Contacts of the strand formed by residues 256 - 266 (chain A) in PDB entry 5MJ6
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 ASN 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A LEU* 4.1 3.0 - - - +
198A VAL 3.4 6.2 - - - +
199A GLN* 2.7 33.8 + - - +
224A ALA* 3.0 38.8 + - + +
254A GLY 4.1 0.2 + - - -
255A HIS* 1.3 72.7 - - - +
257A TYR* 1.3 71.7 + - - +
1D NAG 1.4 65.9 + - + +
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Residues in contact with TYR 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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196A ILE 3.7 0.2 - - - +
197A SER* 3.7 1.6 - - - -
198A VAL* 2.9 49.1 + - + +
200A ALA* 4.3 6.3 - - + -
221A PHE* 3.7 33.7 - + + -
222A MET 3.4 6.5 - - - +
223A SER* 3.5 36.6 - - - -
224A ALA* 4.3 1.8 - - - +
250A ALA 4.0 4.7 + - - -
251A LEU* 3.4 30.4 - - + -
252A LEU* 2.9 25.9 + - - +
255A HIS* 3.4 43.5 - + + +
256A ASN* 1.3 76.7 - - - +
258A THR* 1.3 64.9 + - - +
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Residues in contact with THR 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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195A THR* 3.7 28.3 - - + -
196A ILE 3.7 4.0 - - - +
197A SER* 4.2 12.1 + - - -
220A THR 4.0 0.5 - - - +
221A PHE* 3.7 6.1 - - - -
222A MET* 2.8 54.3 + - + +
224A ALA* 5.0 3.7 - - - +
257A TYR* 1.3 76.7 + - - +
259A LEU* 1.3 65.1 - - - +
260A LYS* 4.2 4.2 + - + +
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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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194A VAL 3.6 1.6 - - - +
195A THR* 3.4 2.6 - - - +
196A ILE* 2.8 50.0 + - + +
198A VAL* 5.3 8.3 - - + -
207A ILE* 4.3 19.7 - - + -
209A LEU* 3.9 17.9 - - + -
219A VAL* 4.1 10.8 - - + -
220A THR 3.6 13.5 - - - +
221A PHE* 4.3 15.7 - - + -
245A ILE* 3.8 41.7 - - + -
258A THR* 1.3 74.4 - - - +
260A LYS* 1.3 61.2 + - - +
261A ILE* 4.2 10.1 - - + -
306A PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 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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193A SER* 3.3 24.2 + - - +
194A VAL 3.4 4.5 - - - +
195A THR* 3.4 24.0 + - + +
218A ARG* 3.7 1.7 - - - +
219A VAL* 3.2 5.5 - - - +
220A THR* 2.8 54.6 + - + +
229A GLU* 5.0 7.2 - - - +
258A THR* 4.2 4.2 + - + -
259A LEU* 1.3 75.3 - - - +
261A ILE* 1.3 65.1 + - - +
262A GLU* 3.9 20.9 - - - +
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Residues in contact with ILE 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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193A SER* 3.6 1.4 - - - -
194A VAL* 3.0 42.3 + - + -
196A ILE* 5.2 2.0 - - + -
209A LEU* 4.3 17.0 - - + -
216A ILE* 3.9 31.6 - - + -
218A ARG 3.5 2.7 - - - +
219A VAL* 4.3 13.5 - - + -
234A ILE* 5.3 0.2 - - + -
243A ILE* 4.3 10.5 - - + -
245A ILE* 4.4 9.9 - - + -
259A LEU* 4.3 9.9 - - + -
260A LYS* 1.3 79.0 - - - +
262A GLU* 1.3 64.8 + - - +
263A TYR* 3.7 7.2 - - + -
304A PRO* 3.7 36.6 - - + -
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Residues in contact with GLU 262 (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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191A ARG* 5.6 4.2 + - - -
192A GLY 3.5 5.8 - - - +
193A SER* 3.8 21.5 - - - +
216A ILE* 3.6 3.5 - - - +
217A SER* 2.9 34.6 + - - +
218A ARG* 2.7 65.9 + - - +
260A LYS* 3.9 20.0 - - + +
261A ILE* 1.3 71.5 - - - +
263A TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 263 (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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179A LEU* 4.0 0.9 - - - +
181A LEU* 3.8 13.7 - - - +
190A PHE* 3.9 13.5 - + - -
191A ARG* 3.6 5.5 - - - +
192A GLY* 2.7 59.3 + - - +
193A SER 4.1 3.6 - - - -
194A VAL* 4.4 4.9 - - + -
214A HIS* 3.5 36.8 - + + -
215A ASN 3.2 15.3 - - - +
216A ILE* 3.9 15.3 - - + +
217A SER* 4.1 5.1 + - - +
261A ILE* 3.7 16.4 - - + -
262A GLU* 1.3 75.8 - - - +
264A SER* 1.3 63.4 + - - +
302A ALA 2.6 23.6 + - - -
303A PHE* 3.2 11.5 - - + +
304A PRO* 3.6 22.0 - - + -
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Residues in contact with SER 264 (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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190A PHE 3.5 7.4 - - - -
191A ARG* 4.0 17.0 - - - +
214A HIS* 3.8 1.6 - - - -
215A ASN* 2.8 57.7 + - - +
263A TYR* 1.3 76.8 - - - +
265A ALA* 1.3 64.0 + - - +
1134A NAG 4.9 0.4 - - - -
1J NAG 4.3 7.6 + - - -
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Residues in contact with ALA 265 (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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189A THR* 3.4 6.8 - - - -
190A PHE* 2.7 63.1 + - + +
213A GLY 3.5 18.4 - - - +
214A HIS* 3.8 12.3 - - + -
263A TYR* 4.7 0.2 - - - -
264A SER* 1.3 77.3 - - - +
266A ASN* 1.3 64.0 + - - +
301A SER 5.0 2.0 - - - +
1134A NAG 4.2 5.6 - - - -
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Residues in contact with ASN 266 (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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188A MET 3.8 4.8 - - - +
189A THR* 4.1 14.9 - - - +
190A PHE* 3.6 13.0 - - - -
213A GLY 4.7 0.8 + - - -
265A ALA* 1.3 78.7 - - - +
267A ILE* 1.3 68.2 + - - +
268A SER* 3.6 3.8 + - - -
274A PHE 4.8 0.5 - - - +
301A SER 5.4 1.6 - - - +
1134A NAG 1.5 66.4 + - + +
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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