Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 2A1X
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 ILE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A TYR* 5.1 1.2 + - - -
146A PHE* 5.2 1.3 - - - +
147A THR* 4.9 0.2 - - - -
178A LEU* 3.9 13.0 - - + -
181A PHE* 4.6 15.0 - - + -
183A PHE* 3.5 43.1 - - + +
184A ARG* 5.1 0.2 - - - -
185A PRO 3.7 11.2 - - - +
186A SER* 3.3 28.5 + - - +
187A ASP 3.3 4.3 + - - +
188A LEU* 1.3 80.5 - - - +
190A VAL* 1.3 71.0 + - - +
259A HIS* 4.6 2.9 - - - -
260A PRO* 3.4 26.0 - - + +
281A HIS* 4.9 5.4 - - + -
282A PHE 3.2 12.3 - - - +
283A ALA* 3.9 13.7 - - + -
287A CYS* 4.5 2.2 - - - -
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Residues in contact with VAL 190 (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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61A TYR* 3.8 13.9 - - - +
143A VAL* 3.8 32.3 - - + -
146A PHE* 3.8 37.0 - - + -
147A THR* 4.2 4.0 - - + -
189A ILE* 1.3 77.9 - - - +
191A CYS* 1.3 71.8 + - - +
192A ALA 3.8 0.2 + - - -
257A PHE* 4.2 4.0 - - + -
258A PHE 3.7 16.2 - - - +
260A PRO* 5.1 0.4 - - - -
280A CYS 3.7 0.7 - - - +
281A HIS* 3.2 3.0 - - - -
282A PHE* 2.7 48.6 + - + -
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Residues in contact with CYS 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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157A MET* 5.7 0.7 - - - -
177A ASP* 4.3 0.4 - - - +
190A VAL* 1.3 75.8 - - - +
192A ALA* 1.3 63.0 + - - +
193A TRP* 4.1 14.1 - - - -
256A VAL 3.5 1.7 - - - +
257A PHE* 3.3 7.3 - - - -
258A PHE* 3.0 68.3 + - + +
259A HIS 6.0 0.4 - - - -
260A PRO* 5.7 0.8 - - + +
279A SER* 4.5 7.0 - - - -
280A CYS 3.4 7.0 - - - -
281A HIS* 3.4 37.0 - - + +
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Residues in contact with ALA 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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133A TYR* 2.7 26.4 + - + +
139A ILE* 4.3 6.3 - - + -
190A VAL 3.8 0.6 + - - -
191A CYS* 1.3 72.9 - - - +
193A TRP* 1.3 59.1 + - - +
255A THR* 4.5 2.0 - - + -
256A VAL 3.6 4.3 - - - -
257A PHE* 4.0 22.9 - - + -
279A SER* 3.1 1.4 - - - -
280A CYS 2.7 29.4 + - - -
282A PHE* 3.7 27.1 - - + -
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Residues in contact with TRP 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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157A MET* 5.0 2.5 - - + -
159A ILE* 3.6 9.4 - - + +
191A CYS* 4.1 13.9 - - - -
192A ALA* 1.3 73.4 - - - +
194A THR* 1.3 62.6 + - - +
195A ALA 4.2 1.6 - - - -
199A ILE* 3.7 28.0 - - + -
206A LEU* 3.6 35.3 - - + +
248A LEU 6.0 0.2 - - - -
250A MET* 3.6 30.9 - - + +
255A THR* 3.4 1.7 - - - +
256A VAL* 2.9 51.4 + - + +
258A PHE* 4.2 5.8 - + + -
275A ARG* 3.9 8.5 - - - -
277A ALA* 3.4 22.0 - - + -
278A ILE 3.6 2.7 - - - -
279A SER* 3.7 18.2 - - - -
451A AKG 3.1 37.3 + - + +
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Residues in contact with THR 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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73A VAL* 4.2 6.9 - - + +
78A ILE* 3.9 18.2 - - + -
133A TYR* 3.0 29.8 + - + -
193A TRP* 1.3 75.4 - - - +
195A ALA* 1.3 77.6 + - - +
196A MET 3.4 0.2 + - - -
253A GLY 3.7 12.6 - - - +
254A ASP 3.3 12.8 - - - +
255A THR* 3.0 20.3 + - - +
277A ALA* 3.3 4.3 - - - -
278A ILE* 2.8 39.1 + - + +
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Residues in contact with ALA 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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78A ILE* 4.0 1.9 - - - +
193A TRP* 4.5 0.4 - - - -
194A THR* 1.3 77.8 - - - +
196A MET* 1.3 55.7 + - - +
197A GLU 3.3 20.2 - - - +
199A ILE* 3.5 23.3 - - + -
250A MET* 3.7 19.5 - - + +
251A GLU 3.5 19.1 - - - +
253A GLY 2.8 27.9 + - - -
254A ASP 3.0 7.8 + - - +
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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