Contacts of the helix formed by residues 259 - 273 (chain C) in PDB entry 4IYM
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 ASP 259 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C ASP 3.9 0.2 + - - -
258C ALA* 1.3 70.3 - - - +
260C LEU* 1.3 58.5 + - - +
261C ASP* 3.3 13.9 + - - +
262C GLN* 3.0 53.9 + - + +
263C ALA* 2.9 26.9 + - - +
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Residues in contact with LEU 260 (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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254C ILE* 3.7 28.7 - - + -
255C MSE 4.9 1.3 - - - +
256C PRO 5.7 2.0 - - - +
258C ALA* 3.1 12.8 + - + +
259C ASP* 1.3 72.6 + - - +
261C ASP* 1.3 57.4 + - - +
263C ALA* 3.4 3.3 + - - +
264C ALA* 2.9 31.0 + - - +
292C THR* 3.8 21.8 - - + +
295C ARG* 3.7 46.0 - - + +
296C LEU* 4.1 17.9 - - + +
299C LYS* 3.9 18.5 - - - -
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Residues in contact with ASP 261 (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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259C ASP* 3.3 8.5 + - - +
260C LEU* 1.3 74.2 + - - +
262C GLN* 1.3 64.6 + - + +
264C ALA* 3.4 4.6 + - - +
265C ASN* 3.0 35.7 + - - +
295C ARG* 5.5 2.5 + - - -
299C LYS* 2.6 36.1 + - - +
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Residues in contact with GLN 262 (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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259C ASP* 3.0 40.1 + - + +
261C ASP* 1.3 76.9 - - + +
263C ALA* 1.3 56.7 + - - +
265C ASN* 3.8 5.5 - - - +
266C ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 263 (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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252C MSE 4.2 7.7 - - - +
254C ILE* 4.3 30.5 - - + -
258C ALA* 5.2 2.5 - - + -
259C ASP 2.9 13.4 + - - +
260C LEU* 3.6 11.4 - - - +
261C ASP 3.3 0.2 - - - -
262C GLN* 1.3 74.7 - - - +
264C ALA* 1.3 59.9 + - - +
266C ALA* 3.1 7.8 + - - +
267C LEU* 2.9 34.4 + - - +
296C LEU* 4.6 4.5 - - + -
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Residues in contact with ALA 264 (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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260C LEU 2.9 19.5 + - - +
261C ASP* 3.4 4.0 + - - +
263C ALA* 1.3 70.9 - - - +
265C ASN* 1.3 64.2 + - - +
267C LEU* 3.2 5.1 + - - +
268C ILE* 3.2 26.5 + - - +
296C LEU* 3.9 10.0 - - + +
299C LYS* 3.8 30.3 - - + -
300C LEU* 3.6 14.7 - - + +
303C MSE 3.9 12.1 - - + -
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Residues in contact with ASN 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 ASP* 3.0 25.7 + - - +
262C GLN* 3.9 6.8 - - - +
264C ALA* 1.3 74.1 - - - +
266C ALA* 1.3 62.9 + - - +
268C ILE* 3.4 6.7 + - - +
269C GLY* 3.4 16.6 + - - -
303C MSE 3.2 28.4 - - - +
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Residues in contact with ALA 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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252C MSE 4.0 16.4 - - + -
262C GLN 2.9 19.7 + - - +
263C ALA* 3.1 7.6 + - - +
265C ASN* 1.3 76.8 - - - +
267C LEU* 1.3 57.2 + - - +
269C GLY* 3.4 2.0 + - - -
270C ALA* 2.8 33.6 + - + +
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Residues in contact with LEU 267 (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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252C MSE 3.7 23.3 - - + -
254C ILE* 4.4 0.7 - - + -
263C ALA 2.9 16.0 + - - +
264C ALA 3.2 8.0 + - - +
266C ALA* 1.3 73.1 - - - +
268C ILE* 1.3 59.8 + - - +
270C ALA* 4.5 1.3 - - - +
271C GLY* 2.7 33.2 + - - +
272C TYR* 4.2 3.9 - - - -
282C ILE* 3.6 31.4 - - + -
285C ALA* 3.9 20.9 - - + +
296C LEU* 3.8 33.4 - - + -
300C LEU* 3.9 20.6 - - + -
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Residues in contact with ILE 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 ALA 3.2 13.8 + - - +
265C ASN* 3.7 7.9 - - - +
266C ALA 3.3 0.4 - - - -
267C LEU* 1.3 74.6 - - - +
269C GLY* 1.3 63.4 + - - +
272C TYR* 3.1 34.3 + - + +
273C GLY 4.0 0.3 + - - -
300C LEU* 3.8 16.2 - - + +
303C MSE 3.7 43.5 - - + +
304C VAL* 3.8 26.7 - - + +
307C LEU* 4.0 25.5 - - + +
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Residues in contact with GLY 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 ASN 3.4 10.3 + - - -
266C ALA 3.8 2.0 - - - -
268C ILE* 1.3 79.5 - - - +
270C ALA* 1.3 56.8 + - - +
273C GLY* 2.9 30.5 + - - -
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Residues in contact with ALA 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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252C MSE 5.2 2.5 - - + -
266C ALA 2.8 22.4 + - - +
267C LEU* 4.4 0.9 - - - +
269C GLY* 1.3 73.9 - - - +
271C GLY* 1.3 60.8 + - - +
273C GLY 4.6 2.0 + - - +
278C ARG* 5.9 0.9 - - - -
280C MSE 5.3 2.9 - - - +
281C ALA* 3.4 14.1 - - - +
282C ILE* 3.1 43.2 + - + +
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Residues in contact with GLY 271 (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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267C LEU* 2.7 24.0 + - - -
270C ALA* 1.3 76.1 - - - +
272C TYR* 1.3 73.2 + - - +
273C GLY 3.8 0.2 - - - -
276C GLY* 3.7 18.1 + - - -
281C ALA* 4.9 0.5 - - - +
282C ILE* 3.4 20.1 - - - +
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Residues in contact with TYR 272 (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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267C LEU 4.5 4.7 - - - -
268C ILE* 3.1 29.9 + - + +
271C GLY* 1.3 86.3 - - - +
273C GLY* 1.3 63.6 + - - +
275C ALA* 2.9 22.9 + - - -
276C GLY 3.9 3.4 - - - +
304C VAL* 3.7 42.6 - - + +
307C LEU* 3.9 32.3 - - + -
318C ASP 4.8 1.0 - - - +
319C MSE 3.4 22.4 - - - +
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Residues in contact with GLY 273 (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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95C ASP* 5.5 2.0 - - - -
268C ILE 4.0 0.6 + - - -
269C GLY* 2.9 22.4 + - - -
270C ALA 4.6 2.5 - - - +
271C GLY 5.0 0.3 - - - -
272C TYR* 1.3 75.0 - - - +
274C SER* 1.3 70.2 + - - -
276C GLY* 3.0 13.9 + - - -
277C GLU 4.2 0.3 + - - -
278C ARG* 4.3 10.6 - - - +
281C ALA* 5.4 0.2 - - - +
318C ASP 4.9 6.5 - - - -
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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