Contacts of the strand formed by residues 238 - 251 (chain A) in PDB entry 3KJO
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 PHE 238 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A CYS 3.4 3.4 - - - +
167A GLN* 3.7 40.4 - - + -
236A GLY 4.2 6.7 - - - -
237A SER* 1.3 76.1 - - - +
239A LEU* 1.3 61.8 + - - +
277A VAL* 3.6 9.0 - - - +
278A LEU* 2.8 41.4 + - + +
280A GLU* 4.4 17.9 - - + -
285A VAL* 3.5 26.0 - - + -
288A LEU* 3.6 23.1 - - + -
289A LYS* 3.7 37.9 - - + -
292A LEU* 4.1 12.6 - - + -
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Residues in contact with LEU 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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164A LEU 3.5 0.6 - - - +
165A THR* 3.3 4.0 - - - -
166A CYS* 2.9 48.1 + - - +
168A LEU* 3.8 28.5 - - + -
181A LEU* 4.8 1.8 - - + -
183A VAL* 4.7 1.1 - - + -
233A LEU* 3.9 29.2 - - + -
237A SER* 3.7 23.6 - - - +
238A PHE* 1.3 82.7 - - - +
240A ARG* 1.3 63.1 + - - +
241A ILE* 4.0 12.8 - - + -
275A ILE* 4.4 10.3 - - + -
276A ARG 3.6 5.2 - - - +
277A VAL* 3.9 21.3 - - + -
278A LEU* 3.9 8.7 - - - +
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Residues in contact with ARG 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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73A TYR* 3.0 30.5 + - - +
74A LYS* 3.5 22.6 - - - +
150A LEU* 4.3 3.0 - - - +
163A ASP* 4.5 14.7 - - + +
164A LEU 3.2 6.7 - - - +
165A THR* 3.0 25.4 + - - +
239A LEU* 1.3 74.7 - - - +
241A ILE* 1.3 63.9 + - - +
242A TYR* 3.5 42.8 - - + +
275A ILE* 3.5 3.8 - - - +
276A ARG 2.9 34.2 + - - +
278A LEU* 3.9 20.3 - - + +
282A ASN* 4.7 1.6 + - - +
284A ASP* 2.8 34.7 + - - +
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Residues in contact with ILE 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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162A PHE 3.7 2.9 - - - +
163A ASP* 3.3 2.9 - - - -
164A LEU* 2.8 42.3 + - + +
166A CYS* 4.3 14.1 - - - -
181A LEU* 4.5 18.8 - - + -
183A VAL* 4.6 2.9 - - + -
220A ILE* 3.4 31.9 - - + -
222A VAL* 6.1 0.2 - - + -
239A LEU* 4.5 12.6 - - + -
240A ARG* 1.3 74.8 - - - +
242A TYR* 1.3 61.1 + - - +
244A LEU* 4.1 17.8 + - + -
265A LEU* 4.1 33.4 - - + -
274A GLY 3.7 3.8 - - - +
275A ILE* 4.4 9.9 - - + +
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Residues in contact with TYR 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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32A PHE* 3.5 24.6 - + - -
34A PRO* 4.0 20.6 - - + -
72A ILE 4.0 2.6 + - - -
73A TYR* 2.6 40.1 + - - +
74A LYS* 5.0 1.3 - - + -
163A ASP* 3.4 23.8 - - - +
240A ARG* 3.5 36.7 - - + +
241A ILE* 1.3 70.7 - - - +
243A SER* 1.3 72.9 + - - +
244A LEU 3.4 0.5 + - - -
265A LEU* 3.5 6.6 - - - +
271A TYR 5.4 0.9 - - - +
272A GLY* 3.3 20.2 - - - +
273A ARG* 3.3 13.2 - - - -
274A GLY 2.9 20.2 + - - +
276A ARG* 3.8 23.3 - - + +
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Residues in contact with SER 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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161A TYR* 3.7 10.2 - - - +
162A PHE 3.3 10.4 + - - +
163A ASP* 2.9 16.2 + - - -
242A TYR* 1.3 75.0 - - - +
244A LEU* 1.3 66.5 + - - +
245A HIS* 3.6 1.4 + - - +
264A HIS 4.6 1.2 - - - +
265A LEU* 4.0 4.2 - - - +
271A TYR* 3.9 17.7 + - - +
273A ARG* 3.5 24.5 - - - +
9B T 2.6 39.2 + - - -
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Residues in contact with LEU 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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160A GLN 3.6 1.0 - - - +
