Contacts of the helix formed by residues 255 - 266 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253P ASP 3.9 9.6 - - - +
254P VAL* 1.3 78.4 - - - +
256P VAL* 1.3 65.6 + - - +
257P GLU* 3.4 18.8 + - - +
258P GLN* 3.2 37.6 + - - +
259P VAL* 3.2 23.2 + - - +
299P VAL* 3.9 7.0 - - - -
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Residues in contact with VAL 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P THR* 1.3 70.6 - - - +
257P GLU* 1.3 79.5 + - - +
259P VAL* 3.1 6.2 + - - +
260P ASN* 2.9 41.4 + - - +
294P ALA 5.1 1.6 - - - +
297P THR* 3.9 34.2 - - + +
298P ARG* 4.2 1.3 - - - -
299P VAL* 3.7 26.6 - - + +
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Residues in contact with GLU 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P THR* 3.4 21.3 + - - +
256P VAL* 1.3 87.7 + - + +
258P GLN* 1.3 63.0 - - + +
260P ASN* 3.4 6.1 + - - +
261P GLU* 3.0 32.7 + - + +
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Residues in contact with GLN 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167P PHE* 3.7 19.6 - - + -
251P LYS* 5.9 1.8 - - - +
253P ASP 3.8 7.0 + - - +
254P VAL* 3.3 14.4 - - - +
255P THR* 3.2 39.8 + - - +
257P GLU* 1.3 76.5 - - + +
259P VAL* 1.3 63.9 - - - +
261P GLU* 3.9 4.9 - - - +
262P ALA* 3.1 24.8 + - - +
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Residues in contact with VAL 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163P LEU* 4.8 4.9 - - + -
167P PHE* 4.0 16.2 - - + -
249P LEU* 5.3 0.2 - - + -
254P VAL* 3.7 20.2 - - + -
255P THR 3.2 12.3 + - - +
256P VAL 3.1 8.4 + - - +
258P GLN* 1.3 77.1 - - - +
260P ASN* 1.3 63.7 + - - +
262P ALA* 3.3 3.5 + - - +
263P MET* 3.1 36.7 + - + +
292P PHE* 4.4 6.1 - - + -
297P THR* 3.9 10.8 - - + -
299P VAL* 5.1 0.4 - - + -
308P VAL* 3.9 18.8 - - + -
310P VAL* 3.6 30.7 - - + -
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Residues in contact with ASN 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P VAL* 2.9 35.4 + - - +
257P GLU* 3.4 6.5 + - - +
259P VAL* 1.3 76.7 - - - +
261P GLU* 1.3 56.6 + - + +
263P MET* 3.2 1.7 + - - +
264P LYS 2.9 23.2 + - - -
273P TYR* 3.3 27.4 + - - +
292P PHE* 3.3 13.9 - - - -
294P ALA* 3.4 30.2 + - - +
297P THR* 2.7 23.8 + - - -
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Residues in contact with GLU 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257P GLU* 3.0 23.1 + - + +
258P GLN* 3.9 5.8 - - - +
260P ASN* 1.3 72.9 - - + +
262P ALA* 1.3 68.5 + - - +
264P LYS* 3.1 18.3 + - + +
265P ASN* 2.9 42.4 + - - +
273P TYR* 5.4 0.4 - - - -
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Residues in contact with ALA 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P VAL* 3.7 18.9 - - + +
166P ASP* 3.3 25.5 - - - +
167P PHE* 4.1 11.2 - - + -
258P GLN 3.1 16.0 + - - +
259P VAL 3.7 3.8 - - - +
260P ASN 3.3 0.2 - - - -
261P GLU* 1.3 79.9 - - - +
263P MET* 1.3 61.8 + - - +
265P ASN* 3.5 10.0 + - - +
266P ALA* 3.3 21.1 + - - +
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Residues in contact with MET 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P VAL* 3.4 33.9 - - + +
162P VAL* 3.6 24.2 - - + -
163P LEU* 3.7 22.7 - - + -
167P PHE* 5.9 0.4 - - + -
259P VAL* 3.1 18.7 + - + +
260P ASN 3.5 6.3 - - - +
262P ALA* 1.3 74.3 - - - +
264P LYS* 1.3 66.3 + - - +
266P ALA* 3.2 11.0 + - - -
267P SER* 3.4 9.4 + - - -
271P PHE* 3.7 30.0 - - + -
273P TYR* 4.2 4.2 - - + +
292P PHE* 3.5 47.5 - - + +
310P VAL* 4.9 0.7 - - + -
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Residues in contact with LYS 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260P ASN 2.9 13.4 + - - +
261P GLU* 3.6 20.0 + - - +
263P MET* 1.3 76.2 - - - +
265P ASN* 1.3 66.5 + - - +
267P SER* 2.9 26.1 + - - +
273P TYR* 3.6 46.1 - - + +
275P GLU* 5.7 0.7 - - - +
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Residues in contact with ASN 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261P GLU* 2.9 37.3 + - - +
262P ALA* 3.8 8.7 - - - +
264P LYS* 1.3 80.9 - - - +
266P ALA* 1.3 59.3 + - - +
267P SER 3.3 3.7 + - - +
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Residues in contact with ALA 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P VAL* 3.4 33.2 - - + -
262P ALA 3.3 5.4 + - - +
263P MET 3.2 9.2 + - - +
264P LYS 3.1 1.0 - - - -
265P ASN* 1.3 74.2 - - - +
267P SER* 1.3 65.8 + - - +
268P ASN* 3.5 13.9 + - - -
271P PHE* 3.8 14.7 - - + +
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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