Contacts of the strand formed by residues 190 - 194 (chain A) in PDB entry 3D8U
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A THR* 4.5 3.6 - - - +
182A LEU* 3.7 17.9 - - + -
183A ILE* 4.6 5.4 - - + -
187A PHE 3.5 24.5 - - - +
188A LYS* 3.5 5.1 + - - +
189A ASN* 1.3 75.4 + - - +
191A GLY* 1.3 63.1 + - - +
209A TRP* 3.4 35.2 + - + +
213A MSE 3.5 31.4 - - - +
222A HIS* 4.1 3.5 + - - +
249A LEU* 4.2 2.0 - - - -
251A ALA* 3.8 11.2 - - + -
253A VAL* 3.6 25.1 - - + +
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Residues in contact with GLY 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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190A VAL* 1.3 79.6 - - - +
192A PHE* 1.3 61.3 + - - +
222A HIS* 2.8 15.7 - - - -
242A LEU* 4.1 4.9 - - - -
249A LEU* 3.6 18.3 - - - +
251A ALA 3.3 11.8 + - - -
252A LEU* 3.5 7.4 - - - -
253A VAL 2.9 23.9 + - - -
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Residues in contact with PHE 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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175A GLY* 5.7 0.2 - - - -
179A THR* 5.7 0.2 - - + -
191A GLY* 1.3 73.3 - - - -
193A ILE* 1.3 64.4 + - - +
194A GLY* 3.9 23.6 - - - -
202A LEU* 4.1 12.1 - - + -
205A GLN* 3.9 20.9 - - + -
206A LEU* 3.9 29.8 - - + -
209A TRP* 3.6 34.3 - + + -
222A HIS 2.7 8.5 + - - -
223A PHE* 3.0 12.6 - - + -
224A LEU 2.8 34.5 + - - +
225A THR* 4.8 1.6 - - + -
242A LEU* 4.3 2.2 - - - +
253A VAL* 3.5 29.8 - - + -
255A SER* 4.6 2.7 - - - -
283A LEU* 3.8 19.3 - - + -
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Residues in contact with ILE 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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192A PHE* 1.3 77.8 - - - +
194A GLY* 1.3 61.2 + - - +
224A LEU* 3.5 10.3 - - + +
234A LEU* 3.9 26.7 - - + +
235A GLY* 3.8 11.4 - - - +
238A GLY* 3.6 10.3 - - - -
239A LEU* 3.5 28.9 - - - +
242A LEU* 4.4 8.7 - - + -
252A LEU* 3.5 29.8 - - + +
253A VAL 2.9 12.8 + - - +
254A CYS* 3.3 4.7 - - - -
255A SER* 3.0 23.9 + - - -
259A ILE* 3.6 24.0 - - + +
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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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192A PHE* 3.9 11.5 - - - -
193A ILE* 1.3 76.4 - - - +
195A ALA* 1.3 61.8 + - - +
202A LEU* 4.0 2.7 - - - -
224A LEU 3.0 10.9 + - - -
225A THR* 3.1 31.7 - - - -
226A THR 3.2 4.9 + - - -
234A LEU* 4.0 9.6 - - - +
255A SER* 3.4 12.8 - - - -
259A ILE* 4.4 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