Contacts of the helix formed by residues 91 - 100 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.4 3.1 - - - +
90A ASN* 1.3 87.4 - - + +
92A THR* 1.3 56.8 + - - +
93A SER* 4.1 20.2 - - - +
94A GLU* 2.7 49.4 + - + +
95A LEU* 3.2 7.9 + - - +
378C ASP* 3.7 21.1 - - + +
385C ILE* 4.0 7.2 - - - -
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Residues in contact with THR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 1.3 71.1 - - - +
93A SER* 1.3 61.6 + - - +
95A LEU* 3.2 13.4 + - + +
96A ILE* 3.0 30.8 + - + +
374C ALA* 3.6 22.5 - - + +
377C VAL* 3.1 20.6 - - - +
378C ASP* 2.9 24.0 + - - -
385C ILE* 4.1 6.8 - - - +
398C GLN* 4.0 1.8 + - - +
401C ILE* 3.4 35.0 - - + -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LYS* 2.8 21.8 + - - +
92A THR* 1.3 80.9 - - - +
94A GLU* 1.3 60.2 + - - +
96A ILE* 3.3 12.2 + - - +
97A ASP* 3.1 33.4 + - - +
378C ASP* 4.6 2.9 + - - -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 4.4 7.8 - - + +
90A ASN* 3.2 45.8 + - - +
91A LYS* 2.7 32.7 + - + +
93A SER* 1.3 78.6 + - - +
95A LEU* 1.3 63.7 + - - +
97A ASP* 3.0 13.6 + - - +
98A PHE* 2.9 23.6 + - - +
103A ARG* 3.5 43.6 + - - +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.8 43.2 - - + -
91A LYS 3.2 4.3 + - - +
92A THR* 3.2 18.1 + - + +
94A GLU* 1.3 77.3 - - - +
96A ILE* 1.3 64.3 + - - +
98A PHE* 3.2 5.5 + - + +
99A LYS* 2.9 31.0 + - + +
385C ILE* 4.8 11.9 - - + -
397C ASP* 5.9 0.2 - - + -
398C GLN* 5.4 4.0 - - + +
401C ILE* 3.5 31.2 - - + -
402C MET* 3.9 35.9 - - + -
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A THR* 3.0 29.6 + - + +
93A SER* 3.4 10.8 - - - +
95A LEU* 1.3 77.0 - - - +
97A ASP* 1.3 51.7 + - - +
99A LYS* 2.9 8.9 + - - -
100A GLU* 2.7 60.1 + - + +
102A ARG* 4.1 7.2 - - - +
370C LEU* 4.9 10.1 - - + -
371C LEU* 6.1 2.5 - - + -
401C ILE* 3.9 23.1 - - + -
405C TRP* 3.8 22.4 - - + +
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.1 22.7 + - - +
94A GLU* 3.0 18.9 + - - +
96A ILE* 1.3 76.4 - - - +
98A PHE* 1.3 61.3 + - - +
100A GLU 3.0 8.1 + - - -
102A ARG* 2.9 61.8 + - + +
103A ARG* 3.9 23.2 + - + +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.8 25.1 - + + -
94A GLU 2.9 12.1 + - - +
95A LEU* 3.5 8.5 - - + +
97A ASP* 1.3 75.6 - - - +
99A LYS* 1.3 83.1 + - + +
100A GLU 3.0 0.2 - - - -
101A LYS* 3.1 15.9 + - - +
103A ARG* 3.7 26.4 - - + +
105A SER* 3.0 41.1 - - - -
106A PHE 4.9 0.2 - - - -
107A GLU* 3.4 44.9 - - + -
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 2.9 25.4 + - + +
96A ILE* 2.9 9.9 + - - +
98A PHE* 1.3 88.2 - - + +
100A GLU* 1.3 58.7 + - - +
101A LYS* 3.4 12.8 + - - +
107A GLU* 3.3 25.4 + - - -
401C ILE* 3.9 17.4 + - + +
402C MET* 2.6 34.8 + - - +
403C SER* 4.4 4.8 - - - +
405C TRP* 3.5 29.5 - - + +
602C PMC 4.7 1.6 + - - -
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 2.7 28.8 + - + +
97A ASP 3.0 1.3 + - - +
99A LYS* 1.3 80.8 - - - +
101A LYS* 1.3 71.0 + - - +
102A ARG* 2.8 55.5 + - - +
405C TRP* 3.1 25.7 + - + +
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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