Contacts of the strand formed by residues 238 - 245 (chain A) in PDB entry 4GB1
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 ASP 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ILE 2.9 32.8 + - - +
236A GLN 4.4 5.4 - - - +
237A GLY* 1.3 79.4 - - - +
239A CYS* 1.3 61.9 + - - +
240A TYR* 3.2 11.3 - - - +
258A LYS* 3.3 38.2 + - + -
259A ALA 3.2 5.2 - - - +
260A ASN* 3.1 29.1 + - - +
265A ILE* 3.8 14.8 - - - +
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Residues in contact with CYS 239 (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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185A CYS* 3.8 15.0 - - - -
187A ASP* 3.9 14.1 - - - -
192A MET* 4.0 26.0 - - + -
209A TYR* 6.1 1.1 - - - -
233A THR 3.3 4.3 - - - -
234A CYS* 2.0 42.8 - - - -
237A GLY 4.2 3.8 - - - -
238A ASP* 1.3 75.0 - - - +
240A TYR* 1.3 60.6 + - - +
241A TRP* 3.3 6.6 - - - -
258A LYS* 3.4 1.7 - - - -
259A ALA 2.7 41.1 + - - +
260A ASN* 6.1 0.2 - - - -
261A GLN 6.1 1.1 - - - -
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Residues in contact with TYR 240 (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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228A GLN* 4.3 0.9 - - - +
232A CYS* 3.5 15.8 - - - +
233A THR* 2.9 26.8 + - - +
235A ILE* 4.2 22.8 + - + +
238A ASP* 3.2 22.5 - - + +
239A CYS* 1.3 73.0 - - - +
241A TRP* 1.3 68.6 + - - +
256A ILE* 5.0 5.8 - - + -
257A TYR 3.2 5.6 - - - +
258A LYS* 3.1 43.3 + - + -
282A CYS* 6.0 0.5 - - - +
289A VAL* 4.0 27.2 - - + +
307A ILE* 4.5 11.0 - - + -
308A SER 4.4 1.6 - - - -
310A PRO* 3.5 30.9 - - + +
312A LEU* 3.7 24.2 - - + -
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Residues in contact with TRP 241 (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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183A THR* 4.0 13.0 - - + -
192A MET* 4.0 19.1 - - + -
194A VAL* 4.1 23.5 - - + +
207A ILE* 4.2 18.8 - - + -
217A VAL* 5.0 2.2 - - + -
227A THR* 3.8 11.0 - - - -
228A GLN* 3.4 13.9 - - - +
232A CYS* 4.1 9.9 - - + -
239A CYS 3.3 20.2 - - - -
240A TYR* 1.3 83.8 - - - +
242A VAL* 1.3 66.4 + - - +
243A MET* 3.5 36.1 - - + -
255A ARG 3.7 0.3 - - - +
256A ILE* 3.5 4.2 - - - +
257A TYR* 2.9 60.3 + + + +
258A LYS 4.6 0.9 - - - -
259A ALA* 3.6 28.9 - - + -
264A ILE* 4.6 7.4 - - + -
282A CYS* 5.9 0.4 - - - -
307A ILE* 5.9 0.4 - - - -
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Residues in contact with VAL 242 (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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227A THR* 3.2 24.9 + - - -
228A GLN* 3.2 12.1 + - - +
241A TRP* 1.3 80.3 - - - +
243A MET* 1.3 70.1 + - - +
244A THR* 5.4 0.4 - - - +
254A TYR* 5.0 0.9 - - + -
255A ARG 3.3 10.5 - - - +
256A ILE* 5.1 1.8 - - - -
270A ILE* 4.1 17.0 - - + -
277A ILE* 4.4 10.3 - - + -
280A CYS* 3.9 32.8 - - + -
282A CYS* 4.5 0.2 - - - -
291A CYS* 4.2 20.4 - - - -
305A LEU* 4.3 7.0 - - + -
307A ILE* 4.2 16.4 - - + -
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Residues in contact with MET 243 (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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194A VAL* 4.6 2.7 - - + -
196A VAL* 4.0 10.8 - - + -
205A ALA* 3.8 23.6 - - + -
217A VAL* 4.8 6.7 - - + -
220A TRP* 3.7 15.7 - - + -
225A LEU* 3.6 30.7 - - + -
226A ARG 3.2 15.3 - - - +
227A THR* 4.0 7.4 - - - +
241A TRP* 3.5 29.8 - - + +
242A VAL* 1.3 82.1 - - - +
244A THR* 1.3 63.9 + - - +
254A TYR* 3.2 5.5 - - - +
255A ARG 2.8 35.2 + - - +
257A TYR* 3.7 22.2 - - + -
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Residues in contact with THR 244 (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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220A TRP* 3.9 2.2 - - - -
225A LEU* 3.6 3.5 - - - +
226A ARG* 3.1 71.6 + - - +
242A VAL* 5.4 0.3 - - - +
243A MET* 1.3 78.2 + - - +
245A ASP* 1.3 62.6 + - - +
252A ALA* 4.1 14.6 - - + -
253A GLN 3.2 9.6 - - - +
254A TYR* 3.9 5.2 - - + +
277A ILE* 2.6 32.0 + - - +
278A GLU* 4.0 7.7 - - + -
279A GLU 5.1 0.5 + - - -
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Residues in contact with ASP 245 (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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219A SER* 3.3 8.7 + - - -
220A TRP* 2.8 60.6 + - + +
221A ALA* 2.9 18.1 + - + +
222A GLY 3.7 0.4 + - - -
223A ASP 3.1 33.6 + - - +
225A LEU* 3.8 10.3 + - - +
244A THR* 1.3 74.4 - - - +
246A GLY* 1.3 57.7 + - - +
252A ALA* 4.3 2.0 - - - -
253A GLN* 2.8 37.2 + - - +
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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