Contacts of the helix formed by residues 245 - 258 (chain A) in PDB entry 5KYT
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 HIS 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A MET* 3.6 2.7 - - - -
197A ASN 5.6 3.4 - - - -
242A PRO* 3.3 23.1 + - + +
243A PHE 3.1 0.6 - - - -
244A HIS* 1.3 90.8 + + + +
246A GLY* 1.3 57.3 + - - +
247A PHE* 3.1 25.7 + - + +
248A GLY 3.1 3.0 + - - +
249A MET* 2.8 32.6 + - - +
343A THR* 4.3 5.8 + - - -
526A LEU* 6.5 0.7 - - + -
527A THR* 3.7 27.2 + - + +
601A SLU 2.7 60.6 + - + -
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Residues in contact with GLY 246 (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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196A MET* 3.5 18.1 - - - +
245A HIS* 1.3 79.2 + - - +
247A PHE* 1.3 62.1 + - - +
250A PHE* 3.1 38.0 + - - +
343A THR* 4.9 9.3 + - - +
346A THR 4.1 6.2 - - - +
347A SER* 5.1 0.2 + - - -
601A SLU 3.7 15.9 + - - -
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Residues in contact with PHE 247 (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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241A VAL* 3.4 23.3 - - + -
245A HIS* 3.1 19.9 + - + +
246A GLY* 1.3 77.1 - - - +
248A GLY* 1.3 51.5 + - - +
251A THR* 2.7 32.8 + - + +
286A LEU* 3.7 33.7 - - + -
287A LEU 3.5 21.3 - - - -
288A VAL* 3.9 8.1 - - + -
314A SER 4.2 0.2 - - - -
315A GLY* 3.6 38.8 - - - -
316A GLY* 4.5 3.4 - - - -
527A THR* 4.8 2.2 - - + -
601A SLU 3.4 54.5 - + - -
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Residues in contact with GLY 248 (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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241A VAL* 3.4 17.5 - - - +
242A PRO 3.3 19.8 + - - -
243A PHE* 4.1 6.3 - - - -
245A HIS 3.1 3.6 + - - -
247A PHE* 1.3 77.3 - - - +
249A MET* 1.3 65.5 + - - +
251A THR* 3.6 4.5 - - - -
252A THR* 2.7 32.5 + - - -
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Residues in contact with MET 249 (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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88A PHE* 4.2 14.6 - - + -
89A PHE* 3.7 19.2 - - + -
92A VAL* 4.2 10.3 - - + -
104A PRO* 3.6 30.7 - - + -
194A LEU* 3.7 15.5 - - + -
196A MET* 3.9 11.2 - - + -
243A PHE 3.5 18.8 + - - +
245A HIS 2.8 20.8 + - - +
248A GLY* 1.3 74.9 - - - +
250A PHE* 1.3 88.1 + - + +
252A THR* 4.0 1.2 - - - -
253A LEU* 3.1 45.5 + - - +
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Residues in contact with PHE 250 (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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194A LEU* 3.7 30.1 - - + -
196A MET* 4.4 8.7 - - + -
210A LEU* 3.7 31.0 - - + -
214A THR* 5.0 0.4 - - - -
215A ALA* 4.2 17.5 - - + -
218A ARG* 2.9 37.2 + - + +
219A PHE* 5.6 0.7 - + - -
246A GLY* 3.1 17.9 + - - +
249A MET* 1.3 87.4 - - + +
251A THR* 1.3 64.9 + - - +
253A LEU* 4.1 14.3 - - + +
254A GLY 3.4 11.3 + - - -
346A THR* 3.1 38.8 - - + -
347A SER* 3.9 20.0 - - - +
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Residues in contact with THR 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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218A ARG* 3.9 10.4 + - - +
239A SER* 5.1 0.3 + - - -
247A PHE* 2.7 26.9 + - + +
248A GLY* 3.4 6.9 + - - -
