Contacts of the helix formed by residues 278 - 289 (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 278 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PRO* 3.8 28.3 - - + -
113B SER* 4.6 0.2 - - - +
115B ASP* 2.4 33.4 + - + +
118B TYR* 4.8 4.0 - - - +
1282B SIA 3.7 19.3 - - + +
184C HIS* 6.4 0.2 - - - -
262C LYS* 5.7 0.2 - - - +
276C THR 3.2 0.6 + - - -
277C THR* 1.3 89.0 - - + +
279C SER* 1.3 66.5 + - - +
280C ALA 3.4 1.8 + - - -
281C VAL* 2.9 23.3 + - + +
282C MET* 2.9 28.6 + - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1282B SIA 3.8 7.3 - - - +
180C THR* 3.6 12.0 - - - -
182C ASP* 2.6 39.9 + - - -
184C HIS* 3.8 6.3 - - - -
262C LYS* 3.3 23.9 + - - -
278C THR* 1.3 71.4 - - - +
280C ALA* 1.3 58.9 + - - +
282C MET* 3.0 16.4 + - - +
283C VAL* 2.8 34.7 + - - +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PRO* 3.8 28.7 - - + -
60B LEU* 3.8 6.2 - - + +
115B ASP* 3.8 19.1 - - - +
184C HIS* 3.8 25.7 - - + +
278C THR* 3.3 0.8 + - - -
279C SER* 1.3 78.3 - - - +
281C VAL* 1.3 62.5 + - - +
283C VAL* 4.0 3.7 - - - +
284C HIS* 3.0 26.2 + - - +
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Residues in contact with VAL 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 4.7 5.4 - - + -
113B SER* 3.3 26.0 - - - +
115B ASP* 3.9 7.6 - - + -
275C LYS* 4.2 40.4 - - + +
277C THR* 4.2 9.2 - - - +
278C THR* 2.9 34.2 + - + +
280C ALA* 1.3 76.5 - - - +
282C MET* 1.3 63.7 + - - +
284C HIS* 3.3 7.9 + - - +
285C CYS* 3.0 23.7 + - + +
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Residues in contact with MET 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C PHE* 4.8 8.3 - - + -
180C THR* 4.2 10.5 - - + -
262C LYS* 3.6 36.8 - - + -
265C ALA* 4.1 7.2 - - + +
266C GLU* 3.9 24.5 - - + -
269C ALA* 3.5 29.2 - - + -
274C CYS* 4.9 0.6 - - - -
275C LYS 3.6 20.4 - - - +
276C THR* 3.9 9.2 - - - +
278C THR 2.9 13.6 + - - +
279C SER* 3.3 18.6 - - - +
281C VAL* 1.3 75.2 - - - +
283C VAL* 1.3 65.8 + - - +
285C CYS* 2.9 16.9 + - - +
286C LEU* 2.9 19.0 + - + +
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PHE* 4.4 10.2 - - + -
178C PHE* 4.3 9.0 - - + -
180C THR* 3.8 13.5 - - + -
184C HIS* 3.5 24.0 - - + +
185C SER* 3.6 17.9 - - - -
279C SER 2.8 24.9 + - - +
280C ALA* 4.0 5.8 - - - +
282C MET* 1.3 70.6 - - - +
284C HIS* 1.3 57.8 + - - +
286C LEU* 3.5 3.4 + - - +
287C ARG* 3.0 73.4 + - - +
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Residues in contact with HIS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.8 18.7 - - + +
61B GLY* 3.6 28.9 + - - -
3384B SO4 3.1 47.0 + - - -
280C ALA 3.0 19.5 + - - +
281C VAL* 3.6 5.4 - - + +
283C VAL* 1.3 77.1 - - - +
285C CYS* 1.3 61.7 + - + +
287C ARG* 3.5 1.1 + - - +
288C GLN* 2.9 56.7 + - + +
3385C SO4 3.1 39.7 + - - +
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Residues in contact with CYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3384B SO4 5.3 0.7 - - - -
273C GLY 4.2 3.6 - - - -
274C CYS* 2.0 54.1 - - + -
275C LYS 4.7 2.7 - - - +
281C VAL* 3.0 14.3 + - + +
282C MET* 2.9 7.4 + - - +
284C HIS* 1.3 79.4 - - + +
286C LEU* 1.3 63.6 + - - +
288C GLN* 3.0 22.0 + - - +
289C LYS* 3.4 16.2 + - - +
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 2.7 27.1 + - - -
65C PHE* 3.7 20.2 - - + -
174C ILE* 5.3 1.6 - - + -
178C PHE* 3.5 45.1 - - + -
268C ILE* 4.7 7.4 - - + +
269C ALA* 4.6 12.8 - - + -
272C ALA* 3.6 31.2 - - + -
274C CYS* 4.2 9.9 - - - -
282C MET 2.9 16.8 + - - +
283C VAL* 4.0 1.3 - - - +
285C CYS* 1.3 78.0 - - - +
287C ARG* 1.3 52.0 + - - +
289C LYS* 3.2 12.3 + - + +
294C LEU* 3.6 21.3 - - + +
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Residues in contact with ARG 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLY* 4.3 13.7 - - - +
62C PRO* 3.5 23.3 + - + -
64C ARG* 2.8 46.1 + - + +
65C PHE* 3.7 25.6 + - + +
66C THR* 4.0 7.3 - - - +
184C HIS 4.0 7.5 + - - -
283C VAL* 3.0 56.2 + - - +
284C HIS 3.9 6.3 - - - +
285C CYS 3.2 0.4 - - - -
286C LEU* 1.3 76.7 - - - +
288C GLN* 1.3 64.6 + - - +
289C LYS 3.3 1.3 - - - +
3385C SO4 2.8 41.6 + - - +
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY* 5.7 1.4 - - - -
3384B SO4 5.2 4.6 + - - +
284C HIS* 2.9 52.8 + - + +
285C CYS* 3.0 11.8 + - - +
287C ARG* 1.3 82.9 + - - +
289C LYS* 1.3 63.2 + - + +
290C THR* 3.9 2.9 + - - +
293C GLU* 4.7 1.4 - - - +
3184C SO4 5.2 1.1 + - - -
3385C SO4 3.9 12.3 + - - -
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Residues in contact with LYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 3.0 24.3 + - - -
272C ALA* 3.4 26.8 + - + +
273C GLY 3.9 8.4 + - - -
274C CYS* 3.9 16.2 - - - -
285C CYS* 3.6 15.9 - - - +
286C LEU* 3.2 19.2 + - + +
287C ARG 4.0 0.3 - - - +
288C GLN* 1.3 81.0 - - - +
290C THR* 1.3 63.8 + - - +
293C GLU* 3.6 30.0 + - + +
294C LEU* 3.8 22.2 - - + -
3184C SO4 3.5 4.0 + - - -
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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
------------------------------------------------------------
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