Contacts of the strand formed by residues 139 - 144 (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 VAL 139 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 4.8 0.2 - - + -
17E PHE* 3.5 28.3 - - + -
19E ILE* 5.3 2.9 - - + -
26E VAL* 4.0 12.6 - - + -
232E MET* 4.0 8.1 - - + -
233E TYR 3.5 16.4 - - - +
234E ILE* 4.5 3.4 - - + -
235E PRO* 3.9 2.9 - - - -
119F TYR* 3.8 0.9 + - - -
133F GLY* 3.5 6.8 - - - -
134F GLY* 3.0 46.3 + - - +
135F TYR* 3.9 13.7 - - + -
137F GLN 3.9 4.8 - - - +
138F LYS* 1.3 86.6 - - + +
140F ASN* 1.3 67.4 + - - +
141F VAL* 4.0 11.9 - - + -
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Residues in contact with ASN 140 (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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231E ARG 4.0 0.2 - - - +
232E MET* 3.2 7.1 - - - +
233E TYR* 2.8 78.2 + - + -
235E PRO* 4.1 20.2 - - - +
119F TYR* 2.7 34.7 + - - -
120F ILE* 4.2 5.7 - - - +
131F THR* 3.6 12.5 - - + +
132F ARG 3.5 2.9 - - - -
137F GLN 5.5 0.3 - - - +
139F VAL* 1.3 76.2 - - - +
141F VAL* 1.3 61.2 + - - +
142F GLU 4.1 0.2 - - - -
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Residues in contact with VAL 141 (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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125E GLN* 5.0 3.4 - - - +
229E VAL* 4.1 30.5 - - + -
231E ARG 3.5 2.9 - - - -
232E MET* 3.7 23.3 - - + -
130F ALA 3.7 0.5 - - - +
131F THR* 3.3 5.2 - - - -
132F ARG* 2.7 46.8 + - + +
133F GLY 3.9 2.0 - - - +
134F GLY* 3.8 28.7 - - - +
139F VAL* 4.0 0.7 - - + -
140F ASN* 1.3 75.5 - - - +
142F GLU* 1.3 61.0 + - - +
143F VAL* 4.0 16.6 + - + +
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Residues in contact with GLU 142 (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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229E VAL* 3.5 4.3 - - - +
230E ARG* 2.6 61.1 + - + -
231E ARG* 2.8 63.0 + - + +
233E TYR* 3.9 10.8 + - + -
122F GLU* 5.7 3.3 - - - +
124F GLN* 4.8 2.0 - - - +
129F VAL* 3.7 17.2 - - + +
130F ALA 3.4 1.3 - - - -
131F THR* 3.3 24.2 + - + +
140F ASN 4.1 0.6 - - - -
141F VAL* 1.3 72.4 - - - +
143F VAL* 1.3 54.4 + - - +
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Residues in contact with VAL 143 (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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227E SER* 4.3 13.7 - - - -
228E ARG 3.1 14.1 - - - +
229E VAL* 4.2 10.3 - - + +
230E ARG* 4.5 2.2 - - - -
115F ALA* 4.2 11.7 - - + -
129F VAL* 3.4 6.2 - - - +
130F ALA* 2.8 46.7 + - + +
132F ARG* 5.1 11.0 - - + -
141F VAL* 4.1 21.1 - - + +
142F GLU* 1.3 78.9 - - - +
144F ASP* 1.3 63.3 - - - +
145F PHE* 3.7 24.8 - - + -
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Residues in contact with ASP 144 (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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227E SER* 3.6 1.9 - - - -
228E ARG* 2.8 58.1 + - - +
230E ARG* 3.7 26.8 + - + +
127F GLU* 4.5 17.3 - - + +
128F LEU 3.5 17.5 - - - +
129F VAL* 4.6 6.5 - - + -
143F VAL* 1.3 75.5 - - - +
145F PHE* 1.3 69.5 + - - +
146F PRO* 3.5 8.9 - - - +
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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