Contacts of the helix formed by residues 250 - 258 (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 THR 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ASP 5.0 5.2 + - - +
245A PRO 3.6 17.3 - - - +
246A GLY* 3.8 1.8 - - - -
247A ALA* 3.1 41.0 + - - +
248A LEU 3.1 3.8 + - - +
249A THR* 1.3 82.2 - - - +
251A GLY* 1.3 72.1 + - - +
252A ARG 3.3 0.5 + - - -
253A MET* 3.2 15.2 + - - +
254A ARG* 3.2 22.1 + - - +
1005A MG 4.0 12.5 - - - -
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Residues in contact with GLY 251 (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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250A THR* 1.3 77.1 - - - +
252A ARG* 1.3 62.4 + - - -
254A ARG* 3.1 9.1 + - - +
255A ASP* 3.0 31.3 + - - +
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Residues in contact with ARG 252 (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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136A MET* 3.7 31.0 - - + +
137A PRO 4.2 9.7 + - - -
138A ILE* 4.2 3.0 - - - +
139A GLU* 4.3 10.3 - - - +
142A ASP* 2.8 44.3 + - - +
250A THR 3.3 0.8 + - - -
251A GLY* 1.3 71.4 - - - -
253A MET* 1.3 65.4 + - - +
255A ASP* 3.3 10.9 + - - +
256A PHE* 3.0 23.2 + - - +
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Residues in contact with MET 253 (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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133A ALA 3.0 28.5 - - - +
134A ILE* 4.0 7.0 - - + -
135A ALA* 3.5 33.2 - - + +
136A MET* 3.9 23.7 - - + +
138A ILE* 3.8 27.1 - - + -
142A ASP* 5.8 3.1 - - + +
248A LEU* 3.8 26.7 - - + +
249A THR* 3.6 16.4 - - - -
250A THR 3.2 8.7 + - - +
252A ARG* 1.3 79.3 - - - +
254A ARG* 1.3 62.3 + - - +
256A PHE* 3.3 3.7 + - - +
257A CYS* 3.0 24.2 + - - -
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Residues in contact with ARG 254 (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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240A PHE* 4.0 10.1 - - + -
242A ASN* 2.8 43.2 + - - +
243A ALA 3.0 21.4 + - - -
244A GLU* 3.5 23.0 + - - -
245A PRO 4.6 2.0 + - - -
249A THR* 3.6 23.9 + - - +
250A THR* 3.2 34.0 + - - +
251A GLY 3.1 13.1 + - - +
253A MET* 1.3 79.6 - - - +
255A ASP* 1.3 63.7 + - - +
257A CYS* 3.3 2.6 + - - +
258A ARG* 2.9 50.5 + - - +
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Residues in contact with ASP 255 (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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251A GLY* 3.0 18.9 + - - +
252A ARG* 3.3 11.4 + - - +
254A ARG* 1.3 79.9 - - - +
256A PHE* 1.3 64.1 + - - +
258A ARG* 3.3 23.5 + - - +
259A THR* 3.4 15.7 + - - +
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Residues in contact with PHE 256 (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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135A ALA* 3.7 15.9 - - + -
136A MET* 3.6 29.4 - - + -
228A ALA* 3.6 30.7 - - + -
229A GLY* 5.4 0.2 - - - -
232A SER* 4.0 13.7 - - - -
252A ARG 3.0 13.4 + - - +
253A MET 3.5 8.3 - - - +
255A ASP* 1.3 76.5 - - - +
257A CYS* 1.3 58.6 + - - +
259A THR* 2.5 41.1 + - + -
260A TRP* 3.4 44.7 - + - -
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Residues in contact with CYS 257 (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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130A TYR* 3.3 32.8 - - + +
135A ALA* 3.5 30.5 - - - -
240A PHE* 4.5 9.9 - - + -
249A THR* 4.2 12.3 - - - -
253A MET 3.0 21.2 + - - +
254A ARG* 3.7 4.9 - - - +
256A PHE* 1.3 75.4 - - - +
258A ARG* 1.3 58.7 + - - +
260A TRP* 2.9 34.6 + - - +
263A GLN* 3.0 15.1 + - - -
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Residues in contact with ARG 258 (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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240A PHE* 4.2 6.5 - - + -
242A ASN* 3.4 22.8 - - - +
244A GLU* 5.7 0.4 + - - -
254A ARG* 2.9 41.1 + - - +
255A ASP* 3.6 15.2 + - - +
256A PHE 3.2 0.8 - - - -
257A CYS* 1.3 75.4 - - - +
259A THR* 1.3 59.4 + - + +
260A TRP 3.3 2.8 + - - +
263A GLN* 4.0 7.1 + - - +
265A GLU* 2.8 43.2 + - - +
267A THR* 4.8 1.0 + - - -
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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