Contacts of the strand formed by residues 241 - 248 (chain A) in PDB entry 1KT8
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 MET 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TYR* 5.5 0.4 - - - -
182A VAL* 5.3 3.6 - - + -
224A GLN* 3.1 34.8 - - - +
237A GLU* 3.1 7.3 - - - +
238A VAL* 2.8 44.7 + - + +
239A GLY 3.5 0.4 + - - -
240A THR* 1.3 88.1 - - - +
242A ASN* 1.3 62.7 + - - +
310A GLY* 4.0 9.2 - - - +
311A SER 3.1 22.0 - - - +
312A GLY* 4.3 3.4 - - - +
314A ALA* 6.4 1.1 - - + -
315A CYS* 4.1 17.5 - - + +
318A CYS* 3.6 34.3 - - + -
320A VAL* 6.2 1.3 - - + -
400A ILP 3.8 8.8 + - - -
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Residues in contact with ASN 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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236A THR 5.2 0.2 - - - -
237A GLU* 3.5 15.1 - - - +
238A VAL* 4.3 0.2 - - - -
241A MET* 1.3 74.8 - - - +
243A ILE* 1.3 59.9 + - - +
244A PHE* 4.5 2.9 - - + -
258A THR* 4.9 1.8 - - - +
265A ILE* 3.9 10.7 - - + +
266A LEU 3.0 15.2 - - - +
268A GLY* 3.2 34.6 - - - +
271A ARG* 3.4 28.2 - - + +
310A GLY* 3.0 6.8 - - - -
311A SER* 2.8 42.6 + - - +
400A ILP 3.5 17.1 - - - -
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Residues in contact with ILE 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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184A LEU* 5.3 3.6 - - + -
226A LEU* 3.6 25.8 - - + -
235A LEU* 3.7 26.0 - - + +
236A THR 3.3 29.5 + - - +
237A GLU* 4.1 2.9 - - - +
238A VAL* 4.1 14.6 - - + -
241A MET 3.9 0.2 + - - -
242A ASN* 1.3 76.3 - - - +
244A PHE* 1.3 68.4 + - - +
245A VAL* 5.0 3.8 - - + -
258A THR* 2.7 26.4 + - - -
259A PRO* 3.3 19.7 - - + +
291A ILE* 5.2 2.0 - - + +
308A VAL* 4.5 15.9 - - + -
309A PHE 3.6 8.3 - - - +
320A VAL* 6.1 0.4 - - + -
323A ILE* 5.9 0.7 - - + -
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Residues in contact with PHE 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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242A ASN* 4.6 2.0 - - + -
243A ILE* 1.3 78.0 - - - +
245A VAL* 1.3 68.5 + - - +
256A LEU* 3.9 27.6 - - + -
257A VAL 3.5 2.9 - - - -
258A THR* 3.6 17.5 - - - -
271A ARG* 3.6 39.0 - - + -
274A LEU* 4.0 11.7 - - + -
275A LEU* 3.6 25.6 - - + -
308A VAL* 3.4 7.5 - - - +
309A PHE* 2.8 68.1 + + + +
311A SER* 3.4 31.0 - - - -
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Residues in contact with VAL 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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235A LEU* 5.0 2.7 - - + -
243A ILE* 5.0 9.6 - - + -
244A PHE* 1.3 80.3 - - - +
246A TYR* 1.3 62.9 + - - +
247A TRP* 3.5 41.5 + - + -
255A GLU 3.7 1.6 - - - +
256A LEU* 3.4 5.5 - - - +
257A VAL* 2.9 45.9 + - + +
291A ILE* 4.0 23.6 - - + -
296A LEU* 4.8 8.3 - - + -
305A VAL* 4.8 3.6 - - + -
307A GLU 3.6 6.1 - - - +
308A VAL* 4.3 19.7 - - + -
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Residues in contact with TYR 246 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PHE 4.4 0.2 - - - -
245A VAL* 1.3 70.4 - - - +
247A TRP* 1.3 63.6 + - - +
254A LEU* 3.5 35.1 - - + +
255A GLU 3.5 15.3 - - - -
256A LEU* 4.1 5.4 - - + -
284A PHE* 4.0 23.9 - + - -
305A VAL* 4.1 1.6 - - - +
306A ARG* 3.0 62.8 + - + +
307A GLU* 2.8 47.9 + - + +
309A PHE* 4.8 1.3 - - + -
340A GLU* 5.2 3.8 + - + -
341A LEU* 3.7 38.9 - - + +
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Residues in contact with TRP 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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245A VAL* 3.5 21.5 - - + -
246A TYR* 1.3 77.7 - - - +
248A THR* 1.3 62.6 + - - +
249A HIS* 4.1 22.1 - + - +
254A LEU* 3.5 9.2 - - - +
255A GLU* 2.6 73.2 + - + +
257A VAL* 3.6 22.4 - - + +
289A ARG* 4.3 6.3 - - - -
291A ILE* 4.2 16.6 - - + -
295A GLN* 4.0 28.3 - - + -
296A LEU* 4.2 12.1 - - + -
299A ALA* 3.5 33.0 - - + -
304A ARG* 3.3 18.6 - - - +
305A VAL* 3.8 10.1 - - + -
306A ARG* 4.3 2.5 - - - +
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Residues in contact with THR 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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247A TRP* 1.3 75.2 - - - +
249A HIS* 1.3 63.0 + - - +
252A GLY* 3.3 39.3 - - - +
253A VAL 3.6 8.3 - - - +
254A LEU* 4.0 12.8 - - + +
304A ARG* 2.8 50.9 + - - +
306A ARG* 5.6 1.7 + - - +
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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