Contacts of the strand formed by residues 235 - 246 (chain A) in PDB entry 5NJ8
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 LEU 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A TYR* 4.8 5.4 - - + +
146A LEU* 4.3 8.5 - - + -
224A LEU* 2.9 34.0 + - - +
226A CYS* 3.5 27.3 - - + +
231A SER* 5.0 14.8 - - - +
233A GLY 3.3 2.9 + - - -
234A PHE* 1.3 73.8 - - - +
236A ALA* 1.3 81.7 + - - +
237A MET* 3.6 20.4 + - + +
271A PRO* 4.6 11.4 - - + -
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Residues in contact with ALA 236 (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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221A ILE* 5.6 6.1 - - + -
222A CYS 4.0 0.4 - - - +
223A ARG* 3.6 28.0 - - + -
234A PHE 3.5 3.2 + - - +
235A LEU* 1.3 88.5 - - - +
237A MET* 1.3 60.5 + - - +
271A PRO 4.8 0.2 - - - -
272A LEU* 3.9 15.7 + - - +
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Residues in contact with MET 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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125A PHE* 3.4 35.2 - - + -
145A TYR* 5.7 3.1 - - - -
146A LEU* 3.7 26.0 - - + -
221A ILE* 3.5 6.5 - - - +
222A CYS* 2.4 44.7 + - - +
224A LEU* 3.8 22.0 - - + -
235A LEU* 4.3 13.0 - - + +
236A ALA* 1.3 76.3 - - - +
238A ASN* 1.3 62.4 + - - +
239A PHE* 4.2 5.3 + - + -
269A ALA* 4.0 20.6 - - + -
270A THR 3.3 13.7 - - - +
271A PRO* 3.5 17.5 - - + -
272A LEU 4.3 6.5 - - - -
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Residues in contact with ASN 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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219A CYS* 4.2 14.6 - - - -
220A PHE 2.9 22.8 + - - +
221A ILE* 4.1 18.8 - - + +
237A MET* 1.3 76.7 - - - +
239A PHE* 1.3 69.5 + - - +
240A GLN* 3.4 5.4 + - - +
269A ALA* 4.7 0.9 - - - -
270A THR* 2.6 58.9 + - - +
272A LEU 5.2 5.8 - - - +
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Residues in contact with PHE 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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127A LEU* 3.7 27.6 - - + -
158A VAL* 6.5 0.7 - - + -
170A PHE* 4.1 14.1 - + - -
218A ARG 4.1 0.3 - - - +
219A CYS* 3.3 3.1 - - - -
220A PHE* 2.9 75.7 + + + +
222A CYS* 3.6 17.0 - - + -
224A LEU* 3.3 47.3 - - + -
237A MET* 4.9 5.6 - - + -
238A ASN* 1.3 71.5 - - - +
240A GLN* 1.3 59.2 + - - +
241A GLY 4.0 0.4 - - - -
265A LEU* 6.0 1.3 - - + -
267A ALA* 4.6 15.9 - - + -
268A ILE 3.4 10.8 - - - +
269A ALA* 4.3 16.4 - - + -
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Residues in contact with GLN 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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217A GLU* 6.3 1.4 - - - +
218A ARG 3.9 2.0 + - - -
219A CYS* 4.0 25.7 - - + +
238A ASN* 3.4 6.5 + - - +
239A PHE* 1.3 71.9 - - - +
241A GLY* 1.3 62.5 + - - +
267A ALA* 4.1 0.4 - - - -
268A ILE* 2.9 37.0 + - + +
270A THR* 4.7 13.2 - - + -
171B ALA 3.8 14.0 + - - +
172B ALA* 3.7 26.7 + - - +
173B ASP* 6.0 0.2 + - - -
342B ARG* 4.1 13.4 + - - +
343B LEU 5.4 3.2 + - - -
345B VAL* 4.4 26.2 - - + +
