Contacts of the strand formed by residues 257 - 265 (chain A) in PDB entry 2J2M
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 GLU 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ARG 5.5 1.0 - - - +
219A PRO* 3.8 1.0 - - - +
220A LYS* 3.0 55.2 + - + +
221A GLU* 4.7 3.8 + - - +
255A PHE* 3.4 17.6 + - + +
256A PRO* 1.3 74.3 - - - +
258A TRP* 1.3 70.9 + - - +
259A ASP* 6.1 0.4 - - - +
296A THR* 4.5 10.7 + - - +
297A MET 3.0 7.6 - - - +
298A THR* 2.6 35.7 + - + +
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Residues in contact with TRP 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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94A PHE* 3.6 27.1 - + - -
113A PHE* 3.4 24.9 - + - -
190A TYR 3.3 21.8 - - - -
191A ARG* 3.8 12.8 - - - -
193A MET 2.8 23.6 + - - -
217A TRP* 3.6 25.4 - - + -
218A VAL 3.3 8.3 - - - +
219A PRO* 3.5 24.7 - - + +
220A LYS 4.5 0.9 - - - +
246A THR* 5.8 0.9 - - + -
256A PRO* 3.5 34.8 - - + -
257A GLU* 1.3 81.2 - - - +
259A ASP* 1.3 64.8 + - - +
296A THR* 3.2 5.2 - - - -
297A MET* 2.8 46.8 + - + +
299A LEU* 3.7 17.3 - - + -
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Residues in contact with ASP 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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69A LYS* 5.0 1.9 + - - -
216A ARG 3.3 1.7 - - - +
217A TRP* 3.2 7.6 - - - -
218A VAL* 2.9 42.8 + - + +
220A LYS* 5.1 10.0 + - - +
257A GLU* 6.1 0.3 - - - +
258A TRP* 1.3 76.3 - - - +
260A LEU* 1.3 60.7 + - - +
261A PHE* 3.6 25.1 - - + -
293A HIS* 2.9 25.0 + - - +
295A GLY 3.4 2.0 - - - -
296A THR* 3.2 18.9 - - - +
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Residues in contact with LEU 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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66A PHE* 3.7 37.9 - - + -
80A PHE* 6.2 0.2 - - + -
81A LEU* 5.8 2.0 - - + -
117A PHE* 5.2 0.7 - - + -
124A TRP* 4.8 16.2 - - + -
126A PHE* 5.4 0.7 - - + -
203A TRP* 6.0 1.3 - - + -
215A LEU* 3.9 29.2 - - + -
216A ARG 3.3 12.8 - - - +
217A TRP* 3.7 35.9 - - + +
258A TRP 4.0 1.2 + - - -
259A ASP* 1.3 70.8 - - - +
261A PHE* 1.3 58.7 + - - +
293A HIS* 3.6 2.8 - - - -
294A VAL* 2.7 50.1 + - + +
295A GLY 2.8 12.3 + - - +
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Residues in contact with PHE 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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215A LEU* 3.6 8.3 - - - +
216A ARG* 2.8 40.9 + - + -
218A VAL* 3.6 34.1 - - + -
259A ASP* 3.6 25.4 - - + -
260A LEU* 1.3 77.9 - - - +
262A VAL* 1.3 60.7 + - - +
291A PHE* 3.5 35.9 - + + -
292A GLN 3.2 5.8 - - - +
293A HIS* 3.5 44.0 - + + -
294A VAL* 4.3 2.2 - - - -
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Residues in contact with VAL 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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72A MET* 3.9 14.6 - - - -
75A TYR* 5.1 0.9 - - + -
203A TRP* 3.8 26.9 - - + -
213A ILE* 3.9 17.5 - - + -
214A LYS 3.4 10.1 - - - +
215A LEU* 3.9 3.8 - - + -
261A PHE* 1.3 74.9 - - - +
263A GLN* 1.3 65.0 - - - +
264A VAL* 4.2 12.8 - - + -
290A PRO 3.6 3.1 - - - +
291A PHE* 4.5 0.4 - - - -
292A GLN* 2.9 53.8 + - + +
294A VAL* 3.9 17.7 - - + -
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Residues in contact with GLN 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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212A TYR 3.5 0.3 - - - +
213A ILE* 2.9 10.7 - - - +
214A LYS* 2.8 44.1 + - + +
216A ARG* 2.6 33.0 + - - +
262A VAL* 1.3 73.4 - - - +
264A VAL* 1.3 61.9 + - - +
284A TRP* 2.9 50.1 + - + +
285A PHE 3.8 1.0 + - - -
289A ILE* 2.6 25.2 + - + +
290A PRO 3.4 18.4 - - - +
291A PHE* 3.4 24.3 - - + -
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Residues in contact with VAL 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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75A TYR* 3.5 52.5 - - + +
211A VAL* 3.6 26.2 - - + -
212A TYR 3.4 2.0 - - - -
213A ILE* 4.3 5.8 - - + -
262A VAL* 4.2 15.7 - - + -
263A GLN* 1.3 78.0 - - - +
265A LEU* 1.3 64.0 + - - +
266A ASP* 4.4 1.2 + - + +
289A ILE* 3.7 18.8 - - - +
290A PRO 4.7 1.0 + - - -
292A GLN* 3.9 14.6 - - - +
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Residues in contact with LEU 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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211A VAL* 4.7 0.2 - - - -
212A TYR* 2.8 40.7 + - + +
264A VAL* 1.3 77.3 - - - +
266A ASP* 1.3 70.8 + - - +
269A ASP* 4.0 17.9 - - + +
270A VAL* 4.2 9.6 - - + -
273A PHE* 3.6 32.5 - - + -
277A PRO* 3.6 36.3 - - + -
284A TRP* 3.6 31.6 - - + -
289A ILE* 4.0 8.7 - - + -
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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