.5 + - - +
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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
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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