Contacts of the strand formed by residues 190 - 195 (chain A) in PDB entry 2OMZ
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 GLN 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASN* 3.2 6.7 + - - +
168A ARG* 3.4 31.2 - - + +
169A LEU 3.1 23.4 + - - -
188A LEU* 4.0 4.5 - - - +
189A GLN* 1.3 85.2 - - + +
191A LEU* 1.3 62.4 + - - +
209A LEU* 4.4 0.2 - - - -
210A GLU* 6.0 0.2 - - + -
211A ARG* 3.3 18.1 - - + +
14B LYS* 3.8 27.9 - - - +
15B GLY* 3.2 35.4 + - - +
16B PRO* 4.1 11.0 - - + -
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Residues in contact with LEU 191 (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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169A LEU* 3.3 36.6 - - + +
171A LEU* 5.2 1.1 - - + -
182A LEU* 3.9 15.3 - - + -
188A LEU* 4.2 12.6 - - + -
190A GLN* 1.3 74.7 - - - +
192A SER* 1.3 74.1 + - - +
193A PHE* 3.9 15.0 - - + -
203A LEU* 3.8 29.2 - - + -
206A LEU* 4.6 0.9 - - + -
209A LEU* 3.6 24.0 - - + -
211A ARG 3.0 7.3 + - - +
212A LEU* 3.4 14.8 - - + +
213A ASP 2.9 23.7 + - - -
16B PRO* 3.7 6.0 - - - +
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Residues in contact with SER 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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169A LEU 3.1 7.8 + - - +
170A GLU* 3.2 23.2 - - - +
171A LEU* 2.9 23.2 + - - +
172A SER* 3.8 13.4 + - - -
191A LEU* 1.3 79.8 - - - +
193A PHE* 1.3 68.7 + - - +
213A ASP* 3.2 24.9 - - - -
16B PRO* 3.8 14.4 - - - +
17B PHE 4.2 3.9 + - - -
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Residues in contact with PHE 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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171A LEU* 3.6 23.3 - - + -
172A SER* 3.8 9.3 - - - +
176A ILE* 4.7 4.7 - - + -
179A ILE* 3.8 26.7 - - + -
182A LEU* 3.9 9.4 - - + -
191A LEU* 3.9 28.0 - - + -
192A SER* 1.3 80.7 - - - +
194A GLY* 1.3 59.2 + - - +
197A VAL* 3.6 39.5 - - + -
200A LEU* 3.7 16.8 - - + -
203A LEU* 4.1 5.4 - - + -
212A LEU* 4.2 2.2 - - + -
213A ASP 3.5 8.0 + - - +
214A ILE* 3.5 29.8 - - + -
215A SER 4.2 4.0 - - - +
217A ASN* 2.9 24.7 + - - -
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Residues in contact with GLY 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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171A LEU 3.3 6.8 + - - +
172A SER* 4.3 6.1 - - - -
173A SER 4.6 0.4 - - - -
174A ASN* 3.2 30.5 - - - +
176A ILE* 3.2 22.0 + - - +
193A PHE* 1.3 80.1 - - - +
195A ASN* 1.3 61.0 + - - -
196A GLN 3.9 1.3 - - - -
215A SER 5.2 1.1 - - - -
216A SER 5.0 0.2 - - - -
217A ASN* 3.4 9.0 - - - -
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Residues in contact with ASN 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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173A SER* 5.2 7.6 - - - +
174A ASN 3.0 27.5 + - - +
175A THR* 3.9 7.5 - - - +
176A ILE 3.8 1.8 + - - +
194A GLY* 1.3 73.5 + - - -
196A GLN* 1.3 84.1 + - - +
216A SER* 3.2 25.6 - - - +
217A ASN* 3.3 17.4 - - - -
218A LYS* 4.2 5.9 - - - -
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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