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Residues in contact with GLY 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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217A GLU* 3.9 4.4 - - - +
218A ARG* 2.5 39.5 + - - +
239A PHE 4.0 1.2 - - - -
240A GLN* 1.3 78.1 + - - +
242A LYS* 1.3 61.4 + - - +
243A LEU 4.1 0.4 - - - -
265A LEU* 4.6 3.8 - - - -
266A PHE 3.4 12.8 - - - -
267A ALA* 3.6 10.9 - - - +
171B ALA 3.4 10.8 - - - -
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Residues in contact with LYS 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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211A GLU 5.5 1.3 - - - -
212A ASN* 2.8 46.9 + - - +
213A SER 5.1 0.2 - - - -
216A MET 4.4 2.7 - - - -
217A GLU* 3.4 37.0 + - + +
218A ARG 4.6 0.7 - - - +
241A GLY* 1.3 73.4 - - - +
243A LEU* 1.3 72.8 + - - +
244A LYS* 3.4 15.1 + - + +
265A LEU* 4.4 0.2 - - - -
266A PHE* 2.9 28.7 + - - +
170B GLU* 3.8 33.6 + - + +
171B ALA* 3.8 4.3 + - - +
173B ASP* 5.7 3.3 + - - +
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Residues in contact with LEU 243 (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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131A THR* 6.3 0.2 - - + -
173A GLN 4.1 10.8 - - - +
174A LEU* 3.3 28.0 - - - +
176A TRP* 5.6 5.2 - - + +
211A GLU 4.8 1.6 - - - +
216A MET* 3.4 51.2 + - + +
218A ARG* 4.4 13.6 - - + +
241A GLY 4.1 0.6 + - - -
242A LYS* 1.3 77.6 - - - +
244A LYS* 1.3 60.8 + - - +
263A LEU* 3.6 32.5 - - + -
264A ALA 3.3 23.1 - - - +
265A LEU* 3.9 21.2 - - + +
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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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82A PHE* 5.0 8.7 - - + -
86A ALA* 5.8 3.0 - - - +
211A GLU 4.7 12.6 - - - +
216A MET* 5.1 1.3 - - - -
242A LYS* 3.4 15.7 + - + +
243A LEU* 1.3 80.5 - - - +
245A TYR* 1.3 70.6 + - - +
247A HIS* 6.4 0.7 - - - -
263A LEU* 4.7 1.3 - - - -
264A ALA* 2.9 30.0 + - - +
266A PHE* 3.5 35.3 - - + -
166B HIS* 4.3 5.1 + - - -
170B GLU* 2.5 49.0 + - + +
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Residues in contact with TYR 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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82A PHE* 3.8 9.4 - - - -
176A TRP* 5.9 0.2 - - - -
209A PRO* 3.4 36.2 + - + +
210A PRO 4.4 12.6 - - - -
211A GLU* 4.9 10.2 + - + +
216A MET* 5.4 0.7 - - + -
244A LYS* 1.3 84.9 - - - +
246A LEU* 1.3 59.8 + - - +
247A HIS* 3.5 36.2 + + + +
261A PRO* 4.0 24.0 - - + -
262A GLN 3.7 14.8 - - - -
263A LEU* 3.7 37.4 - - + +
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Residues in contact with LEU 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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78A ARG* 3.6 27.6 - - - +
82A PHE* 3.6 16.2 - - + -
130A THR* 5.1 6.1 - - + -
136A PHE* 4.3 20.4 - - + -
244A LYS 3.6 1.2 + - - -
245A TYR* 1.3 71.6 - - - +
247A HIS* 1.3 80.1 + - - +
249A GLN* 4.3 6.1 - - + +
261A PRO* 4.2 2.4 - - - +
262A GLN* 2.7 46.7 + - + +
263A LEU 3.8 3.1 - - - +
264A ALA* 3.7 22.9 - - + -
266A PHE* 3.5 26.7 - - + -
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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