Contacts of the helix formed by residues 111 - 119 (chain C) in PDB entry 2OB1
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 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C LYS* 4.6 1.2 - - - +
82C THR* 3.8 23.2 + - - +
85C ILE* 3.6 23.1 - - - +
86C ASP* 2.7 32.2 + - - +
89C ILE* 3.6 23.8 - - - -
109C ASP* 2.7 46.8 + - - +
110C LEU* 1.3 77.1 - - - +
112C MET* 1.3 63.2 + - - +
113C LEU 3.0 1.0 + - - -
114C PRO* 3.1 14.3 - - + +
115C LEU* 3.3 22.3 - - + +
124C TYR* 3.5 13.7 + - + +
199C ILE* 4.1 13.7 - - - +
201C GLU* 2.9 23.8 + - - -
2004C PO4 3.2 31.8 + - - +
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Residues in contact with MET 112 (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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109C ASP 3.6 25.1 - - - +
110C LEU* 3.1 23.8 + - + +
111C ARG* 1.3 78.5 - - - +
113C LEU* 1.3 71.3 + - + +
115C LEU* 4.0 2.5 - - - -
116C LEU* 2.9 44.6 + - + +
124C TYR* 3.5 46.3 - - + -
126C ASP* 4.0 8.3 - - - +
136C LYS* 4.1 1.1 - - - -
140C LEU* 4.0 13.9 - - + -
150C LEU* 4.4 2.0 - - + -
169C TYR* 3.5 39.7 - - + +
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Residues in contact with LEU 113 (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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44C TRP* 3.5 40.9 - - + -
110C LEU* 2.9 25.3 + - + +
112C MET* 1.3 88.9 - - + +
114C PRO* 1.4 67.2 - - + +
116C LEU* 4.2 2.5 - - + +
117C GLN* 3.3 21.3 + - - +
140C LEU* 5.5 0.4 - - + -
146C LEU* 3.5 31.6 - - + -
149C SER* 3.6 14.1 - - - +
150C LEU* 3.6 42.8 - - + -
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Residues in contact with PRO 114 (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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33C LEU* 3.8 25.6 - - + -
37C LEU* 4.1 13.5 - - + -
41C TYR* 4.2 23.8 - - + -
44C TRP* 3.7 15.6 - - + -
45C HIS* 6.5 0.2 - - + -
110C LEU 3.4 10.3 - - - +
111C ARG* 3.1 21.8 - - + +
113C LEU* 1.4 87.1 - - + +
115C LEU* 1.3 51.6 - - + +
117C GLN* 3.1 3.0 + - + +
118C MET* 2.8 45.5 + - + +
2004C PO4 5.2 0.2 - - - +
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Residues in contact with LEU 115 (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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86C ASP* 6.1 1.6 - - - +
89C ILE* 4.0 42.6 - - + -
90C LEU* 4.5 6.1 - - + -
93C LEU* 4.2 1.8 - - + -
101C VAL* 4.9 2.7 - - + -
111C ARG* 3.3 24.6 + - + +
112C MET* 4.0 3.4 - - - +
113C LEU 3.3 0.6 - - - -
114C PRO* 1.3 80.2 - - + +
116C LEU* 1.3 58.6 + - - +
118C MET* 3.3 8.6 + - + -
119C PHE* 2.8 57.8 + - + +
122C LEU* 4.2 19.1 - - + -
124C TYR* 4.0 22.7 - - + -
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Residues in contact with LEU 116 (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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112C MET* 2.9 41.6 + - + +
113C LEU* 4.3 2.2 - - - +
115C LEU* 1.3 75.7 - - - +
117C GLN* 1.3 63.5 + - + +
119C PHE 3.8 3.2 + - - +
120C PRO* 4.7 0.3 - - - +
122C LEU* 3.5 30.1 - - + +
124C TYR* 4.2 2.0 - - + -
149C SER 6.0 1.6 - - - +
150C LEU* 3.9 15.0 - - + -
168C ARG* 2.8 69.4 + - + +
169C TYR* 3.9 22.2 - - + -
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Residues in contact with GLN 117 (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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37C LEU* 3.5 22.8 - - + +
40C LYS* 3.0 29.6 + - - +
44C TRP* 3.5 23.9 - - - -
113C LEU 3.3 9.9 + - - +
114C PRO* 3.1 9.8 + - + +
116C LEU* 1.3 80.1 - - - +
118C MET* 1.3 61.5 + - - +
119C PHE 3.6 1.0 + - - -
120C PRO* 5.1 3.1 - - - +
149C SER* 4.4 16.1 - - - +
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Residues in contact with MET 118 (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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31C GLN 4.3 6.3 - - - +
32C ARG* 3.2 43.5 + - - +
33C LEU* 4.3 0.9 - - + -
34C SER 5.8 0.4 - - - -
37C LEU* 3.6 21.3 - - + -
90C LEU* 4.2 12.3 - - + -
114C PRO* 2.8 40.5 + - + +
115C LEU* 4.3 5.4 - - + +
117C GLN* 1.3 75.6 - - - +
119C PHE* 1.3 92.7 + - + +
120C PRO* 3.6 9.6 - - - +
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Residues in contact with PHE 119 (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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32C ARG* 3.8 32.8 - - - -
90C LEU* 3.8 26.5 - - + -
93C LEU* 3.5 55.6 - - + -
94C VAL* 6.0 0.2 - - - -
97C GLU* 5.2 7.2 - - - +
115C LEU* 2.8 23.9 + - + +
116C LEU 3.8 2.3 - - - +
117C GLN 3.4 0.6 - - - -
118C MET* 1.3 98.8 - - + +
120C PRO* 1.4 57.1 - - + +
121C HIS 3.2 2.0 - - - +
122C LEU* 3.0 27.3 + - + +
168C ARG* 2.7 26.1 + - - -
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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