Contacts of the helix formed by residues 261 - 275 (chain C) in PDB entry 5UQ9
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 LYS 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C TYR* 3.2 5.9 + - - -
258C ALA 5.0 6.0 + - - +
259C GLY* 5.4 4.7 - - - -
260C GLN* 1.3 75.7 + - - +
262C GLY* 1.3 69.3 + - - +
264C GLY* 3.2 13.0 + - - -
265C LYS* 3.7 37.0 + - - +
285C VAL* 5.9 0.3 - - - +
288C ARG* 5.0 3.2 + - + +
289C CYS* 4.1 28.1 - - - +
292C SER* 3.9 23.8 + - - -
275D GLY* 4.6 10.5 + - - -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C GLN* 3.2 22.7 + - - -
261C LYS* 1.3 82.6 - - - +
263C THR* 1.3 60.1 + - - -
265C LYS* 3.4 7.4 - - - +
266C TRP* 3.0 26.8 + - - -
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Residues in contact with THR 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 4.3 12.8 + - - +
184C LYS* 5.6 0.2 - - + -
185C MET* 3.9 27.5 - - + +
188C ASN* 3.3 41.2 + - + +
192C TYR* 4.6 2.4 + - - -
260C GLN* 4.8 6.7 + - - +
262C GLY* 1.3 71.3 - - - -
264C GLY* 1.3 63.8 + - - +
265C LYS 3.4 0.4 - - - -
266C TRP* 3.6 9.8 + - + +
267C THR* 3.2 21.3 + - - -
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Residues in contact with GLY 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ASN 5.0 1.6 - - - -
189C GLY* 5.1 1.3 - - - -
192C TYR* 3.5 41.3 + - - -
261C LYS 3.2 5.4 + - - -
263C THR* 1.3 80.3 - - - +
265C LYS* 1.3 62.8 + - - +
267C THR* 3.4 12.0 + - - -
268C ALA 3.7 4.3 + - - -
281C ILE* 4.7 1.2 - - - +
285C VAL* 3.2 18.9 - - - +
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C LYS* 3.7 35.2 + - - +
262C GLY 3.4 15.3 - - - +
264C GLY* 1.3 75.7 - - - +
266C TRP* 1.3 89.2 + - + +
268C ALA* 3.1 5.0 + - - +
269C ILE* 2.8 40.5 + - + +
285C VAL* 3.9 21.9 - - + +
289C CYS* 5.5 1.8 - - - -
272D LEU* 2.2 41.6 + - + +
273D GLU* 4.2 11.5 + - - -
275D GLY* 4.5 8.3 - - - +
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Residues in contact with TRP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLU* 4.8 18.8 + - + -
107C ARG* 6.1 4.0 - - - -
185C MET* 3.7 20.4 - - + +
262C GLY* 3.0 32.4 + - - -
263C THR* 3.6 9.8 + - + +
264C GLY 3.3 1.0 - - - -
265C LYS* 1.3 93.3 - - + +
267C THR* 1.3 57.5 + - - +
269C ILE* 3.6 33.4 - - + +
270C SER* 3.0 28.6 + - - -
273D GLU* 5.0 11.7 - - + -
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Residues in contact with THR 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C MET* 2.8 30.1 + - - +
186C VAL* 4.1 14.8 - - + -
189C GLY* 3.5 25.3 - - - -
263C THR 3.2 10.8 + - - -
264C GLY 3.4 5.5 + - - -
265C LYS 3.2 0.8 - - - -
266C TRP* 1.3 79.2 - - - +
268C ALA* 1.3 57.6 + - - +
270C SER* 3.6 2.9 + - - -
271C ALA* 3.2 23.9 + - - +
278C VAL* 5.4 1.9 - - + +
281C ILE* 4.3 17.0 - - + -
341C LEU* 3.8 19.6 - - + +
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C GLY 3.7 6.1 + - - +
265C LYS 3.1 5.4 + - - +
267C THR* 1.3 75.2 - - - +
269C ILE* 1.3 65.7 + - - +
271C ALA* 3.2 8.8 + - - +