250A PHE* 1.3 79.1 - - - +
252A THR* 1.3 62.1 + - - +
254A GLY* 3.1 3.5 + - - -
255A TYR* 2.9 45.9 + - - +
286A LEU* 3.4 31.1 - - + +
347A SER* 5.3 0.2 - - - +
601A SLU 3.6 35.9 - - + -
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Residues in contact with THR 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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42A PHE* 3.7 27.8 - - + -
89A PHE* 3.4 31.0 - - + -
239A SER* 4.8 3.6 + - - -
243A PHE* 3.4 18.8 - - + -
248A GLY* 2.7 23.4 + - - -
251A THR* 1.3 78.2 + - - +
253A LEU* 1.3 65.5 + - - +
255A TYR* 3.1 12.8 + - - +
256A LEU* 3.0 22.8 + - + +
262A VAL* 4.5 10.3 - - + +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.7 19.0 - - + +
89A PHE* 3.6 28.3 - - + -
92A VAL* 4.4 6.5 - - + -
93A LEU* 4.2 11.7 - - + -
96A LEU* 4.4 14.4 - - + -
194A LEU* 4.7 3.4 - - + -
215A ALA* 5.2 2.2 - - + -
219A PHE* 3.9 23.6 - - + -
249A MET* 3.1 36.5 + - - +
250A PHE* 4.2 23.1 - - + +
252A THR* 1.3 76.3 - - - +
254A GLY* 1.3 61.0 + - - +
256A LEU* 3.3 7.9 + - + +
257A ILE* 3.0 26.7 + - - +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A ARG* 5.4 0.4 - - - -
219A PHE* 4.3 6.6 - - - -
222A ALA* 3.7 24.7 - - - -
250A PHE 3.4 9.1 + - - -
251A THR 3.1 8.1 + - - -
253A LEU* 1.3 79.0 - - - +
255A TYR* 1.3 57.0 + - - +
257A ILE* 3.2 7.7 + - - +
258A CYS* 2.9 35.1 + - - -
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A TYR* 4.3 0.7 - - - -
218A ARG* 5.5 4.7 - - - -
222A ALA* 6.3 0.9 - - + -
229A ASN* 3.8 21.4 + - - -
237A ILE* 3.7 36.2 - - + +
239A SER* 4.9 5.2 - - - -
251A THR* 2.9 41.4 + - - +
252A THR* 3.1 12.5 + - - +
254A GLY* 1.3 75.9 - - - +
256A LEU* 1.3 61.8 + - - +
258A CYS* 3.2 2.9 + - - +
259A GLY 3.1 3.3 + - - -
260A PHE* 2.9 54.2 + + + -
262A VAL* 3.7 27.8 - - + -
284A THR* 4.5 5.5 - - - +
286A LEU* 3.7 30.9 - - + +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 4.5 3.1 - - + -
30A MET* 4.2 20.3 - - + +
33A TYR* 3.3 12.0 - - - -
41A ALA* 4.1 9.9 - - + +
42A PHE* 3.7 39.3 - - + -
53A TYR* 3.5 31.7 + - + +
89A PHE* 4.6 10.3 - - + -
93A LEU* 4.1 30.7 - - + -
252A THR* 3.0 18.2 + - + +
253A LEU* 3.7 11.9 - - - +
254A GLY 3.2 0.2 - - - -
255A TYR* 1.3 74.0 - - - +
257A ILE* 1.3 64.7 + - - +
259A GLY 3.0 10.2 + - - -
262A VAL* 5.0 2.7 - - + -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLN* 3.4 36.8 - - + +
26A LEU* 3.5 22.0 - - + +
29A ALA* 3.7 14.3 - - + +
32A ARG* 4.9 0.3 + - - -
33A TYR* 2.7 26.2 + - - -
219A PHE* 3.8 29.2 - - + +
222A ALA* 5.5 0.2 - - + -
223A ARG* 3.3 46.7 + - + +
231A ILE* 4.2 3.3 - - - +
253A LEU 3.0 10.7 + - - +
254A GLY* 3.4 10.8 - - - +
256A LEU* 1.3 76.2 - - - +
258A CYS* 1.3 50.9 + - - +
259A GLY 3.3 0.2 - - - -
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Residues in contact with CYS 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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33A TYR* 3.3 12.4 + - - -
222A ALA* 3.8 23.3 - - - -
223A ARG* 3.8 18.4 - - - -
229A ASN* 3.8 11.9 - - - -
231A ILE* 3.6 25.4 - - + +
232A ILE 5.3 0.9 - - - +
254A GLY 2.9 17.8 + - - +
255A TYR* 3.5 9.4 - - - +
256A LEU 3.1 0.8 - - - -
257A ILE* 1.3 75.5 - - - +
259A GLY* 1.3 60.3 + - - +
260A PHE* 3.3 32.5 + - + -
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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