Contacts of the strand formed by residues 259 - 266 (chain A) in PDB entry 1KB9
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 ALA 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 1.3 75.7 - - - +
260A TRP* 1.3 61.8 + - - +
261A ILE* 4.2 4.5 + - + +
332A THR 3.9 0.5 - - - +
333A ALA* 3.4 3.8 - - - -
334A THR* 3.0 39.1 + - + +
337A VAL* 4.8 2.2 - - + -
340A ILE* 3.9 15.7 - - + -
436A THR 3.5 5.4 - - - -
438A GLN 3.5 22.7 - - - +
439A ILE* 3.9 14.4 - - + -
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Residues in contact with TRP 260 (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 HIS* 3.7 35.4 - + + +
157A PRO* 3.8 31.7 - - + +
160A VAL* 3.7 21.0 - - + +
256A LEU* 3.8 26.2 - - + -
257A PRO* 4.5 8.7 - - + -
258A LYS* 3.4 53.9 - - + +
259A ALA* 1.3 73.7 - - - +
261A ILE* 1.3 62.0 + - - +
332A THR 3.4 6.1 - - - +
333A ALA* 3.7 24.7 - - + +
435A GLY* 3.1 4.9 - - - -
436A THR* 3.0 38.6 + - + +
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Residues in contact with ILE 261 (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 VAL* 4.0 1.8 - - - -
259A ALA* 4.5 6.7 - - + +
260A TRP* 1.3 83.6 - - - +
262A SER* 1.3 87.0 + - - +
263A LEU* 3.9 17.5 - - + +
330A PHE* 4.5 4.5 - - + -
331A SER* 3.2 2.6 - - - -
332A THR* 2.8 55.2 + - + +
334A THR* 5.8 2.5 - - + -
340A ILE* 5.1 8.5 - - + -
343A LEU* 6.2 0.4 - - + -
344A ILE* 3.9 22.7 - - + -
433A ILE* 4.8 7.0 - - + -
434A ALA 3.4 10.1 - - - +
435A GLY* 4.6 1.1 - - - -
439A ILE* 4.4 16.2 - - + -
442A LEU* 4.8 18.2 - - + -
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Residues in contact with SER 262 (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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157A PRO 4.8 1.7 + - - -
160A VAL* 3.4 20.1 - - - +
161A LEU* 4.1 10.4 + - - +
164A LEU* 3.9 26.1 - - - +
261A ILE* 1.3 76.3 + - - +
263A LEU* 1.3 63.1 + - - +
330A PHE 3.3 7.2 - - - -
331A SER* 2.8 24.7 + - - -
432A ALA 4.0 0.2 - - - +
433A ILE* 3.6 2.1 - - - -
434A ALA 3.0 30.4 + - - +
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Residues in contact with LEU 263 (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* 4.8 0.7 - - - -
261A ILE* 3.9 17.0 - - + +
262A SER* 1.3 76.9 - - - +
264A ALA* 1.3 67.4 + - - +
318A PHE* 4.5 0.2 - - - -
329A GLY* 3.2 1.6 - - - -
330A PHE* 2.9 41.2 + - + +
344A ILE* 4.2 14.4 - - + -
348A LEU* 4.3 10.1 - - + -
351A TRP* 4.0 21.3 - - + -
431A ILE* 4.0 26.0 - - + -
432A ALA 3.3 10.8 - - - +
433A ILE* 4.0 13.9 - - + -
442A LEU* 6.1 1.1 - - + -
448A ILE* 3.5 29.4 - - + -
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Residues in contact with ALA 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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164A LEU* 4.0 20.6 - - + +
244A PHE* 3.8 3.4 - - - -
263A LEU* 1.3 81.9 - - - +
265A VAL* 1.3 68.7 + - - +
318A PHE* 4.3 2.7 - - + -
327A LEU* 4.2 11.7 - - + -
328A TRP 3.3 22.7 - - - +
329A GLY* 3.8 3.1 - - - +
351A TRP* 5.2 0.7 - - - -
431A ILE* 3.4 3.5 - - - -
432A ALA* 2.8 33.9 + - - +
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Residues in contact with VAL 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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244A PHE* 3.8 9.6 - - - -
264A ALA* 1.3 77.6 - - - +
266A GLU* 1.3 71.7 + - - +
267A GLY 3.0 0.9 + - - -
327A LEU* 3.5 6.6 - - - +
328A TRP* 2.8 41.5 + - + +
351A TRP* 5.1 4.3 - - + -
425A ARG* 3.5 26.0 - - + +
426A LEU* 3.6 19.1 - - + -
429A GLN* 4.9 1.6 - - + -
430A ASP 3.7 16.8 - - - +
431A ILE* 3.8 2.9 - - + -
452A MET* 3.5 32.5 - - + -
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Residues in contact with GLU 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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242A ALA 5.6 0.5 - - - +
243A ALA* 5.3 2.1 - - - -
244A PHE* 3.7 48.3 + - + +
265A VAL* 1.3 77.0 - - - +
267A GLY* 1.3 66.6 + - - +
324A ASP 5.5 0.2 - - - +
325A SER* 3.3 26.9 + - - +
326A GLY 3.7 3.8 - - - +
425A ARG* 3.3 44.0 + - - +
430A ASP 5.0 0.6 + - - -
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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