Contacts of the strand formed by residues 251 - 256 (chain E) in PDB entry 1K9A
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 LEU 251 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ARG* 5.5 1.4 + - - -
188E TRP* 3.4 32.6 - - + -
237E ALA* 4.3 3.8 - - - +
240E MET* 3.9 29.9 + - + +
241E THR* 3.7 32.3 - - + +
243E LEU 5.8 0.2 + - - -
249E VAL 3.8 3.2 + - - -
250E GLN* 1.3 99.7 + - - +
252E LEU* 1.3 60.5 + - - +
253E GLY 3.6 26.5 - - - +
254E VAL* 4.4 10.3 - - + -
264E ILE* 3.8 21.1 - - + -
265E VAL 3.7 8.7 - - - +
266E THR* 4.4 3.4 - - - -
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ARG* 3.8 21.6 + - - +
188E TRP* 4.0 6.6 - - - -
190E LEU* 3.4 15.4 - - + +
214E TYR* 6.3 2.5 - - + -
218E LYS 5.2 0.2 - - - +
219E VAL* 3.6 23.1 - - + -
250E GLN* 4.1 9.6 - - + +
251E LEU* 1.3 82.4 - - - +
253E GLY* 1.3 60.9 + - - +
265E VAL* 2.9 16.6 + - + +
266E THR 3.4 31.0 - - - +
267E GLU* 3.6 11.4 - - + +
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Residues in contact with GLY 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E TRP* 3.1 20.0 - - - -
190E LEU* 3.3 16.3 - - - +
251E LEU* 3.6 7.7 - - - +
252E LEU* 1.3 84.5 - - - +
254E VAL* 1.3 65.0 + - - +
265E VAL* 3.0 27.5 + - - +
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Residues in contact with VAL 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PHE* 3.9 40.6 - - + -
188E TRP* 2.7 15.4 + - + +
189E ALA* 3.8 3.5 - - - -
190E LEU 3.0 24.0 + - - +
233E PHE* 3.3 31.9 - - + -
237E ALA* 4.1 12.3 - - + -
251E LEU* 4.4 14.6 - - + -
253E GLY* 1.3 79.0 - - - +
255E ILE* 1.3 68.1 + - - +
256E VAL* 4.1 10.5 + - + -
263E TYR 3.6 4.3 - - - +
264E ILE* 5.1 2.5 - - + -
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Residues in contact with ILE 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E LEU* 4.0 21.5 - - + +
191E ASN 5.0 0.4 - - - -
192E MET* 3.8 42.6 - - + +
195E LEU* 3.3 36.3 - - + -
233E PHE* 4.2 0.9 - - - -
254E VAL* 1.3 79.4 - - - +
256E VAL* 1.3 66.8 + - - +
257E GLU* 4.2 11.7 - - + +
261E GLY 3.3 3.8 - - - +
262E LEU* 3.5 1.6 - - - -
263E TYR* 2.8 53.4 + - + +
265E VAL* 3.8 17.0 - - + -
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Residues in contact with VAL 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU* 4.2 23.1 - - + -
150E MET* 4.6 9.9 - - + -
180E GLN* 4.6 17.3 - - + -
183E PHE* 5.7 5.4 - - + -
233E PHE* 4.1 23.1 - - + -
254E VAL* 4.1 9.8 + - + -
255E ILE* 1.3 79.8 - - - +
257E GLU* 1.3 67.6 + - - +
258E GLU* 3.6 1.9 + - - -
261E GLY 3.4 3.8 - - - -
262E LEU* 4.0 14.4 - - + -
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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
------------------------------------------------------------
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