Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 2OQH
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 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASP* 3.4 19.9 + - - +
166B ALA* 3.3 8.2 - - + +
167B VAL* 2.8 28.2 + - - +
186B ARG* 5.1 0.9 - - - +
191B GLY 3.9 2.7 + - - +
192B VAL* 1.3 75.1 - - - +
194B LEU* 1.3 59.4 + - - +
195B ARG* 4.9 1.0 - - - +
220B GLU* 3.4 38.8 + - + +
322B ALA* 6.0 2.4 - - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ILE* 5.6 0.4 - - + -
167B VAL* 3.5 26.2 - - + +
169B LEU* 5.3 2.2 - - + +
182B LEU* 3.8 39.7 - - + +
185B VAL* 3.9 21.1 - - + -
186B ARG* 3.7 38.4 - - + +
192B VAL* 3.2 8.7 + - + +
193B ASN* 1.3 72.7 - - - +
195B ARG* 1.3 67.6 + - - +
217B LEU* 5.1 0.7 - - + -
219B LEU* 3.4 28.5 - - + -
220B GLU 2.8 32.2 + - - +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 2.9 23.3 + - - -
166B ALA* 3.5 19.2 - - - +
167B VAL 2.9 11.3 + - - +
168B LYS* 3.5 21.8 - - + -
169B LEU* 3.0 24.0 + - - +
182B LEU* 3.9 6.9 - - - +
193B ASN* 5.2 0.6 - - - +
194B LEU* 1.3 80.1 - - - +
196B VAL* 1.3 64.1 + - - +
219B LEU* 4.7 2.7 - - - -
220B GLU* 2.8 39.4 + - + +
221B TYR* 3.4 43.8 + - + +
295B ASN* 3.4 11.6 - - - +
321B ARG* 4.5 0.2 - - - +
322B ALA* 2.8 32.5 + - - +
324B ASP* 3.3 15.4 + - - -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 4.6 1.1 - - - -
169B LEU* 3.4 24.5 - - + +
171B GLY* 4.4 11.7 - - - -
178B ASP* 5.0 1.8 - - + -
182B LEU* 3.6 31.6 - - + -
195B ARG* 1.3 76.8 - - - +
197B ASP* 1.3 64.0 + - - +
198B PRO* 3.8 6.0 - - + +
202B TRP* 4.8 9.6 - - + -
214B LEU* 4.4 3.8 - - + -
219B LEU* 4.1 12.1 - - + -
221B TYR 3.7 2.4 + - - -
222B LEU* 3.3 27.1 - - + -
223B GLU* 2.9 27.9 + - - +
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LYS* 3.4 28.2 + - + -
169B LEU 2.9 10.1 + - - +
170B LYS* 3.8 3.6 - - - -
171B GLY 2.9 17.1 + - - +
196B VAL* 1.3 76.5 - - - +
198B PRO* 1.3 58.7 - - - +
199B ASN* 3.0 45.1 + - - +
223B GLU* 3.2 39.9 - - + +
224B ASP* 4.0 3.3 - - - +
246B ASN* 4.9 1.6 + - - -
297B HIS* 5.9 0.9 - - - -
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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