Contacts of the strand formed by residues 271 - 276 (chain A) in PDB entry 4KXA
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 TRP 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LYS* 3.8 30.8 - - - +
108A PRO 3.6 26.7 - - - -
109A LEU* 4.0 12.6 - - + -
248A THR* 3.9 21.1 - - + -
249A HIS* 3.4 22.7 - - - -
250A PRO* 3.6 25.8 - - + -
251A LYS* 4.9 0.4 - - - +
266A SER* 3.8 2.3 - - - -
267A VAL* 3.0 38.7 + - + -
268A ASP* 3.0 33.0 + - - +
269A ASP 5.2 0.2 - - - -
270A LYS* 1.3 93.3 - - + +
272A THR* 1.3 65.3 + - - +
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Residues in contact with THR 272 (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 THR* 3.3 1.6 - - - -
249A HIS* 2.7 62.8 + - + +
251A LYS* 3.5 21.4 - - - +
264A GLU* 4.3 18.4 - - + +
265A GLU 3.6 11.4 - - - +
266A SER* 5.1 3.5 + - - +
267A VAL* 4.3 3.1 - - - -
270A LYS 4.3 0.2 + - - -
271A TRP* 1.3 76.3 + - - +
273A ARG* 1.3 69.8 + - - +
274A THR* 4.0 3.8 - - - +
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Residues in contact with ARG 273 (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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105A HIS* 3.1 29.3 + - + +
246A SER* 3.3 27.4 + - - -
247A ILE 3.3 8.5 - - - +
248A THR* 2.9 23.8 - - - +
263A LYS 3.6 1.9 - - - +
264A GLU* 3.4 2.8 - - - -
265A GLU* 2.8 67.3 + - + +
267A VAL* 4.0 11.9 - - + +
272A THR* 1.3 72.9 - - - +
274A THR* 1.3 62.8 + - - +
275A THR* 3.8 9.8 + - - +
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Residues in contact with THR 274 (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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246A SER* 3.2 3.3 - - - -
247A ILE 2.8 34.6 + - - -
249A HIS* 2.6 31.5 + - - -
255A ALA* 3.8 14.0 + - + +
261A VAL* 4.0 25.4 - - + -
263A LYS 3.6 2.7 - - - -
264A GLU* 4.2 11.9 + - + +
272A THR* 4.0 5.2 - - - +
273A ARG* 1.3 71.4 - - - +
275A THR* 1.3 62.1 + - - +
276A PHE* 3.8 31.8 - - + -
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Residues in contact with THR 275 (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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244A THR* 5.8 4.0 - - - -
245A ILE 3.7 9.4 - - - +
246A SER* 3.7 15.4 - - - -
261A VAL* 3.8 1.9 - - - -
262A ALA* 2.7 33.9 + - + +
263A LYS* 2.8 47.6 + - + +
265A GLU* 4.6 1.2 + - - -
273A ARG* 3.8 16.4 + - - +
274A THR* 1.3 75.1 - - - +
276A PHE* 1.3 66.0 + - - +
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Residues in contact with PHE 276 (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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244A THR* 4.2 11.3 - - - +
245A ILE* 2.8 41.0 + - + +
247A ILE* 3.5 27.1 - - + -
255A ALA 3.7 20.0 - - - -
256A LEU* 3.6 17.5 - - + -
257A SER* 3.6 30.5 - - - -
259A MET* 3.6 24.7 - - + -
260A PRO 3.5 10.1 - - - +
261A VAL* 3.9 13.0 - - + -
262A ALA* 3.9 2.9 - - - +
274A THR* 3.8 27.4 - - + -
275A THR* 1.3 82.7 - - - +
277A GLU* 1.3 67.8 + - - +
278A LYS 3.9 0.3 + - - -
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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