Contacts of the helix formed by residues 255 - 266 (chain Q) in PDB entry 3K9Q
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 255 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253Q ASP 4.0 8.1 - - - +
254Q VAL* 1.3 78.6 - - - +
256Q VAL* 1.3 66.7 + - - +
257Q GLU* 3.3 18.8 + - - +
258Q GLN* 3.0 47.1 + - - +
259Q VAL* 3.2 15.2 + - - +
299Q VAL* 3.9 6.5 - - - -
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Residues in contact with VAL 256 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Q THR* 1.3 73.9 - - - +
257Q GLU* 1.3 71.5 + - + +
259Q VAL* 3.2 2.6 + - - +
260Q ASN* 2.9 48.6 + - - +
294Q ALA 5.1 0.9 - - - +
297Q THR* 3.7 35.8 - - + +
298Q ARG* 4.2 1.3 - - - -
299Q VAL* 3.7 27.9 - - + +
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Residues in contact with GLU 257 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Q THR* 3.3 21.7 + - - +
256Q VAL* 1.3 88.8 + - + +
258Q GLN* 1.3 59.1 + - + +
260Q ASN* 3.8 5.9 - - - +
261Q GLU* 2.9 34.9 + - + +
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Residues in contact with GLN 258 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Q PHE* 3.7 18.0 - - + -
251Q LYS* 5.3 4.6 - - - +
252Q GLN 5.4 0.2 - - - +
253Q ASP 3.8 6.8 + - - +
254Q VAL* 3.3 13.9 - - - +
255Q THR* 3.0 39.3 + - - +
257Q GLU* 1.3 73.8 - - + +
259Q VAL* 1.3 65.5 + - - +
261Q GLU* 4.1 4.1 - - - +
262Q ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 259 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163Q LEU* 4.6 7.4 - - + -
167Q PHE* 3.9 16.2 - - + -
249Q LEU* 5.3 0.4 - - + -
254Q VAL* 3.6 22.4 - - + -
255Q THR 3.2 13.3 + - - +
256Q VAL 3.6 6.5 - - - +
258Q GLN* 1.3 76.3 - - - +
260Q ASN* 1.3 64.7 + - - +
262Q ALA* 3.2 4.0 + - - +
263Q MET* 3.1 31.0 + - + +
292Q PHE* 4.5 6.3 - - + -
297Q THR* 4.0 9.9 - - + -
299Q VAL* 5.1 0.4 - - + -
308Q VAL* 4.0 15.7 - - + -
310Q VAL* 3.7 30.5 - - + -
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Residues in contact with ASN 260 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256Q VAL* 2.9 37.1 + - - +
257Q GLU* 3.9 5.7 - - - +
259Q VAL* 1.3 76.1 - - - +
261Q GLU* 1.3 56.7 + - - +
263Q MET* 3.2 2.4 + - - +
264Q LYS* 3.0 23.9 + - - +
273Q TYR* 3.3 27.5 - - - +
275Q GLU* 5.8 0.4 + - - -
292Q PHE* 3.3 14.3 - - - -
294Q ALA* 3.3 29.1 + - + +
297Q THR* 2.7 24.1 + - - -
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Residues in contact with GLU 261 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257Q GLU* 2.9 22.4 + - + +
258Q GLN* 4.2 4.3 - - - +
260Q ASN* 1.3 72.5 - - - +
262Q ALA* 1.3 58.3 + - - +
264Q LYS* 3.2 26.6 + - + +
265Q ASN* 2.8 53.5 + - - +
273Q TYR* 5.4 0.2 - - - -
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Residues in contact with ALA 262 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162Q VAL* 3.7 20.8 - - + +
166Q ASP* 3.4 25.8 - - - +
167Q PHE* 4.0 11.4 - - + -
258Q GLN 3.1 18.9 + - - +
259Q VAL 3.6 4.0 - - - +
261Q GLU* 1.3 76.5 - - - +
263Q MET* 1.3 61.5 + - - +
265Q ASN* 3.6 10.5 + - - +
266Q ALA* 3.4 17.5 + - - +
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Residues in contact with MET 263 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159Q VAL* 3.5 33.7 - - + +
162Q VAL* 3.6 25.4 - - + -
163Q LEU* 3.8 22.4 - - + -
167Q PHE* 5.9 0.4 - - + -
259Q VAL* 3.1 18.4 + - + +
260Q ASN 3.5 7.0 - - - +
261Q GLU 3.2 0.2 - - - -
262Q ALA* 1.3 73.8 - - - +
264Q LYS* 1.3 65.3 + - - +
266Q ALA* 3.1 14.0 + - - +
267Q SER* 3.5 8.5 + - - -
271Q PHE* 3.7 29.4 - - + -
273Q TYR* 4.3 2.6 - - + +
292Q PHE* 3.5 45.3 - - + -
310Q VAL* 4.9 0.7 - - + -
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Residues in contact with LYS 264 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260Q ASN 3.0 10.1 + - - +
261Q GLU* 3.2 25.1 + - + +
263Q MET* 1.3 76.0 - - - +
265Q ASN* 1.3 66.5 + - - +
267Q SER* 3.0 23.9 + - - +
273Q TYR* 3.6 52.7 - - + +
275Q GLU* 5.6 1.3 - - - +
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Residues in contact with ASN 265 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261Q GLU* 2.8 44.6 + - - +
262Q ALA* 3.8 9.1 - - - +
263Q MET 3.3 0.2 - - - -
264Q LYS* 1.3 79.5 - - - +
266Q ALA* 1.3 57.7 + - - +
267Q SER 3.6 2.8 + - - +
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Residues in contact with ALA 266 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162Q VAL* 3.4 32.3 - - + -
262Q ALA 3.4 3.6 + - - +
263Q MET 3.1 10.6 + - - +
265Q ASN* 1.3 76.7 - - - +
267Q SER* 1.3 64.0 + - - +
268Q ASN* 3.6 13.9 + - - -
271Q PHE* 3.8 14.5 - - + -
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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