Contacts of the strand formed by residues 236 - 242 (chain A) in PDB entry 2Q4E
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 THR 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 5.7 0.2 - - - +
154A LYS 3.0 3.6 + - - -
155A THR* 2.9 38.0 + - - -
156A VAL* 3.1 1.2 + - - +
228A SER* 5.8 4.0 - - - -
229A LEU 3.6 9.0 - - - -
230A SER* 3.4 17.9 - - - -
231A TRP* 3.4 8.4 - - - -
234A GLY 4.8 4.6 + - - +
235A ARG* 1.3 80.7 - - - +
237A ALA* 1.3 69.2 + - - +
238A THR* 6.3 0.2 - - - -
211B PHE* 6.4 0.2 - - + -
212B PRO 3.9 14.4 - - - +
213B GLY* 4.3 13.9 - - - +
240B TYR* 4.2 11.9 + - + -
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Residues in contact with ALA 237 (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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155A THR* 3.6 5.8 - - - -
156A VAL* 2.9 34.8 - - + +
196A THR* 3.9 11.2 - - + +
228A SER* 2.8 27.2 - - - -
229A LEU* 2.9 11.7 + - + +
231A TRP* 3.5 15.7 - - + -
236A THR* 1.3 81.3 + - - +
238A THR* 1.3 65.0 + - - +
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Residues in contact with THR 238 (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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155A THR* 5.6 0.2 - - - +
156A VAL 2.9 7.3 + - - +
157A GLN* 3.1 34.6 - - - +
158A SER* 2.8 24.8 + - - -
196A THR* 4.2 0.9 + - - -
211A PHE* 3.9 16.8 - - + -
227A ALA 3.0 11.9 - - - +
228A SER* 4.0 11.4 - - - -
229A LEU* 5.2 0.7 - - - -
236A THR* 6.3 0.2 - - - -
237A ALA* 1.3 86.5 - - - +
239A ILE* 1.3 67.7 + - - +
211B PHE* 4.1 17.0 - - + -
238B THR* 5.4 5.5 + - + -
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Residues in contact with ILE 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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158A SER* 2.9 10.8 - - - -
185A LEU* 4.7 3.4 - - + -
189A GLY* 4.4 11.7 - - - +
192A ALA* 3.4 25.4 - - + -
193A ILE* 3.6 39.9 - - + +
196A THR* 3.8 13.2 - - - +
211A PHE* 3.7 7.3 - - - -
225A CYS 5.5 1.6 - - - +
226A GLY* 3.5 14.5 - - - -
227A ALA* 3.1 20.9 + - + +
229A LEU* 4.8 9.6 - - + -
238A THR* 1.3 80.2 - - - +
240A TYR* 1.3 66.5 + - - +
241A CYS* 5.7 0.7 - - - -
346A VAL* 4.4 23.6 - - + -
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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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158A SER 2.7 11.3 + - - +
159A CYS* 3.2 16.4 - - + -
160A PHE* 2.8 33.1 + - - +
161A SER* 5.5 4.9 - - - -
192A ALA* 4.3 3.4 - - - +
211A PHE* 4.5 10.5 - + + -
224A SER* 4.9 8.2 - - - -
225A CYS* 3.8 24.5 - - - -
226A GLY* 4.0 9.0 - - - -
239A ILE* 1.3 80.2 - - - +
241A CYS* 1.3 66.5 + - - +
242A SER* 5.1 10.3 - - - -
154B LYS* 4.0 9.2 + - + +
155B THR* 3.3 41.5 - - + -
234B GLY 4.2 3.5 + - - -
236B THR* 2.8 28.6 + - - -
254B ILE* 5.4 2.2 - - + -
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Residues in contact with CYS 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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160A PHE 2.8 6.7 - - - +
161A SER* 4.3 0.4 - - - -
184A ALA* 3.4 29.4 - - - -
185A LEU* 3.6 11.0 - - - -
188A ALA* 3.5 11.7 - - + -
189A GLY* 3.3 31.0 - - - +
224A SER* 3.3 1.3 - - - -
225A CYS* 3.1 48.6 + - - -
239A ILE* 5.7 1.8 - - - -
240A TYR* 1.3 78.9 - - - +
242A SER* 1.3 63.8 + - - +
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Residues in contact with SER 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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160A PHE 3.1 5.5 + - - -
161A SER* 2.8 36.4 - - - -
162A PHE* 3.2 4.9 + - - -
184A ALA* 4.1 3.0 - - - +
188A ALA* 4.7 2.5 - - - +
223A LEU 3.1 10.7 + - - -
224A SER* 3.5 14.4 - - - -
240A TYR* 5.1 8.5 - - - -
241A CYS* 1.3 78.2 - - - +
243A PHE* 1.3 64.3 + - - +
244A LEU* 2.8 24.8 + - - +
245A ALA* 3.4 11.4 + - - +
154B LYS* 5.8 1.5 - - - +
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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