Contacts of the helix formed by residues 91 - 100 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F PHE* 3.4 3.2 - - - +
90F ASN* 1.3 83.7 - - + +
92F THR* 1.3 67.7 + - - +
93F SER* 4.0 20.3 + - - +
94F GLU* 2.8 40.1 + - + +
95F LEU* 3.2 8.5 + - - +
378H ASP* 3.5 22.4 - - + +
385H ILE* 3.9 7.0 - - - -
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Residues in contact with THR 92 (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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91F LYS* 1.3 68.6 - - - +
93F SER* 1.3 62.9 + - - +
95F LEU* 2.9 25.7 + - + +
96F ILE* 2.9 21.5 + - + +
374H ALA* 3.6 25.0 - - + +
377H VAL* 3.1 21.5 - - - +
378H ASP* 2.8 24.3 + - - -
385H ILE* 4.0 6.8 - - - +
398H GLN* 3.8 4.7 + - - +
401H ILE* 3.6 27.1 - - + -
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Residues in contact with SER 93 (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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91F LYS* 2.9 22.6 + - - +
92F THR* 1.3 79.9 - - - +
94F GLU* 1.3 65.1 + - - +
96F ILE* 3.2 13.7 + - - +
97F ASP* 3.1 28.5 + - - +
378H ASP* 4.4 3.4 + - - -
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F PHE* 4.4 5.5 - - + -
90F ASN* 3.0 47.7 + - - +
91F LYS* 2.8 28.9 + - + +
93F SER* 1.3 78.4 + - - +
95F LEU* 1.3 64.7 + - - +
97F ASP* 3.1 13.3 + - - +
98F PHE* 3.0 22.3 + - - +
103F ARG* 3.7 44.4 + - - +
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Residues in contact with LEU 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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89F PHE* 3.7 44.3 - - + -
91F LYS 3.2 5.3 + - - +
92F THR* 2.9 21.7 + - + +
94F GLU* 1.3 76.8 - - - +
96F ILE* 1.3 63.0 + - - +
98F PHE* 3.2 5.8 + - + +
99F LYS* 3.0 32.4 + - + +
385H ILE* 4.6 15.3 - - + -
398H GLN* 5.5 4.5 - - + +
401H ILE* 3.8 26.2 - - + -
402H MET* 4.0 33.4 - - + -
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Residues in contact with ILE 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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92F THR* 2.9 32.0 + - + +
93F SER* 3.5 10.8 - - - +
95F LEU* 1.3 76.5 - - - +
97F ASP* 1.3 52.4 + - - +
99F LYS* 3.0 8.0 + - - +
100F GLU* 2.8 62.0 + - + +
102F ARG* 4.2 5.8 - - - +
370H LEU* 4.9 11.7 - - + -
371H LEU* 6.1 3.1 - - + -
401H ILE* 4.0 24.2 - - + -
405H TRP* 4.0 18.2 - - + +
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Residues in contact with ASP 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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93F SER* 3.1 21.4 + - - +
94F GLU* 3.1 19.2 + - - +
96F ILE* 1.3 75.6 - - - +
98F PHE* 1.3 60.8 + - - +
100F GLU 3.0 8.1 + - - -
102F ARG* 2.8 63.4 + - + +
103F ARG* 3.9 22.2 + - + +
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Residues in contact with PHE 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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89F PHE* 3.9 22.2 - + + -
94F GLU 3.0 12.2 + - - +
95F LEU* 3.5 10.3 - - + +
96F ILE 3.2 0.2 - - - -
97F ASP* 1.3 76.0 - - - +
99F LYS* 1.3 84.0 + - + +
101F LYS* 3.0 16.3 + - - +
103F ARG* 3.7 32.0 - - + +
105F SER* 2.9 41.3 - - - -
106F PHE 5.0 0.2 - - - -
107F GLU* 3.5 40.8 - - + -
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Residues in contact with LYS 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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95F LEU* 3.0 25.4 + - + +
96F ILE* 3.0 9.5 + - - +
98F PHE* 1.3 91.0 - - + +
100F GLU* 1.3 57.6 + - - +
101F LYS* 3.3 13.8 + - - +
107F GLU* 2.9 27.2 + - - -
401H ILE* 3.8 19.7 + - + +
402H MET* 2.8 32.0 + - - +
403H SER* 4.6 3.4 - - - +
405H TRP* 3.7 28.3 - - + +
607H PMC 4.9 1.6 + - - -
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Residues in contact with GLU 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 ILE* 2.8 32.7 + - + +
97F ASP 3.7 0.4 - - - +
98F PHE 3.0 0.6 - - - -
99F LYS* 1.3 80.0 - - - +
101F LYS* 1.3 70.7 + - - +
102F ARG* 2.8 53.6 + - - +
405H TRP* 3.2 23.3 + - + +
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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