Contacts of the strand formed by residues 181 - 185 (chain A) in PDB entry 3ONC
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 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 10.1 - - + -
12A MET* 4.0 17.9 - - - -
106A LEU* 3.8 32.5 - - + -
108A LEU* 4.4 9.2 - - + -
157A GLY* 3.4 3.0 - - - -
158A ILE* 2.9 30.3 + - - +
179A PRO* 3.4 2.0 - - - +
180A ALA* 1.3 85.7 - - + +
182A ASN* 1.3 70.3 + - - +
183A GLN* 3.9 5.4 - - + +
204A ILE* 3.6 6.1 - - - -
205A VAL* 3.0 16.6 - - + +
207A THR* 3.6 21.3 - - - +
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ILE* 3.2 24.0 - - + +
159A SER* 3.6 4.3 - - - -
160A ASN 3.6 1.7 + - - -
161A PHE 3.1 40.4 + - - -
166A VAL* 3.7 13.7 - - - +
181A VAL* 1.3 73.5 - - - +
183A GLN* 1.3 63.2 + - - +
184A ILE* 3.7 12.7 + - + +
195A LEU* 4.2 3.0 - - - +
199A CYS* 3.7 17.6 - - - -
204A ILE* 3.5 12.6 - - + +
205A VAL 3.0 6.2 + - - +
206A VAL* 3.3 13.8 - - + +
207A THR 3.1 18.0 + - - -
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Residues in contact with GLN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A HIS* 6.1 0.2 + - - -
43A ASP* 3.0 23.6 + - - -
75A VAL* 4.8 1.6 - - - +
77A LYS* 3.3 5.7 - - - -
106A LEU* 6.2 0.4 - - - +
108A LEU* 3.6 24.2 - - + +
158A ILE 3.0 7.5 + - - -
159A SER* 2.8 27.8 + - - +
160A ASN 2.9 13.2 + - - -
181A VAL* 3.9 2.8 - - + +
182A ASN* 1.3 70.3 + - - +
184A ILE* 1.3 61.9 + - - +
207A THR* 3.3 28.0 - - + +
209A TYR* 3.9 9.1 - - + -
260A ILE* 3.6 16.5 - - - +
500A NAP 2.9 40.2 + - - -
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASN* 4.1 13.0 - - - +
161A PHE 4.5 0.2 - - - +
182A ASN* 3.6 27.6 - - - +
183A GLN* 1.3 81.0 - - - +
185A GLU* 1.3 65.5 + - - +
186A CYS* 4.7 2.5 - - + -
192A GLN* 3.8 35.2 - - + +
195A LEU* 3.9 23.8 - - + -
196A ILE* 4.2 7.9 - - + -
206A VAL* 3.8 28.3 - - + -
207A THR 2.9 10.2 + - - +
208A ALA* 3.4 1.9 - - - -
209A TYR* 2.8 30.5 + - - -
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Residues in contact with GLU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASN* 4.8 0.6 + - - -
184A ILE* 1.3 74.3 - - - +
186A CYS* 1.3 64.3 + - - +
187A HIS* 2.8 29.2 + - + +
190A LEU* 3.7 17.9 - - + +
192A GLN* 2.9 28.8 + - - +
209A TYR* 3.4 34.4 + - + +
210A SER* 4.4 2.0 - - - -
295A TRP 3.7 0.2 - - - +
296A ARG* 3.5 15.4 + - - +
297A VAL* 2.8 32.3 + - - +
298A CYS* 2.9 29.0 + - - +
311A PHE* 6.4 0.2 - - + -
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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