Contacts of the helix formed by residues 290 - 302 (chain C) in PDB entry 1YA8
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 290 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A GLN* 6.2 0.7 - - - +
64C ARG* 4.3 0.7 - - - -
288C GLN 5.1 2.7 - - - +
289C LYS* 1.3 76.7 - - - +
291C GLU* 1.3 65.6 + - - +
292C GLU* 3.4 13.4 + - - +
293C GLU* 2.9 53.3 + - + +
294C LEU* 3.1 12.5 + - - +
3184C SO4 3.1 17.5 - - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 3.5 20.4 + - - +
64C ARG* 4.4 0.7 - - - +
88C THR* 3.2 31.9 + - + +
112C LEU* 4.0 17.8 - - - +
113C SER* 3.4 2.6 - - - -
114C GLU* 2.7 57.7 + - - +
175C TRP* 3.5 9.9 - - + +
289C LYS 3.9 0.2 + - - -
290C THR* 1.3 70.8 - - - +
292C GLU* 1.3 71.8 + - - +
294C LEU* 3.2 1.6 + - - -
295C LEU* 3.1 20.0 + - + +
3184C SO4 2.8 19.7 + - - +
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Residues in contact with GLU 292 (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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275A LYS* 2.3 44.3 + - - -
290C THR* 3.1 11.4 + - - +
291C GLU* 1.3 89.2 + - - +
293C GLU* 1.3 62.0 + - + +
295C LEU* 3.2 11.4 + - + +
296C GLU* 3.0 29.0 + - + +
3184C SO4 4.4 4.2 + - - -
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Residues in contact with GLU 293 (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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288C GLN 4.7 0.9 - - - +
289C LYS* 3.6 34.0 + - + +
290C THR* 2.9 59.2 + - + +
292C GLU* 1.3 76.1 - - + +
294C LEU* 1.3 59.7 + - - +
296C GLU* 3.1 10.7 + - - +
297C THR* 2.9 31.0 + - - -
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Residues in contact with LEU 294 (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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64C ARG* 3.4 38.6 - - - +
65C PHE* 4.6 8.3 - - + -
174C ILE* 3.8 18.8 - - + +
175C TRP* 3.5 33.4 - - + +
272C ALA* 4.7 6.3 - - + -
286C LEU* 3.6 33.4 - - + +
289C LYS* 3.8 16.4 - - + -
290C THR 3.1 13.4 + - - +
291C GLU 3.7 1.6 - - - +
293C GLU* 1.3 76.7 - - - +
295C LEU* 1.3 50.9 + - - +
297C THR* 3.6 5.6 - - - +
298C THR* 2.7 34.0 + - - -
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Residues in contact with LEU 295 (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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88C THR* 3.7 20.9 - - + -
89C GLN* 3.5 36.1 - - - +
90C ASP* 4.2 7.4 - - - +
91C PRO* 4.4 8.1 - - + -
112C LEU* 4.0 14.8 - - + -
175C TRP* 3.9 4.0 - - + -
291C GLU* 3.1 13.8 + - + +
292C GLU* 3.5 13.5 - - + +
293C GLU 3.1 0.2 - - - -
294C LEU* 1.3 74.3 - - - +
296C GLU* 1.3 61.3 + - + +
298C THR* 2.9 18.0 + - + +
299C LEU* 2.9 36.8 + - + +
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Residues in contact with GLU 296 (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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292C GLU* 3.0 19.5 + - + +
293C GLU* 3.1 11.0 + - - +
295C LEU* 1.3 78.1 - - + +
297C THR* 1.3 60.8 + - - +
299C LEU* 3.0 13.8 + - + +
300C LYS* 2.9 41.4 + - - +
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Residues in contact with THR 297 (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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174C ILE* 4.2 15.3 - - + -
268C ILE* 4.2 8.1 - - + +
271C THR* 3.8 22.2 + - + -
272C ALA* 3.3 36.2 - - + +
293C GLU 2.9 17.3 + - - -
294C LEU* 3.6 12.4 - - - -
296C GLU* 1.3 74.6 - - - +
298C THR* 1.3 61.0 + - - +
300C LYS* 3.3 13.6 + - - +
301C MET* 3.0 31.8 + - + +
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Residues in contact with THR 298 (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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89C GLN* 5.9 1.8 - - - -
90C ASP* 5.6 7.0 - - + +
145C MET* 4.7 8.1 - - + -
173C GLY* 6.2 1.1 - - - -
174C ILE* 3.7 16.1 + - + +
175C TRP* 4.1 10.4 - - + -
294C LEU 2.7 20.8 + - - -
295C LEU* 2.9 26.6 + - + -
297C THR* 1.3 77.6 - - - +
299C LEU* 1.3 62.4 + - + +
301C MET* 3.6 19.2 - - - +
302C LYS* 3.7 4.2 + - - -
303C PHE* 3.9 22.0 + - + -
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Residues in contact with LEU 299 (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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90C ASP* 3.9 38.4 - - + +
91C PRO* 5.3 4.7 - - + -
295C LEU* 2.9 27.1 + - + +
296C GLU* 3.0 15.0 + - + +
298C THR* 1.3 77.5 - - + +
300C LYS* 1.3 67.4 + - + +
301C MET 3.1 0.4 - - - -
302C LYS* 3.2 21.2 + - - +
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Residues in contact with LYS 300 (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 THR* 4.0 35.5 + - + +
296C GLU* 2.9 33.8 + - - +
297C THR* 3.6 9.4 + - - +
299C LEU* 1.3 75.8 - - + +
301C MET* 1.3 67.0 + - - +
302C LYS* 3.2 17.0 - - - +
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Residues in contact with MET 301 (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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174C ILE* 5.5 1.3 - - + -
264C LEU* 4.8 9.4 - - + -
267C GLN* 5.1 10.5 - - - +
268C ILE* 3.3 35.7 - - + +
271C THR* 4.1 26.5 - - - -
297C THR* 3.0 34.4 + - + +
298C THR* 3.6 2.5 - - - +
299C LEU 3.1 0.4 - - - -
300C LYS* 1.3 77.3 - - - +
302C LYS* 1.3 69.7 + - - +
303C PHE* 3.2 60.4 - - + -
316C GLN* 6.5 0.2 - - + -
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Residues in contact with LYS 302 (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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298C THR 3.7 3.4 + - - -
299C LEU 3.2 15.6 + - - +
300C LYS* 3.2 17.0 - - - +
301C MET* 1.3 79.1 - - - +
303C PHE* 1.3 65.6 + - - +
304C LEU 3.9 0.7 - - - -
305C SER* 3.7 22.0 + - - +
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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