Contacts of the helix formed by residues 244 - 255 (chain B) in PDB entry 7KAC
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 SER 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B GLU* 2.6 35.2 + - - -
243B TRP* 1.3 74.0 - - - +
245B ALA* 1.3 62.8 + - - +
246B ALA* 3.4 15.9 + - - +
247B PHE* 3.3 4.3 + - - +
248B HIS* 3.1 25.6 + - - -
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B SER* 1.3 71.6 - - - +
246B ALA* 1.4 59.2 + - - +
248B HIS* 3.6 9.5 + - - +
249B ASN* 3.0 28.9 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 5.0 0.2 - - - +
244B SER* 3.2 10.6 + - - +
245B ALA* 1.4 77.3 - - - +
247B PHE* 1.4 57.3 + - - +
249B ASN* 3.3 2.8 + - - -
250B PHE* 2.9 24.1 + - - +
271B HIS* 3.2 14.8 - - + -
272B GLN* 4.6 12.1 - - + -
273B LEU* 4.1 26.9 - - + +
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Residues in contact with PHE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B GLU* 3.7 26.0 - - + +
114B ILE* 4.0 20.0 - - + -
205B ALA* 3.9 28.9 - - + -
209B ALA* 4.2 3.6 - - + -
237B LEU* 3.7 19.5 - - + -
243B TRP* 3.5 50.3 - + + -
244B SER* 3.3 8.9 + - - +
246B ALA* 1.4 75.7 - - - +
248B HIS* 1.3 64.0 + - - +
250B PHE* 3.2 2.7 + + + +
251B ILE* 3.1 43.1 + - + +
273B LEU* 3.7 24.3 - - + +
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Residues in contact with HIS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ARG* 6.0 1.0 - - - +
237B LEU* 3.7 36.1 + - + +
239B GLU 3.9 5.8 - - - -
240B LYS* 2.8 44.8 + - + +
243B TRP* 3.5 12.6 + - + +
244B SER 3.1 26.6 + - - -
245B ALA* 3.9 8.7 - - - +
247B PHE* 1.3 74.0 - - - +
249B ASN* 1.3 58.2 + - - +
251B ILE* 3.5 4.6 + - - +
252B LYS* 3.0 27.3 + - - +
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ALA 3.0 18.9 + - - +
246B ALA* 3.8 4.9 - - - +
248B HIS* 1.3 74.8 - - - +
250B PHE* 1.3 58.8 + - - +
252B LYS* 4.1 8.7 - - - +
253B VAL* 2.9 43.1 + - - +
271B HIS* 3.0 24.8 + - + +
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B CYS* 3.8 33.4 - - + -
122B LEU* 4.2 4.7 - - + -
201B LEU* 4.0 16.6 - - + -
202B GLY* 4.9 1.1 - - - -
205B ALA* 4.5 8.3 - - + -
246B ALA 2.9 16.5 + - - +
247B PHE* 3.2 6.0 + + - +
249B ASN* 1.3 74.0 - - - +
251B ILE* 1.3 69.5 + - + +
253B VAL* 3.4 2.9 - - - +
254B THR* 2.9 55.8 + - + +
268B MET* 3.5 25.4 - - + -
271B HIS* 3.5 17.0 + - + -
273B LEU* 3.6 23.8 - - + -
274B VAL* 3.5 25.4 - - + -
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLY 3.8 11.0 - - - +
205B ALA* 3.6 20.6 - - + -
206B ILE* 3.9 18.4 - - + -
235B PRO 4.1 8.7 - - - +
236B ARG* 4.5 8.7 - - + -
237B LEU* 4.0 17.3 - - + +
247B PHE* 3.1 41.1 + - + +
248B HIS* 3.7 8.1 - - - +
250B PHE* 1.3 79.4 - - + +
252B LYS* 1.3 62.5 + - - +
254B THR* 3.1 4.6 + - - -
255B LEU* 2.9 50.2 + - + +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B PRO 6.0 1.1 - - - -
248B HIS 3.0 18.5 + - - +
249B ASN* 3.3 15.5 + - - +
251B ILE* 1.3 77.8 - - - +
253B VAL* 1.3 60.9 + - + +
255B LEU* 3.6 18.2 - - - +
256B THR* 3.7 4.3 + - - -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ASN* 2.9 42.4 + - - +
250B PHE* 3.4 8.3 - - - +
252B LYS* 1.3 75.8 - - + +
254B THR* 1.4 67.0 + - - +
256B THR* 2.7 24.0 + - - -
263B PRO* 3.5 23.2 - - + +
268B MET* 3.7 27.6 - - + -
271B HIS* 4.2 7.9 - - + -
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE* 3.7 28.7 - - + +
199B TRP* 3.5 10.2 + - - -
201B LEU* 5.1 3.1 - - + -
202B GLY* 3.3 20.3 - - - +
250B PHE* 2.9 50.5 + - + +
251B ILE* 3.1 10.4 + - - -
253B VAL* 1.4 74.6 - - - +
255B LEU* 1.4 58.5 + - - +
256B THR 3.4 4.0 + - - -
262B ARG* 3.5 21.1 - - - -
268B MET* 3.8 18.8 - - + -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TRP* 3.3 56.3 - - + +
202B GLY* 4.0 3.8 - - - -
203B ILE* 3.7 13.2 - - + +
206B ILE* 3.9 14.6 - - + -
234B PRO* 3.2 29.2 - - + +
235B PRO* 3.5 33.4 - - + +
251B ILE* 2.9 34.5 + - + +
252B LYS* 3.6 7.8 - - - +
253B VAL 3.2 0.2 - - - -
254B THR* 1.4 79.3 - - - +
256B THR* 1.3 60.9 + - - -
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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