Contacts of the strand formed by residues 252 - 261 (chain A) in PDB entry 4EF5
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 GLN 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A LEU* 3.2 7.1 - - - -
249A GLU* 2.8 41.8 + - + +
250A ASN* 3.8 15.1 + - + +
251A GLY* 1.3 80.4 - - - +
253A ARG* 1.3 68.3 + - - +
254A ALA* 3.2 2.1 + - + +
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Residues in contact with ARG 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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186A TYR* 2.9 31.3 + - - -
190A LEU* 3.7 38.1 - - + +
222A LEU* 3.6 20.4 - - - +
246A GLU* 2.3 60.4 + - + +
247A LEU 3.9 2.5 - - - +
248A LEU* 4.0 4.6 - - + +
251A GLY 4.0 1.6 + - - -
252A GLN* 1.3 73.4 - - - +
254A ALA* 1.3 60.5 + - - +
255A GLY 3.6 5.6 - - - +
256A THR* 3.7 10.5 - - - -
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Residues in contact with ALA 254 (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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247A LEU 2.9 14.2 + - - +
249A GLU* 3.6 35.7 - - + +
252A GLN* 3.2 1.5 + - + -
253A ARG* 1.3 73.7 - - - +
255A GLY* 1.3 56.8 + - - +
330A LEU* 4.1 16.0 - - + +
334A ARG* 3.8 18.0 + - - +
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Residues in contact with GLY 255 (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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246A GLU* 3.3 5.7 - - - +
247A LEU* 3.0 28.4 + - - -
253A ARG* 3.6 4.4 - - - +
254A ALA* 1.3 82.4 - - - +
256A THR* 1.3 69.0 + - - -
330A LEU* 4.3 5.4 - - - +
333A LEU* 4.3 13.2 - - - -
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Residues in contact with THR 256 (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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186A TYR* 3.3 40.9 + - + -
193A ALA 4.3 11.8 + - - +
194A VAL* 4.1 7.8 - - + -
195A SER* 3.4 18.2 + - - -
222A LEU* 3.8 10.3 - - + -
244A ILE* 3.5 23.8 - - + -
245A TYR 3.2 11.0 - - - +
246A GLU* 4.7 0.7 - - - +
253A ARG* 3.7 7.4 + - - -
255A GLY* 1.3 77.0 + - - -
257A CYS* 1.3 67.9 - - - +
333A LEU* 3.8 9.4 - - - +
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Residues in contact with CYS 257 (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* 3.7 7.6 - - - +
195A SER* 4.8 4.0 - - - +
199A TYR* 3.5 31.0 - - - -
244A ILE* 3.4 0.8 - - - -
245A TYR* 2.7 41.4 + - + +
247A LEU* 4.2 6.1 - - + -
256A THR* 1.3 83.7 - - - +
258A VAL* 1.3 60.2 + - - +
259A LEU* 3.5 27.5 + - + -
329A VAL* 4.0 5.4 - - - -
333A LEU* 3.8 20.4 - - + -
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Residues in contact with VAL 258 (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 LEU* 5.1 2.9 - - + -
179A ILE* 3.7 33.4 - - + -
194A VAL* 4.1 12.6 - - + +
195A SER 5.0 1.7 + - - +
197A ARG 4.7 7.7 + - - +
198A LEU* 3.7 22.4 - - + -
199A TYR* 3.0 30.9 + - - +
225A LEU* 4.4 8.3 - - + -
242A ASN* 4.4 14.8 - - + +
243A SER 3.3 22.2 - - - +
244A ILE* 4.3 13.0 - - + -
257A CYS* 1.3 71.8 - - - +
259A LEU* 1.3 61.7 + - - +
260A GLU* 5.3 0.7 - - - +
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Residues in contact with LEU 259 (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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199A TYR* 3.5 29.8 - - + +
201A LEU* 4.1 22.0 - - + -
212A LEU* 4.0 20.1 - - + +
219A ILE* 4.0 32.3 - - + -
243A SER* 3.2 13.0 + - - +
245A TYR* 3.8 33.2 - - + -
247A LEU* 4.4 11.4 - - + -
257A CYS* 3.8 15.0 - - - +
258A VAL* 1.3 75.1 - - - +
260A GLU* 1.3 68.8 + - - +
329A VAL* 4.3 11.2 - - + -
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Residues in contact with GLU 260 (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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163A TYR* 4.6 3.8 + - - -
167A TYR* 2.3 35.3 + - - -
198A LEU* 4.6 11.3 - - + +
199A TYR 2.9 9.8 + - - +
200A ILE* 3.2 14.7 - - + -
201A LEU* 2.6 36.2 + - - -
212A LEU* 4.8 3.3 - - - +
241A SER 3.5 10.9 - - - +
242A ASN* 2.8 30.6 + - - -
243A SER 4.9 1.4 + - - +
258A VAL* 5.3 0.7 - - - +
259A LEU* 1.3 82.4 - - - +
261A TYR* 1.3 63.7 + - - +
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Residues in contact with TYR 261 (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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163A TYR* 4.2 4.3 + - - -
200A ILE* 4.5 1.1 - - - -
201A LEU* 3.6 16.8 - - + -
203A PRO* 3.5 30.7 - - + -
207A GLY 4.0 5.1 + - - -
208A VAL* 3.8 35.9 - - + -
209A PRO* 3.6 30.0 - - + +
212A LEU* 3.6 27.0 - - + +
215A ALA* 3.8 18.2 - - - +
260A GLU* 1.3 82.4 - - - +
262A ALA* 1.3 60.0 + - - +
263A THR* 3.0 13.7 + - - -
265A LEU* 5.7 0.2 - - + -
314A TYR* 3.5 25.1 + - - -
325A LEU* 3.8 6.2 - - - +
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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