Contacts of the helix formed by residues 91 - 98 (chain C) in PDB entry 2O1S
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 ARG 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C HIS* 3.8 2.0 + - - -
86C LYS* 3.0 41.9 + - - +
87C ILE* 4.2 1.5 - - - -
89C THR* 2.9 32.5 + - - +
90C GLY* 1.3 82.3 - - - +
92C ARG* 1.3 65.1 + - - +
93C ASP 3.4 2.2 - - - -
94C LYS* 3.2 11.4 + - + +
95C ILE* 3.1 23.6 + - - +
104C LEU* 3.9 27.1 - - + +
112C GLU* 2.8 33.3 + - - -
113C SER* 3.6 22.7 + - - -
115C TYR* 4.4 0.2 - - - +
116C ASP* 2.7 44.0 + - - -
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.4 34.5 - - - +
11C LEU* 3.5 30.4 + - + -
12C ALA* 3.7 20.8 + - - +
14C VAL 4.1 9.6 + - - +
15C ASP* 3.8 31.7 + - - +
38C TYR* 2.6 45.7 + - + +
87C ILE* 3.4 33.1 + - + +
90C GLY 3.6 2.7 - - - -
91C ARG* 1.3 78.5 - - - +
93C ASP* 1.3 88.5 + - - +
94C LYS 3.4 0.9 + - - -
95C ILE* 3.7 7.1 - - - +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.9 23.7 + - + +
15C ASP* 5.1 1.7 - - - +
38C TYR* 4.0 4.6 + - - -
90C GLY 5.5 0.2 + - - -
91C ARG 3.4 0.2 - - - -
92C ARG* 1.3 120.5 + - - +
94C LYS* 1.3 63.1 + - + +
95C ILE* 3.7 0.4 - - - -
96C GLY 5.3 0.8 + - - -
97C THR* 5.8 0.3 - - - +
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY 5.6 2.0 - - - +
91C ARG* 3.2 16.7 + - + +
93C ASP* 1.3 81.7 - - + +
95C ILE* 1.3 60.6 + - - +
96C GLY 3.1 3.8 - - - -
97C THR* 2.7 45.3 + - + +
104C LEU* 3.5 27.4 - - + +
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Residues in contact with ILE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C TYR* 4.0 4.0 - - + +
42C SER* 3.4 31.6 - - - +
43C VAL* 3.4 23.3 - - + +
83C TYR* 4.0 16.4 - - + +
86C LYS* 4.3 11.4 - - + -
87C ILE* 3.8 27.4 - - + -
91C ARG 3.1 7.5 + - - +
92C ARG 3.7 17.7 - - - +
93C ASP 3.7 0.6 - - - -
94C LYS* 1.3 77.5 - - - +
96C GLY* 1.3 65.8 + - - +
97C THR 3.0 2.0 + - - -
98C ILE* 3.1 43.2 + - + +
104C LEU* 3.8 7.6 - - + -
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Residues in contact with GLY 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C SER* 3.5 24.2 - - - -
43C VAL* 4.6 2.9 - - - -
44C SER* 5.1 7.7 + - - -
93C ASP 5.3 0.8 + - - -
94C LYS 3.0 2.6 + - - -
95C ILE* 1.3 82.1 - - - +
97C THR* 1.3 60.7 + - - +
98C ILE* 3.4 1.9 + - - +
100C GLN* 3.0 17.7 + - - -
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C LYS* 2.7 32.3 + - + +
96C GLY* 1.3 78.0 - - - +
98C ILE* 1.3 66.9 + - - +
99C ARG 3.4 0.3 + - - -
100C GLN* 3.1 30.6 + - - +
103C GLY* 3.5 17.7 - - - -
104C LEU* 3.2 18.2 + - - +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C VAL* 4.2 7.0 - - + -
47C SER* 3.6 10.1 + - - +
83C TYR* 3.3 55.6 - - + +
86C LYS* 3.7 19.1 - - + -
94C LYS 4.0 0.2 + - - -
95C ILE* 3.1 27.1 + - + +
96C GLY 3.4 2.7 - - - +
97C THR* 1.3 80.6 + - - +
99C ARG* 1.3 75.6 + - + +
100C GLN* 3.3 8.3 + - - +
104C LEU* 3.6 12.3 - - + +
105C HIS 3.4 25.8 - - - +
106C PRO* 4.3 1.6 - - + +
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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