Contacts of the helix formed by residues 91 - 100 (chain I) in PDB entry 1I43
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 LYS 91 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89I PHE* 3.4 3.0 - - - +
90I ASN* 1.3 84.6 - - + +
92I THR* 1.3 67.0 + - - +
93I SER* 4.1 17.9 - - - +
94I GLU* 2.8 41.4 + - + +
95I LEU* 3.2 9.4 + - - +
378K ASP* 3.5 23.1 - - + +
385K ILE* 3.9 6.7 - - - -
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Residues in contact with THR 92 (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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91I LYS* 1.3 70.9 - - - +
93I SER* 1.3 61.2 + - - +
95I LEU* 3.2 15.2 + - + +
96I ILE* 3.0 29.7 + - + +
374K ALA* 3.6 22.9 - - + +
377K VAL* 3.2 19.9 - - - +
378K ASP* 2.8 23.2 + - - -
385K ILE* 4.2 6.0 - - - +
398K GLN* 4.0 2.3 + - - +
401K ILE* 3.5 32.5 - - + -
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Residues in contact with SER 93 (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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91I LYS* 2.9 20.7 + - - +
92I THR* 1.3 79.0 - - - +
94I GLU* 1.3 58.7 + - - +
96I ILE* 3.4 12.8 + - - +
97I ASP* 3.1 34.5 + - - +
378K ASP* 4.6 2.5 + - - -
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Residues in contact with GLU 94 (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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89I PHE* 4.5 6.4 - - + -
90I ASN* 3.1 47.5 + - - +
91I LYS* 2.8 29.6 + - + +
93I SER* 1.3 73.6 - - - +
95I LEU* 1.3 67.5 + - - +
97I ASP* 2.9 13.6 + - - +
98I PHE* 2.9 23.4 + - - +
103I ARG* 3.7 41.6 + - - +
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Residues in contact with LEU 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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89I PHE* 3.6 46.5 - - + -
91I LYS 3.2 4.9 + - - +
92I THR* 3.2 21.1 + - + +
94I GLU* 1.3 77.7 - - - +
96I ILE* 1.3 62.1 + - - +
98I PHE* 3.3 7.9 + - + +
99I LYS* 3.0 27.0 + - + +
385K ILE* 4.5 14.4 - - + -
398K GLN* 5.5 4.9 - - + +
401K ILE* 3.9 27.4 - - + -
402K MET* 4.0 33.4 - - + +
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Residues in contact with ILE 96 (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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92I THR* 3.0 31.6 + - + +
93I SER* 3.6 10.8 - - - +
95I LEU* 1.3 74.5 - - - +
97I ASP* 1.3 54.5 + - - +
99I LYS* 3.0 7.3 + - - -
100I GLU* 2.8 64.6 + - + +
102I ARG* 4.3 5.6 - - - +
370K LEU* 4.9 13.0 - - + -
371K LEU* 6.2 1.6 - - + -
401K ILE* 4.0 23.8 - - + -
405K TRP* 4.1 17.5 - - + +
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Residues in contact with ASP 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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93I SER* 3.1 24.9 + - - +
94I GLU* 3.2 17.1 - - - +
96I ILE* 1.3 77.8 - - - +
98I PHE* 1.3 55.9 + - - +
100I GLU 3.2 6.2 + - - -
102I ARG* 2.8 68.8 + - + +
103I ARG* 3.9 21.6 + - + +
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Residues in contact with PHE 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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89I PHE* 3.9 23.8 - + + -
94I GLU 2.9 10.8 + - - +
95I LEU* 3.6 10.8 - - + +
97I ASP* 1.3 76.2 - - - +
99I LYS* 1.3 83.5 + - + +
101I LYS* 3.1 15.8 + - - +
103I ARG* 3.6 31.8 - - + +
105I SER* 3.2 35.0 - - - -
106I PHE 5.1 0.2 - - - -
107I GLU* 3.3 44.2 - - + -
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Residues in contact with LYS 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 LEU* 3.0 24.5 + - + +
96I ILE* 3.0 11.3 + - - +
98I PHE* 1.3 90.4 - - + +
100I GLU* 1.3 57.8 + - - +
101I LYS* 3.3 13.2 + - - +
107I GLU* 3.1 27.6 + - - -
401K ILE* 3.9 17.2 + - + +
402K MET* 2.6 33.2 + - - +
403K SER* 4.6 3.8 - - - +
405K TRP* 3.7 28.0 - - + +
610K PMC 4.8 1.6 + - - -
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Residues in contact with GLU 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 ILE* 2.8 41.8 + - + +
97I ASP 3.8 0.4 - - - +
98I PHE 3.1 0.4 - - - -
99I LYS* 1.3 78.7 - - - +
101I LYS* 1.3 70.5 + - - +
102I ARG* 3.0 44.8 + - - +
405K TRP* 3.2 24.3 + - + +
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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