Contacts of the helix formed by residues 94 - 102 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92I LEU 3.9 0.6 - - - -
93I GLY* 1.3 78.9 - - - +
95I THR* 1.3 67.8 + - - +
96I GLN* 3.7 16.6 - - - +
97I VAL* 3.1 30.7 + - - +
98I ILE* 3.0 23.6 + - - +
45J LEU* 5.0 3.8 - - - -
46J ILE* 5.2 6.5 - - + +
49J GLN* 3.3 25.6 - - + -
107J TYR* 3.9 23.1 - - + +
109J LEU* 3.7 19.0 - - + +
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Residues in contact with THR 95 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I GLY 3.9 1.2 + - - -
94I THR* 1.3 71.6 - - - +
96I GLN* 1.3 85.1 + - - +
98I ILE* 3.3 6.1 + - - +
99I ASN* 2.8 31.4 + - - +
42J ASP* 2.9 32.8 + - - +
45J LEU* 4.1 16.4 - - - +
46J ILE* 6.2 0.4 - - - +
95J THR* 3.8 5.8 + - - -
98J ILE* 3.4 25.0 - - + +
99J ASN* 3.4 15.2 + - - +
102J THR* 4.5 6.3 - - + -
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Residues in contact with GLN 96 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94I THR* 3.7 15.0 - - - +
95I THR* 1.3 93.1 - - - +
97I VAL* 1.3 66.2 + - + +
99I ASN* 3.9 1.9 - - - +
100I SER* 3.1 25.6 + - - -
42J ASP* 5.1 1.6 - - - +
46J ILE* 5.8 3.1 - - - +
99J ASN* 3.4 23.4 + - - +
102J THR* 4.9 7.5 - - - +
104J LEU 5.0 3.4 + - - +
106J SER* 3.2 46.3 + - - +
107J TYR 3.9 4.2 + - - -
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Residues in contact with VAL 97 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ILE* 3.6 27.4 - - + -
92I LEU* 4.1 25.4 - - + +
94I THR* 3.1 27.0 + - - +
96I GLN* 1.3 76.6 - - + +
98I ILE* 1.3 67.5 + - + +
100I SER* 3.5 5.0 + - - -
101I LYS* 2.9 30.8 + - + +
109J LEU* 3.8 24.9 - - + -
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Residues in contact with ILE 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ILE* 3.5 42.8 - - + +
41I ILE* 4.0 26.5 - - + -
42I ASP* 3.8 31.9 - - + +
45I LEU* 5.2 1.6 - - + -
93I GLY* 4.2 9.4 - - - +
94I THR 3.0 19.1 + - - +
95I THR* 3.6 6.3 - - - +
97I VAL* 1.3 76.6 - - + +
99I ASN* 1.3 57.1 + - - +
102I THR* 2.7 38.8 + - - +
45J LEU* 5.3 2.7 - - + -
95J THR* 3.4 21.1 - - - +
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Residues in contact with ASN 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95I THR 2.8 17.7 + - - +
96I GLN 3.9 2.4 - - - +
98I ILE* 1.3 77.8 - - - +
100I SER* 1.3 64.4 + - - +
102I THR* 3.8 13.5 - - - +
95J THR* 3.4 9.8 + - - +
96J GLN* 3.4 39.2 + - - +
99J ASN* 3.7 31.7 + - + +
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Residues in contact with SER 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96I GLN 3.1 16.6 + - - -
97I VAL* 3.5 8.7 + - - -
99I ASN* 1.3 82.0 + - - +
101I LYS* 1.3 72.5 + - - +
102I THR 3.8 0.6 - - - +
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Residues in contact with LYS 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I GLU* 6.4 0.2 - - - +
35I ARG* 5.7 12.0 - - - +
38I ILE* 3.8 30.6 - - + +
97I VAL* 2.9 23.1 + - + +
100I SER* 1.3 88.1 - - - +
102I THR* 1.3 65.2 + - - +
103I PRO* 3.4 7.1 - - - +
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Residues in contact with THR 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38I ILE* 4.0 4.9 - - - +
42I ASP* 2.7 40.2 + - - +
98I ILE* 2.7 28.0 + - - +
99I ASN* 3.8 15.3 - - - +
100I SER 3.8 0.7 - - - +
101I LYS* 1.3 72.4 - - - +
103I PRO* 1.3 69.4 - - - +
104I LEU* 3.1 19.1 + - - +
95J THR* 4.5 7.0 - - + -
96J GLN* 4.9 4.7 - - - +
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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