Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 2NO5
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 ASN 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A LEU* 3.3 27.1 - - - +
5A LEU* 3.9 17.6 - - + +
170A ASN* 3.0 33.9 + - - +
172A VAL 3.0 16.5 + - - +
173A CYS* 3.4 9.5 - - + -
174A PHE* 2.7 33.1 + - - +
189A GLY 4.9 1.4 - - - +
190A PHE* 1.3 74.6 - - - +
192A THR* 1.3 56.3 + - - +
210A LYS* 3.4 30.9 + - + +
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Residues in contact with THR 192 (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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174A PHE 3.5 4.3 - - - +
182A LEU* 3.7 22.4 - - + +
185A ALA* 4.3 9.2 - - + -
186A GLY* 3.5 35.4 - - - +
190A PHE* 3.7 5.6 + - + +
191A ASN* 1.3 76.9 - - - +
193A VAL* 1.3 63.4 + - - +
194A ARG 4.2 0.2 - - - -
207A ALA 4.7 1.2 + - - -
208A PRO 3.5 7.8 + - - -
209A LEU* 3.4 26.9 - - - +
210A LYS* 2.9 36.1 + - - +
211A HIS 3.4 2.8 + - - +
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Residues in contact with VAL 193 (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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173A CYS* 3.3 31.6 - - - -
174A PHE 2.8 12.5 + - - +
175A VAL* 3.3 8.1 - - + +
176A SER 3.2 23.4 + - - -
182A LEU* 3.6 3.8 - - - +
191A ASN 5.2 0.2 - - - -
192A THR* 1.3 78.8 - - - +
194A ARG* 1.3 65.8 + - - +
195A ILE* 3.7 0.6 + - + -
210A LYS* 4.8 5.4 - - + -
211A HIS* 3.4 35.9 - - + +
212A GLN 4.4 0.7 - - - +
213A VAL* 4.5 9.0 - - + -
219A LEU* 4.0 26.5 - - + -
222A LEU* 5.5 7.0 - - + -
223A LEU* 5.6 1.1 - - + -
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Residues in contact with ARG 194 (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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176A SER 3.2 6.3 - - - +
177A SER* 3.9 20.3 + - - -
179A ALA* 4.3 22.7 - - - +
182A LEU* 3.3 23.6 - - + +
192A THR 4.2 0.2 - - - -
193A VAL* 1.3 74.1 - - - +
195A ILE* 1.3 63.8 + - - +
196A ASN* 3.4 32.9 + - - +
200A ASN* 3.7 26.7 + - - +
201A PRO 3.9 16.0 + - - -
202A PRO* 4.6 7.5 - - - +
203A GLU* 4.9 4.0 + - - +
209A LEU* 3.6 22.4 - - + +
211A HIS 3.2 6.7 + - - -
212A GLN* 3.4 18.0 + - + +
213A VAL* 3.0 28.1 + - - +
1015A CNR 4.7 6.7 - - - +
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Residues in contact with ILE 195 (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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15A THR* 4.4 4.9 - - + -
175A VAL* 3.5 31.9 - - + -
176A SER 3.0 7.9 + - - +
177A SER* 3.0 31.5 + - - +
193A VAL* 3.7 0.4 + - + -
194A ARG* 1.3 73.2 - - - +
196A ASN* 1.3 56.3 + - - +
197A ARG* 3.5 33.4 + - + +
213A VAL* 3.4 22.4 - - + -
215A SER* 3.7 30.5 - - - +
216A LEU* 3.8 19.5 - - + -
219A LEU* 3.9 9.0 - - + -
1011A SO4 5.2 0.5 + - - -
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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