Contacts of the helix formed by residues 94 - 102 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LEU* 5.0 4.3 - - - -
46A ILE* 5.3 6.3 - - + -
49A GLN* 3.3 24.9 - - + -
107A TYR* 4.0 22.4 - - + +
109A LEU* 3.7 19.9 - - + +
92B LEU 3.9 0.4 - - - -
93B GLY* 1.3 78.5 - - - +
95B THR* 1.3 66.7 + - - +
96B GLN* 3.7 17.3 - - - +
97B VAL* 3.1 31.5 + - - +
98B ILE* 3.0 22.6 + - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 3.1 31.4 + - - +
45A LEU* 4.1 15.8 - - - +
95A THR* 3.8 5.8 + - - -
98A ILE* 3.5 14.1 - - + +
99A ASN* 3.4 28.7 + - - +
102A THR* 4.6 2.9 - - + -
93B GLY 3.9 1.2 + - - -
94B THR* 1.3 71.1 - - - +
96B GLN* 1.3 92.5 + - - +
98B ILE* 3.2 6.6 + - - +
99B ASN* 2.8 31.4 + - - +
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Residues in contact with GLN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 4.8 1.9 - - - +
46A ILE* 5.9 3.1 - - - +
99A ASN* 3.5 23.6 + - - +
102A THR* 5.0 7.1 - - - +
104A LEU 5.1 2.3 + - - +
106A SER* 3.3 44.2 + - - +
107A TYR 4.0 3.5 + - - -
94B THR* 3.7 15.8 - - - +
95B THR* 1.3 94.6 - - - +
97B VAL* 1.3 62.8 + - + +
99B ASN* 3.9 2.1 - - - +
100B SER* 3.0 26.5 + - - -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 3.8 24.7 - - + -
38B ILE* 3.6 26.6 - - + +
92B LEU* 4.1 23.1 - - + +
94B THR* 3.1 27.4 + - - +
96B GLN* 1.3 76.0 - - + +
98B ILE* 1.3 66.1 + - + +
100B SER* 3.5 6.0 + - - -
101B LYS* 3.0 36.3 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 5.3 2.0 - - + -
95A THR* 3.5 17.3 - - - +
38B ILE* 3.4 41.3 - - + +
41B ILE* 3.9 28.0 - - + -
42B ASP* 3.7 34.5 - - + +
45B LEU* 5.2 1.3 - - + -
92B LEU 4.8 0.2 - - - +
93B GLY* 4.1 9.2 - - - +
94B THR 3.0 23.9 + - - +
95B THR* 3.6 7.4 - - - +
97B VAL* 1.3 77.6 - - + +
99B ASN* 1.3 58.4 + - - +
102B THR* 2.8 37.1 + - - +
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 3.5 12.1 + - - +
96A GLN* 3.5 40.1 + - - +
99A ASN* 3.7 28.5 + - + +
95B THR 2.8 20.7 + - - +
96B GLN 3.9 3.6 - - - +
98B ILE* 1.3 76.5 - - - +
100B SER* 1.3 65.0 + - - +
102B THR* 3.7 13.7 - - - +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLN 3.0 15.1 + - - -
97B VAL* 3.5 7.4 + - - -
99B ASN* 1.3 82.3 + - - +
101B LYS* 1.3 77.3 + - - +
102B THR 3.7 0.8 - - - +
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 4.0 30.1 - - + +
92B LEU* 4.9 11.7 - - - +
97B VAL* 3.0 23.8 + - + +
98B ILE 3.7 0.2 - - - -
100B SER* 1.3 94.4 - - - +
102B THR* 1.3 64.4 + - - +
103B PRO* 3.6 6.1 - - - +
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A THR* 4.6 6.3 - - + -
96A GLN* 5.0 4.5 - - - +
38B ILE* 4.0 5.4 - - - -
42B ASP* 2.7 39.0 + - - +
98B ILE* 2.8 30.7 + - - +
99B ASN* 3.7 14.6 - - - +
100B SER 3.7 0.9 - - - +
101B LYS* 1.3 72.6 - - - +
103B PRO* 1.3 69.5 - - - +
104B LEU* 3.1 18.6 + - - +
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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