Contacts of the helix formed by residues 262 - 279 (chain r) in PDB entry 6QXT
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 LEU 262 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248r ILE 4.6 15.0 - - - +
249r PHE* 5.3 7.6 + - - +
251r GLU 4.6 6.3 + - - +
253r TYR* 5.2 9.0 - - + +
260r MET 4.1 0.2 + - - -
261r TYR* 1.3 74.5 - - - +
263r SER* 1.3 58.2 + - - +
265r ILE* 3.4 6.3 + - - +
266r VAL* 2.9 32.1 + - - +
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Residues in contact with SER 263 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187r MET* 6.4 1.6 - - - -
261r TYR* 3.2 5.5 - - - +
262r LEU* 1.3 80.1 - - - +
264r ASN* 1.3 57.7 + - - +
266r VAL* 3.5 4.4 + - - +
267r SER* 2.9 28.9 + - - -
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Residues in contact with ASN 264 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260r MET* 4.7 12.1 - - + -
261r TYR* 3.4 14.6 + - + +
263r SER* 1.3 79.7 - - - +
265r ILE* 1.3 58.0 + - - +
267r SER* 3.3 6.6 + - - -
268r ASP* 2.9 30.5 + - - +
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Residues in contact with ILE 265 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253r TYR* 6.3 2.9 - - + -
255r TYR* 4.8 19.3 - - + -
260r MET* 4.9 4.7 - - + +
261r TYR 3.1 17.3 + - - +
262r LEU* 3.8 7.9 - - - +
264r ASN* 1.3 76.7 - - - +
266r VAL* 1.3 57.4 + - - +
268r ASP* 3.4 4.8 + - - +
269r TYR* 2.9 31.1 + - - +
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Residues in contact with VAL 266 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187r MET* 5.4 12.6 - - + +
188r PHE* 5.5 8.5 - - + -
191r GLU* 4.4 8.7 - - + +
262r LEU 2.9 20.0 + - - +
263r SER* 4.0 4.5 - - - +
265r ILE* 1.3 76.1 - - - +
267r SER* 1.3 56.7 + - - +
269r TYR* 3.9 4.8 - - - +
270r THR* 2.9 31.9 + - - -
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Residues in contact with SER 267 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191r GLU* 4.8 8.3 - - - +
263r SER 2.9 19.2 + - - -
264r ASN* 3.5 8.1 - - - -
266r VAL* 1.3 77.2 - - - +
268r ASP* 1.3 57.7 + - - +
270r THR* 3.4 5.2 + - - -
271r LYS* 2.9 31.1 + - - +
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Residues in contact with ASP 268 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264r ASN 2.9 16.3 + - - +
265r ILE* 3.9 4.7 - - - +
267r SER* 1.3 75.8 - - - +
269r TYR* 1.3 58.7 + - - +
271r LYS* 3.4 5.6 + - - +
272r LYS* 2.9 31.6 + - - +
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Residues in contact with TYR 269 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265r ILE 2.9 17.7 + - - +
266r VAL* 3.9 6.7 - - - +
268r ASP* 1.3 77.6 - - - +
270r THR* 1.3 57.6 + - - +
272r LYS* 3.4 2.4 + - - +
273r VAL* 2.9 29.0 + - - +
285r PRO* 4.3 21.4 - - + +
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Residues in contact with THR 270 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188r PHE* 5.6 0.9 - - - -
191r GLU* 3.9 27.8 - - - -
192r VAL* 5.1 2.2 - - - -
195r CYS* 6.0 2.5 - - - -
218r ILE* 6.2 4.7 - - - -
266r VAL 2.9 19.8 + - - -
267r SER 3.8 3.1 - - - -
269r TYR* 1.3 76.6 - - - +
271r LYS* 1.3 57.8 + - - +
273r VAL* 3.2 7.2 + - - +
274r ILE* 2.9 30.3 + - - +
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Residues in contact with LYS 271 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195r CYS* 6.1 2.5 - - - -
267r SER 2.9 17.2 + - - +
268r ASP* 3.8 7.0 - - - +
270r THR* 1.3 76.7 - - - +
272r LYS* 1.3 57.7 + - - +
274r ILE* 3.4 4.4 + - - +
275r LYS* 2.9 33.2 + - - +
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Residues in contact with LYS 272 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268r ASP 2.9 17.0 + - - +
269r TYR 3.8 4.3 - - - +
271r LYS* 1.3 75.8 - - - +
273r VAL* 1.3 57.8 + - - +
275r LYS* 4.7 3.6 - - - -
276r ALA* 2.9 32.7 + - - +
283r GLU 4.2 4.3 - - - +
285r PRO* 3.8 24.0 - - + -
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Residues in contact with VAL 273 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218r ILE* 5.9 7.0 - - + -
269r TYR 2.9 18.3 + - - +
270r THR* 3.2 8.0 + - - +
272r LYS* 1.3 77.1 - - - +
274r ILE* 1.3 56.1 + - - +
276r ALA* 3.4 5.2 + - - +
277r LEU* 2.9 29.3 + - - +
285r PRO* 5.1 3.1 - - + +
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Residues in contact with ILE 274 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195r CYS* 4.5 20.6 - - + -
197r CYS* 5.9 4.9 - - + -
270r THR 2.9 15.9 + - - +
271r LYS* 4.0 4.3 - - - +
273r VAL* 1.3 78.1 - - - +
275r LYS* 1.3 57.9 + - - +
277r LEU* 3.1 7.4 + - - +
278r ASN* 2.9 30.5 + - - +
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Residues in contact with LYS 275 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271r LYS 2.9 19.0 + - - +
272r LYS* 4.2 4.0 - - - +
274r ILE* 1.3 77.3 - - - +
276r ALA* 1.3 57.1 + - - +
278r ASN* 3.5 5.6 + - - +
279r GLN* 3.0 32.2 + - - +
282r GLU* 6.2 0.2 - - - -
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Residues in contact with ALA 276 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272r LYS 2.9 21.2 + - - +
273r VAL* 3.7 5.4 - - - +
275r LYS* 1.3 78.8 - - - +
277r LEU* 1.3 55.4 + - - +
279r GLN* 4.8 0.9 - - - -
280r LEU 2.9 8.1 + - - -
281r GLY* 2.6 32.6 + - - +
282r GLU* 4.4 12.3 - - - +
283r GLU 3.2 25.6 - - - +
284r ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 277 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93r ARG 5.7 1.1 - - - +
97r TRP* 5.3 18.1 - - + +
98r LYS 5.9 0.2 + - - -
101r VAL* 5.1 11.4 - - + +
273r VAL 2.9 18.0 + - - +
274r ILE* 3.1 7.6 + - - +
276r ALA* 1.3 76.2 - - - +
278r ASN* 1.3 62.0 + - - +
280r LEU* 3.5 9.8 + - - +
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Residues in contact with ASN 278 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93r ARG* 4.6 23.7 - - + +
274r ILE 2.9 15.2 + - - +
275r LYS* 4.1 5.4 - - - +
277r LEU* 1.3 77.7 - - - +
279r GLN* 1.3 59.4 + - - +
280r LEU* 3.3 2.0 + - - +
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Residues in contact with GLN 279 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275r LYS 3.0 18.9 + - - +
276r ALA 4.4 1.1 - - - +
278r ASN* 1.3 75.0 - - - +
280r LEU* 1.3 72.0 + - - +
281r GLY 3.6 0.2 - - - -
282r GLU* 4.5 18.8 + - + +
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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