Contacts of the strand formed by residues 183 - 189 (chain F) in PDB entry 1O94
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 SER 183 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E PRO* 6.1 0.2 - - - -
142E HIS 5.0 3.4 + - - -
172E VAL* 3.7 16.2 - - - +
173E GLU 3.0 18.4 - - - -
174E ILE* 3.9 14.6 - - - -
175E ASN* 5.3 0.9 - - - +
71F ASP* 3.6 9.3 + - - +
72F PRO* 4.1 15.8 - - - +
73F ASP* 4.8 0.7 + - - -
180F GLN* 4.5 1.1 + - - -
181F SER* 3.1 29.1 + - - +
182F ARG* 1.3 80.5 - - - +
184F GLN* 1.3 63.8 + - - +
185F ASN* 4.4 1.6 + - - -
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Residues in contact with GLN 184 (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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172E VAL* 3.4 2.1 - - - -
173E GLU* 2.7 50.1 + - + +
71F ASP* 5.2 0.7 - - - -
180F GLN* 4.7 13.2 + - - +
181F SER* 6.1 0.2 - - - -
183F SER* 1.3 78.6 - - - +
185F ASN* 1.3 78.8 + - - +
186F LYS* 3.5 20.7 - - - +
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Residues in contact with ASN 185 (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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162E ARG* 5.6 0.2 - - - -
170E GLN* 3.5 26.2 + - - +
171E GLU 3.8 4.3 - - - -
172E VAL* 3.7 19.4 - - - +
67F SER* 4.2 12.6 - - - -
69F ASP* 3.4 19.2 + - - +
70F PHE 2.9 28.4 + - - +
71F ASP* 4.7 6.4 + - - +
72F PRO* 5.8 1.4 - - - +
183F SER* 5.3 1.0 + - - -
184F GLN* 1.3 94.3 + - - +
186F LYS* 1.3 64.2 + - - +
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Residues in contact with LYS 186 (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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159E VAL* 5.6 0.9 - - + -
170E GLN* 4.7 3.8 - - - +
171E GLU* 2.7 47.5 + - + +
173E GLU* 4.0 30.8 + - + +
184F GLN* 3.5 31.4 - - + +
185F ASN* 1.3 84.3 + - - +
187F ASP* 1.3 73.2 + - - +
188F TYR* 3.9 3.1 + - - -
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Residues in contact with ASP 187 (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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170E GLN* 4.6 1.6 - - - -
171E GLU* 3.0 29.9 + - + +
186F LYS* 1.3 85.8 - - - +
188F TYR* 1.3 72.0 + - - +
189F VAL* 3.9 1.4 + - - +
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Residues in contact with TYR 188 (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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162E ARG* 5.4 1.2 + - - -
164E LEU* 3.6 23.6 - - + -
168E MET* 4.0 21.1 - - + -
169E LEU 3.2 10.3 - - - +
170E GLN* 3.5 31.9 + - + +
10F ARG* 3.7 15.2 + - + +
11F ARG* 3.4 46.2 + - + +
69F ASP* 2.4 41.6 + - + +
186F LYS 5.3 2.2 - - - -
187F ASP* 1.3 84.7 - - - +
189F VAL* 1.3 60.3 + - - +
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Residues in contact with VAL 189 (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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161E ARG* 4.2 32.5 - - - +
168E MET* 4.3 13.5 - - - +
169E LEU* 2.7 43.5 + - + +
171E GLU* 5.9 1.8 - - + +
187F ASP 3.9 2.4 + - - +
188F TYR* 1.3 75.9 - - - +
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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