Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 1O9I
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 ASP 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PRO 5.5 0.2 + - - -
23B ARG* 3.7 21.7 - - + +
26B GLN* 5.5 1.9 - - - +
104B MET* 1.3 78.4 - - - +
106B PRO* 1.3 71.8 - - - +
107B GLU* 2.8 27.5 + - - +
108B HIS* 3.0 51.5 + - + +
109B SER* 4.3 1.2 + - - -
117B SER* 4.9 7.8 + - - -
119B ASN* 5.4 0.9 + - - -
120B ASN 4.8 3.6 - - - +
121B PRO* 4.5 9.5 - - - +
122B ASN 6.0 0.4 - - - -
123B GLY* 4.6 14.9 + - - -
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Residues in contact with PRO 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 6.3 0.4 - - - -
101B MET 6.2 0.2 - - - +
104B MET* 3.3 10.5 - - + +
105B ASP* 1.3 88.0 - - - +
107B GLU* 1.3 63.1 + - + +
109B SER* 3.2 20.8 + - - +
110B LEU* 3.2 17.7 + - + +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP* 2.8 21.0 + - - +
106B PRO* 1.3 76.2 - - + +
108B HIS* 1.3 66.1 + - - +
109B SER 3.2 0.2 - - - -
110B LEU* 4.5 4.0 - - + -
111B VAL* 2.9 49.8 + - + +
112B HIS* 3.1 17.5 + - + +
119B ASN* 4.0 19.6 + - - +
123B GLY* 4.9 8.7 - - - +
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Residues in contact with HIS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO 4.9 1.6 + - - -
22B ALA* 4.2 3.1 - - + -
23B ARG* 4.0 22.8 + - - +
26B GLN* 2.8 39.9 + - + +
77B ILE* 4.2 0.8 - - + +
81B LEU* 3.6 36.4 - - + +
104B MET* 5.2 3.5 - - + +
105B ASP* 3.0 36.7 + - + +
107B GLU* 1.3 79.5 - - - +
109B SER* 1.3 52.9 + - - +
112B HIS* 3.5 6.0 - + - +
113B GLY 3.2 6.2 + - - -
114B LEU* 2.7 32.5 + - + -
115B ASN 3.3 20.0 - - - -
117B SER* 4.3 8.7 + - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 3.8 34.9 + - - +
104B MET* 5.4 4.2 - - - +
105B ASP 4.3 0.9 + - - -
106B PRO* 3.2 12.4 + - - +
108B HIS* 1.3 79.6 - - - +
110B LEU* 1.3 73.2 + - - +
113B GLY* 3.1 20.1 + - - -
114B LEU* 3.8 19.9 - - - +
261C LEU* 3.9 14.3 - - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PRO* 3.2 21.0 + - + +
107B GLU* 4.5 3.8 - - + -
109B SER* 1.3 85.1 + - - +
111B VAL* 1.3 68.0 + - + +
113B GLY 5.0 0.2 + - - -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A SER 5.1 0.7 - - - +
134A SER* 3.2 26.8 - - - +
107B GLU* 2.9 44.2 + - + +
110B LEU* 1.3 88.5 - - + +
112B HIS* 1.3 85.6 + - + +
113B GLY 3.6 0.4 - - - -
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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