272C LEU* 3.0 26.3 + - - +
278C VAL* 5.4 2.7 - - - +
281C ILE* 4.9 3.1 - - + +
282C GLY* 3.8 31.2 - - - +
285C VAL* 4.7 2.5 - - + -
272D LEU* 3.6 24.2 - - + -
286D PHE* 4.6 4.5 - - + -
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C LYS* 2.8 26.8 + - + +
266C TRP* 3.6 40.8 - - + +
268C ALA* 1.3 76.1 - - - +
270C SER* 1.3 63.3 + - - +
272C LEU* 3.3 7.1 + - - +
273C GLU* 3.0 39.8 + - - +
269D ILE* 3.9 20.4 - - + +
272D LEU* 3.7 27.8 - - + -
273D GLU* 3.8 25.6 - - + +
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 4.0 5.4 + - - -
107C ARG* 5.9 0.2 - - - -
182C PHE* 3.6 16.8 - - - -
185C MET* 4.1 13.7 - - - -
266C TRP 3.0 19.9 + - - -
267C THR 3.7 4.7 - - - -
268C ALA 3.2 0.2 - - - -
269C ILE* 1.3 78.2 - - - +
271C ALA* 1.3 62.0 + - - +
273C GLU* 3.0 12.6 + - - +
274C TYR* 2.9 51.4 + - - -
341C LEU* 4.0 4.2 - - - +
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C THR 3.2 12.0 + - - +
268C ALA* 3.2 10.5 + - - +
270C SER* 1.3 77.9 - - - +
272C LEU* 1.3 58.0 + - - +
274C TYR* 3.5 0.4 + - - -
275C GLY* 2.8 24.4 + - - -
276C VAL 2.9 30.1 + - - +
278C VAL* 3.6 27.8 - - + -
341C LEU* 3.9 12.5 - - + +
286D PHE* 4.4 5.8 - - + -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ALA 3.0 10.5 + - - +
269C ILE 3.7 2.7 - - - +
270C SER 3.2 0.4 - - - -
271C ALA* 1.3 73.2 - - - +
273C GLU* 1.3 65.8 + - - +
275C GLY* 3.4 10.0 + - - +
286C PHE* 6.2 0.2 - - + -
265D LYS* 3.2 25.8 + - + +
268D ALA* 3.7 25.6 - - + -
269D ILE* 3.6 31.9 - - + +
272D LEU* 3.7 26.0 - - + -
282D GLY* 5.0 2.0 - - - +
285D VAL* 3.7 29.9 - - + +
286D PHE* 3.5 29.4 - - + -
289D CYS* 5.9 0.6 - - - -
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 4.2 1.7 + - - -
107C ARG* 2.8 32.6 + - - -
269C ILE* 3.0 33.9 + - - +
270C SER* 3.0 13.8 + - - +
272C LEU* 1.3 77.1 - - - +
274C TYR* 1.3 69.0 + - + +
260D GLN* 5.3 0.3 - - - +
265D LYS* 3.2 24.3 + - - +
266D TRP* 5.2 11.4 - - + -
269D ILE* 4.0 14.3 - - + +
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Residues in contact with TYR 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 3.5 12.7 + - - -
107C ARG* 5.0 1.8 + - - -
182C PHE* 4.7 4.5 - + - -
270C SER* 2.9 46.2 + - - +
271C ALA 4.4 0.2 - - - +
273C GLU* 1.3 86.3 - - + +
275C GLY* 1.3 62.2 + - - +
276C VAL* 3.4 11.5 + - + +
341C LEU* 4.3 8.1 - - + -
344C GLN* 3.9 28.4 + - + +
345C ALA* 4.4 11.9 - - + -
348C GLU* 3.4 45.3 - - + -
349C PHE* 3.0 33.3 - + - -
260D GLN* 3.5 13.1 + - - +
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Residues in contact with GLY 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C ALA 2.8 9.6 + - - -
272C LEU* 3.4 8.4 + - - -
273C GLU 3.3 3.6 + - - -
274C TYR* 1.3 80.2 - - - +
276C VAL* 1.3 58.1 + - - +
277C PRO* 4.0 1.4 - - - +
260D GLN* 3.3 25.2 + - - +
265D LYS* 5.8 0.4 - - - -
289D CYS* 3.3 34.0 - - - +
293D LEU* 6.2 0.2 - - - +
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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