Contacts of the strand formed by residues 263 - 270 (chain A) in PDB entry 1K63
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 GLN 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TYR* 2.6 35.1 + - - -
238A LYS* 3.4 16.1 - - + +
240A PHE* 3.6 16.7 - - + +
257A CYS 3.0 24.7 + - - -
258A ARG* 4.0 9.3 + - - +
260A TRP* 3.6 29.7 + - - +
261A PRO 4.0 2.9 - - - +
262A ASN* 1.3 77.3 - - - +
264A THR* 1.3 75.8 + - - +
265A GLU* 5.0 4.2 + - + +
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Residues in contact with THR 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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238A LYS 2.9 11.6 + - - -
239A LEU* 3.4 19.9 - - + +
240A PHE 2.8 25.6 + - - -
262A ASN 5.5 0.2 + - - -
263A GLN* 1.3 78.6 - - - +
265A GLU* 1.3 68.7 + - - +
266A ILE* 5.2 4.0 - - + -
289A PHE* 5.1 2.1 - - - -
292A ARG* 3.8 29.5 + - - +
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Residues in contact with GLU 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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239A LEU* 4.8 0.7 - - - -
240A PHE* 3.3 32.9 - - + +
242A ASN* 4.3 1.6 - - + -
258A ARG* 2.8 50.4 + - - +
263A GLN* 4.3 3.7 + - + +
264A THR* 1.3 81.2 - - - +
266A ILE* 1.3 80.0 + - - +
267A THR* 4.0 7.8 + - - -
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Residues in contact with ILE 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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239A LEU* 4.8 6.7 - - + +
240A PHE 3.1 3.5 + - - +
241A ILE* 4.2 21.3 - - + -
242A ASN* 2.8 33.1 + - - +
264A THR* 5.2 4.0 - - + -
265A GLU* 1.3 80.3 - - - +
267A THR* 1.3 58.2 + - - +
268A VAL* 3.6 27.1 - - + -
281A GLU* 3.8 11.0 - - + +
282A ILE* 4.7 0.7 - - - -
285A ALA* 3.5 34.8 - - + -
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Residues in contact with THR 267 (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* 3.0 29.7 + - - +
244A GLU* 3.5 33.0 - - + +
258A ARG* 4.8 0.5 + - - -
265A GLU* 4.0 8.0 + - - -
266A ILE* 1.3 76.0 - - - +
268A VAL* 1.3 75.6 + - - +
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Residues in contact with VAL 268 (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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241A ILE* 4.2 2.9 - - + -
242A ASN 2.9 14.2 + - - +
243A ALA* 3.2 6.6 - - - -
244A GLU* 3.0 24.2 + - - -
266A ILE* 3.6 26.5 - - + -
267A THR* 1.3 82.2 - - - +
269A ALA* 1.3 67.9 + - - +
274A ILE* 4.0 24.2 - - + -
278A SER* 3.8 16.6 - - - -
281A GLU* 4.0 19.3 - - + -
282A ILE* 4.1 13.0 - - + -
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Residues in contact with ALA 269 (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* 4.4 10.5 - - + -
244A GLU* 3.3 11.0 - - - +
268A VAL* 1.3 77.7 - - - +
270A GLY* 1.3 57.8 + - - +
274A ILE* 4.5 1.7 - - - +
277A ASP* 3.7 8.7 - - + +
278A SER* 2.7 31.9 + - - +
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Residues in contact with GLY 270 (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* 3.8 13.9 - - - +
243A ALA* 4.3 0.2 - - - -
244A GLU 2.9 9.7 + - - -
245A PRO* 3.1 9.8 - - - +
246A GLY* 2.8 28.9 + - - -
268A VAL 3.6 1.4 + - - -
269A ALA* 1.3 73.9 - - - +
271A ALA* 1.3 55.0 + - - -
274A ILE* 3.8 16.4 - - - -
277A ASP* 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