Contacts of the strand formed by residues 243 - 253 (chain A) in PDB entry 4X8G
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 GLY 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A THR* 3.0 15.9 + - - +
188A LYS* 4.1 0.9 - - - -
189A THR* 2.8 37.3 + - - -
190A PRO 3.7 2.5 + - - -
191A LYS* 5.1 1.3 - - - -
241A PRO 4.5 1.2 - - - +
242A GLY* 1.3 74.9 - - - -
244A LYS* 1.3 61.0 + - - -
245A HIS* 3.4 2.3 + - - +
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Residues in contact with LYS 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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187A THR 3.5 4.9 - - - -
188A LYS* 4.2 12.1 - - + +
242A GLY 5.5 0.2 - - - -
243A GLY* 1.3 68.7 - - - -
245A HIS* 1.3 59.7 + - - +
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Residues in contact with HIS 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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185A LEU 3.8 1.0 - - - +
186A SER* 3.8 0.4 - - - -
187A THR* 2.8 47.1 + - - +
240A VAL* 3.3 14.4 - - + +
241A PRO* 3.5 43.4 - - + +
242A GLY 5.3 0.4 - - - +
243A GLY 3.4 2.0 + - - +
244A LYS* 1.3 75.6 - - - +
246A ASN* 1.3 79.8 + - - +
247A MET* 3.7 27.6 - - + +
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Residues in contact with ASN 246 (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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184A THR* 5.9 3.4 - - - -
185A LEU 3.3 6.1 - - - +
186A SER* 3.8 19.5 - - - +
245A HIS* 1.3 92.3 + - - +
247A MET* 1.3 61.7 + - - +
248A ASP* 4.4 12.5 - - - +
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Residues in contact with MET 247 (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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184A THR* 3.2 4.5 - - - -
185A LEU* 2.7 46.2 + - + +
215A GLN* 3.0 33.0 - - + +
216A ALA 5.2 3.1 - - - +
238A LEU* 4.8 9.0 - - - -
239A MET 3.8 16.2 - - - +
240A VAL* 3.7 24.0 - - + -
245A HIS* 3.7 21.8 - - + +
246A ASN* 1.3 77.3 - - - +
248A ASP* 1.3 69.9 + - - +
249A PHE* 3.4 31.5 - - + -
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Residues in contact with ASP 248 (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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182A LEU* 4.3 15.8 - - + +
183A MET 3.8 1.6 - - - -
184A THR* 3.3 24.9 - - - +
215A GLN* 3.8 4.7 - - - +
216A ALA* 3.1 45.0 + - + +
246A ASN* 4.4 10.7 - - - +
247A MET* 1.3 76.1 - - - +
249A PHE* 1.3 66.8 + - - +
250A TYR* 4.7 5.6 + - + -
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Residues in contact with PHE 249 (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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117A LEU* 5.3 2.9 - - + -
181A SER 3.9 0.2 - - - +
182A LEU* 3.3 6.9 - - - +
183A MET* 2.6 72.7 + - + +
184A THR 4.8 0.7 - - - -
185A LEU* 3.8 27.4 - - + -
201A LEU* 4.3 12.1 - - + -
213A VAL* 4.2 12.1 - - + -
214A PHE 3.2 15.5 - - - +
215A GLN* 4.0 21.5 - - + -
228A VAL* 4.4 5.2 - - + -
238A LEU* 4.0 27.1 - - + -
247A MET* 3.4 32.3 - - + -
248A ASP* 1.3 77.6 - - - +
250A TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 250 (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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177A LEU* 4.2 53.4 - - + +
180A MET* 4.2 20.9 - - + -
181A SER 3.5 7.9 - - - -
182A LEU* 3.7 34.5 - - + +
213A VAL* 3.6 1.0 - - - -
214A PHE* 2.8 50.7 + - + +
216A ALA* 3.5 34.1 - - + -
225A CYS* 4.8 4.7 - - - -
248A ASP* 4.7 7.1 + - + -
249A PHE* 1.3 75.1 - - - +
251A VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 251 (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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150A LEU* 3.3 23.3 - - + +
180A MET* 3.2 6.5 - - - +
181A SER* 2.8 42.2 + - - +
183A MET* 4.0 24.7 - - + -
211A VAL* 3.6 26.7 - - + -
212A ARG 3.8 3.8 - - - +
213A VAL* 4.2 8.7 - - + -
250A TYR* 1.3 77.2 - - - +
252A GLU* 1.3 63.0 + - - +
267A LEU* 4.0 25.4 - - + -
291A PHE* 4.4 10.5 - - + -
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Residues in contact with GLU 252 (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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150A LEU* 3.8 7.2 - - - -
151A LEU 4.5 2.5 - - - +
153A ASN* 2.7 42.2 + - + +
165A ASP 4.4 2.3 - - - +
166A CYS* 4.3 4.2 - - - -
168A ASP 4.5 1.0 - - - +
180A MET* 3.3 19.3 - - + +
211A VAL* 3.3 7.1 - - - +
212A ARG* 3.0 76.5 + - + +
214A PHE* 3.2 28.6 - - + -
251A VAL* 1.3 74.3 - - - +
253A ALA* 1.3 58.0 + - - +
254A LEU* 4.0 7.6 - - + -
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Residues in contact with ALA 253 (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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150A LEU* 3.7 20.5 - - + +
151A LEU 3.2 28.8 + - - +
152A VAL* 3.8 5.7 - - + +
153A ASN* 3.1 25.2 + - - +
166A CYS* 4.1 0.3 - - - +
210A LYS 3.3 7.4 - - - +
252A GLU* 1.3 73.4 - - - +
254A LEU* 1.3 67.8 + - - +
255A ALA 3.7 1.6 - - - +
293A VAL* 4.1 20.2 - - + -
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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