Contacts of the strand formed by residues 258 - 265 (chain A) in PDB entry 1KYO
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 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS* 1.3 79.0 - - - +
259A TRP* 1.3 63.1 + - - +
260A ILE* 3.8 4.3 + - + +
331A THR 3.8 1.0 - - - +
332A ALA* 3.7 1.7 - - - -
333A THR* 3.1 35.6 + - + +
336A VAL* 4.5 3.1 - - + -
339A ILE* 4.0 16.8 - - + -
435A THR 3.5 7.4 - - - -
437A GLN 3.3 28.0 - - - +
438A ILE* 4.1 6.1 - - + -
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Residues in contact with TRP 259 (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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155A HIS* 3.9 27.8 - + + -
156A PRO* 3.8 34.1 - - + +
159A VAL* 3.9 10.7 - - + +
255A LEU* 3.5 35.4 - - + -
256A PRO* 4.0 10.1 - - + -
257A LYS* 3.5 53.2 - - + +
258A ALA* 1.3 72.7 - - - +
260A ILE* 1.3 63.3 + - - +
331A THR 3.4 7.4 - - - +
332A ALA* 3.6 20.6 - - + +
434A GLY* 3.2 2.6 - - - -
435A THR* 2.9 55.9 + - + +
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Residues in contact with ILE 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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159A VAL* 4.3 0.9 - - - -
258A ALA* 3.9 13.5 - - + +
259A TRP* 1.3 79.5 - - - +
261A SER* 1.3 76.2 + - - +
262A LEU* 4.1 11.7 - - + +
329A PHE* 5.1 2.2 - - + -
330A SER 3.6 0.2 - - - -
331A THR* 2.8 50.3 + - + +
333A THR* 5.3 2.7 - - + -
339A ILE* 5.0 9.0 - - + -
342A LEU* 5.9 0.9 - - + -
343A ILE* 3.9 27.8 - - + -
432A ILE* 5.0 3.1 - - + -
433A ALA 3.3 9.6 - - - +
434A GLY* 4.5 2.0 - - - -
438A ILE* 4.0 19.1 - - + -
441A LEU* 4.7 21.1 - - + -
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Residues in contact with SER 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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156A PRO 4.6 2.9 + - - -
159A VAL* 3.6 21.7 - - - +
160A LEU* 4.4 7.7 + - - -
163A LEU* 4.1 21.4 - - - +
260A ILE* 1.3 74.9 + - - +
262A LEU* 1.3 62.2 + - - +
317A PHE* 5.3 0.4 - - - -
329A PHE 3.5 5.2 - - - -
330A SER* 3.0 29.2 + - - -
431A ALA 3.9 0.5 - - - +
432A ILE* 3.7 1.4 - - - -
433A ALA* 2.8 35.8 + - - +
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Residues in contact with LEU 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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163A LEU* 4.7 2.2 - - - +
260A ILE* 4.1 10.3 - - + +
261A SER* 1.3 76.5 - - - +
263A ALA* 1.3 66.7 + - - +
317A PHE* 5.1 0.2 - - - -
328A GLY* 3.1 2.3 - - - -
329A PHE* 2.8 44.1 + - + +
343A ILE* 4.2 15.9 - - + -
347A LEU* 4.1 17.0 - - + -
350A TRP* 3.6 29.6 - - + -
430A ILE* 4.4 22.0 - - + -
431A ALA 3.4 9.9 - - - +
432A ILE* 4.4 7.4 - - + -
447A ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 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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163A LEU* 4.0 20.1 - - + +
243A PHE* 3.9 2.9 - - - -
262A LEU* 1.3 80.8 - - - +
264A VAL* 1.3 66.2 + - - +
317A PHE* 4.0 5.8 - - + -
326A LEU* 4.1 7.0 - - + -
327A TRP 3.1 28.9 - - - +
328A GLY* 3.7 2.7 - - - +
350A TRP* 5.1 0.2 - - - -
430A ILE* 3.4 6.3 - - - +
431A ALA* 2.9 33.1 + - - -
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Residues in contact with VAL 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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243A PHE* 3.8 11.2 - - - -
263A ALA* 1.3 75.3 - - - +
265A GLU* 1.3 75.6 + - - +
266A GLY 3.0 0.7 + - - -
326A LEU* 3.4 8.0 - - - +
327A TRP* 2.6 40.3 + - + +
350A TRP* 5.2 3.4 - - + -
424A ARG* 3.7 14.8 - - + +
425A LEU* 3.4 35.4 - - + -
428A GLN* 4.9 2.2 - - + -
429A ASP 3.8 17.7 - - - +
430A ILE* 3.9 3.8 - - + -
451A MET* 3.9 21.8 - - + -
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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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242A ALA* 5.1 1.2 - - - -
243A PHE* 3.3 53.9 + - + +
264A VAL* 1.3 76.8 - - - +
266A GLY* 1.3 64.8 + - - +
324A SER* 3.7 18.8 + - - +
325A GLY 3.7 4.0 - - - -
424A ARG* 3.4 50.8 + - - +
429A ASP 4.9 0.2 + - - -
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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