Contacts of the helix formed by residues 278 - 287 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LYS* 5.8 0.4 - - - +
276A THR 3.3 1.1 + - - -
277A THR* 1.3 86.4 - - + +
279A SER* 1.3 67.8 + - - +
280A ALA 4.1 0.2 - - - -
281A VAL* 2.8 30.6 + - + +
282A MET* 2.9 19.9 + - - +
85C PRO* 3.8 28.0 - - + -
115C ASP* 2.4 36.4 + - + +
118C TYR* 4.8 0.7 - - - +
1382C SIA 3.7 26.2 - - + +
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Residues in contact with SER 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A THR* 3.7 16.2 - - - -
182A ASP* 2.9 32.1 + - - -
184A HIS* 4.1 5.8 - - - -
262A LYS* 2.9 29.8 - - - +
278A THR* 1.3 71.6 - - - +
280A ALA* 1.3 62.7 + - - +
282A MET* 3.0 15.8 + - - +
283A VAL* 3.0 28.6 + - - +
1382C SIA 3.0 11.3 + - - -
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A HIS* 3.9 24.6 - - + +
278A THR* 3.2 1.0 + - - -
279A SER* 1.3 78.5 - - - +
281A VAL* 1.3 57.4 + - - +
283A VAL* 3.9 2.8 - - - +
284A HIS* 2.9 31.4 + - - +
58C PRO* 3.7 28.3 - - + -
60C LEU* 4.0 4.6 - - + +
115C ASP* 3.2 20.4 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 4.3 29.6 - - + +
277A THR* 4.1 10.5 - - - +
278A THR* 2.8 37.8 + - - +
280A ALA* 1.3 74.7 - - - +
282A MET* 1.3 66.3 + - - +
284A HIS* 3.3 8.2 + - + +
285A CYS* 3.0 24.8 + - + +
60C LEU* 4.8 5.8 - - + -
113C SER* 3.5 23.6 - - - +
115C ASP* 3.8 7.6 - - + +
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Residues in contact with MET 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A PHE* 4.9 9.2 - - + -
180A THR* 5.0 2.5 - - + -
262A LYS* 3.8 29.2 - - + -
265A ALA* 4.2 8.3 - - + -
266A GLU* 3.5 42.4 - - + +
269A ALA* 3.8 22.2 - - + -
274A CYS* 4.6 0.2 - - - -
275A LYS 3.7 22.4 - - - +
276A THR* 3.8 12.6 - - - +
278A THR 2.9 13.5 + - - +
279A SER* 3.4 20.0 - - - +
281A VAL* 1.3 75.0 - - - +
283A VAL* 1.3 64.6 + - + +
285A CYS* 3.0 8.5 + - - +
286A LEU* 2.9 27.7 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 4.3 10.5 - - + -
178A PHE* 3.8 10.1 - - + -
180A THR* 3.4 12.3 - - + -
184A HIS* 3.8 12.8 - - + +
185A SER* 3.4 29.8 - - - -
279A SER 3.0 16.3 + - - +
280A ALA* 4.0 4.0 - - - +
282A MET* 1.3 75.3 - - - +
284A HIS* 1.3 64.5 + - - +
286A LEU* 4.0 3.1 - - - +
287A ARG* 2.9 68.4 + - + +
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA 2.9 20.3 + - - +
281A VAL* 3.6 7.0 - - + +
283A VAL* 1.3 76.6 - - - +
285A CYS* 1.3 60.7 + - + +
287A ARG* 3.5 6.6 - - - +
288A GLN* 2.8 59.9 + - + +
3185A SO4 3.0 44.1 + - - +
60C LEU* 3.9 22.0 - - + +
61C GLY* 3.7 28.1 + - - -
3184C SO4 2.9 29.1 + - - -
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Residues in contact with CYS 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLY 4.6 1.1 - - - -
274A CYS* 2.0 53.4 - - + -
275A LYS* 4.5 4.3 - - + +
281A VAL* 3.0 15.2 + - + +
282A MET* 3.0 8.2 + - - +
284A HIS* 1.3 75.5 - - + +
286A LEU* 1.3 64.6 + - - +
287A ARG 3.1 1.1 - - - -
288A GLN* 3.0 27.5 + - - +
289A LYS* 3.5 15.4 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG* 3.3 11.1 + - - -
65A PHE* 3.7 21.3 - - + -
174A ILE* 5.3 1.1 - - + -
178A PHE* 3.4 46.2 - - + -
268A ILE* 4.8 7.6 - - + +
269A ALA* 4.6 15.5 - - + -
272A ALA* 3.6 31.0 - - + -
274A CYS* 4.1 9.9 - - - -
282A MET 2.9 17.2 + - - +
283A VAL 4.1 1.6 - - - +
285A CYS* 1.3 75.7 - - - +
287A ARG* 1.3 62.3 + - - +
288A GLN 3.1 0.9 + - - -
289A LYS* 3.1 16.9 + - + +
294A LEU* 3.8 19.3 - - + +
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 4.4 12.9 - - - +
62A PRO* 3.5 22.3 + - + -
64A ARG* 2.7 41.1 + - - +
65A PHE* 3.6 22.7 + - + -
66A THR* 3.5 21.4 - - - +
184A HIS 4.2 8.3 + - - -
283A VAL* 2.9 54.5 + - - +
284A HIS 3.5 8.0 - - - +
285A CYS 3.1 0.2 - - - -
286A LEU* 1.3 76.8 - - - +
288A GLN* 1.3 57.9 + - + +
289A LYS 4.0 0.3 - - - +
3185A SO4 2.9 43.9 + - - +
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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