161A TYR* 3.1 5.7 - - - -
162A PHE* 2.8 52.7 + - + +
164A LEU* 3.8 22.0 - - + -
220A ILE* 3.6 48.5 - - + -
241A ILE* 4.1 19.3 - - + +
242A TYR 3.3 2.7 - - - -
243A SER* 1.3 73.8 - - - +
245A HIS* 1.3 59.1 + - - +
263A PHE* 4.0 21.5 - - + -
264A HIS 3.5 26.9 - - - +
265A LEU* 4.1 4.0 - - - +
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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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159A MET* 3.6 25.4 - - + +
160A GLN* 3.3 14.1 + - - -
161A TYR* 3.4 44.1 + + + -
243A SER 4.6 0.4 - - - +
244A LEU* 1.3 75.1 - - - +
246A THR* 1.3 75.2 + - - +
247A LYS* 4.1 5.1 + - + -
262A GLU 3.6 0.3 - - - +
263A PHE* 3.3 5.2 - - - -
264A HIS* 2.8 49.2 + + + +
266A HIS* 3.4 27.4 - + + +
10B T 3.2 28.8 + + + -
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Residues in contact with THR 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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156A VAL* 4.4 8.3 - - + -
157A GLN 2.8 27.3 + - - +
158A PRO 3.4 3.3 + - - -
159A MET* 3.3 13.7 - - - +
160A GLN* 2.9 23.0 + - + +
162A PHE* 3.5 23.1 - - + -
245A HIS* 1.3 83.6 - - - +
247A LYS* 1.3 62.6 + - - +
261A LEU* 4.4 7.2 - - - -
262A GLU 3.2 7.2 - - - -
263A PHE* 3.5 28.9 - - + -
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Residues in contact with LYS 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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158A PRO 3.4 3.4 - - - -
159A MET* 3.5 28.9 - - + -
245A HIS* 4.9 3.1 - - + +
246A THR* 1.3 77.9 - - - +
248A LEU* 1.3 73.7 + - - +
249A GLN* 3.4 15.3 + - - +
261A LEU* 4.2 1.6 - - - -
262A GLU* 2.8 60.4 + - + +
264A HIS* 4.5 11.2 - - + +
10B T 5.0 13.8 + - - +
11B A 5.6 4.6 + - - -
12B G 4.4 14.5 + - - -
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Residues in contact with LEU 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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158A PRO* 3.0 38.0 + - + +
159A MET* 5.1 1.6 - - - +
191A PHE* 3.9 40.6 - - + -
247A LYS* 1.3 82.5 - - - +
249A GLN* 1.3 62.0 + - - +
250A SER* 4.0 3.6 + - - -
259A LEU* 4.0 28.5 - - + -
260A SER 3.6 19.3 - - - +
261A LEU* 4.1 3.6 - - + -
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Residues in contact with GLN 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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247A LYS* 3.4 15.9 + - - +
248A LEU* 1.3 75.3 + - - +
250A SER* 1.3 71.5 + - - +
251A MET* 3.0 36.8 + - - +
252A ASN* 5.1 0.9 - - - -
258A MET* 3.4 7.9 - - + +
259A LEU* 3.4 6.1 - - - -
260A SER* 2.8 48.6 + - - +
262A GLU* 3.6 30.7 - - - +
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Residues in contact with SER 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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248A LEU* 4.0 4.1 + - - -
249A GLN* 1.3 78.1 + - - +
251A MET* 1.3 63.8 + - - +
257A THR* 3.4 13.6 + - - +
258A MET* 2.9 33.4 + - - +
259A LEU* 4.4 11.2 - - - -
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Residues in contact with MET 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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249A GLN* 3.0 30.6 + - - +
250A SER* 1.3 84.1 - - - +
252A ASN* 1.3 69.7 + - - +
255A ASN* 3.4 41.1 - - + +
256A GLN 3.3 12.1 - - - +
257A THR* 4.1 11.9 - - - +
258A MET* 3.7 3.3 - - - -
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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