Contacts of the helix formed by residues 278 - 289 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A PRO* 3.9 22.0 - - + -
115A ASP* 2.7 33.7 + - + +
118A TYR* 5.1 1.6 - - - +
1182A SIA 4.4 20.4 - - + +
262B LYS* 5.3 0.4 - - - -
276B THR 4.0 3.6 - - - -
277B THR* 1.3 95.6 - - + +
279B SER* 1.3 68.0 + - - +
280B ALA 3.7 0.4 + - - -
281B VAL* 3.0 31.1 + - - +
282B MET* 3.1 15.5 + - - +
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182A SIA 5.4 1.5 - - - +
180B THR* 3.8 11.0 - - - -
182B ASP* 2.7 34.4 + - - -
184B HIS* 3.9 7.0 - - - -
262B LYS* 3.1 30.0 + - - +
278B THR* 1.3 71.6 - - - +
280B ALA* 1.3 57.1 + - - +
282B MET* 2.7 38.7 + - - +
283B VAL* 3.0 16.0 + - - +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.7 28.7 - - + -
60A LEU* 3.6 5.8 - - + +
115A ASP* 3.7 20.0 - - - +
184B HIS* 3.9 27.1 - - + +
278B THR* 3.3 0.8 - - - -
279B SER* 1.3 77.8 - - - +
281B VAL* 1.3 61.2 + - - +
283B VAL* 4.0 4.2 - - - +
284B HIS* 3.2 24.4 + - - +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.6 7.2 - - + -
113A SER* 3.8 20.4 - - - +
114A GLU 5.6 0.7 - - - +
115A ASP* 4.0 9.9 - - + +
3285A SO4 5.8 3.4 - - - +
275B LYS* 4.4 40.6 - - + +
277B THR* 4.4 6.5 - - - +
278B THR* 3.0 32.7 + - - +
279B SER 2.8 1.2 + - - -
280B ALA* 1.3 75.4 - - - +
282B MET* 1.3 67.6 + - - +
284B HIS* 3.4 7.3 + - + +
285B CYS* 3.0 24.2 + - + +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B PHE* 4.9 7.6 - - + -
180B THR* 4.4 9.6 - - + -
262B LYS* 3.4 35.2 - - + -
265B ALA* 4.3 6.3 - - + +
266B GLU* 3.7 39.0 - - + -
269B ALA* 3.9 17.5 - - + -
274B CYS* 5.2 0.4 - - - -
275B LYS 3.6 20.0 - - - +
276B THR* 3.8 11.0 - - - +
278B THR 3.1 9.5 + - - +
279B SER* 2.7 25.2 + - - +
281B VAL* 1.3 70.3 - - - +
283B VAL* 1.3 64.7 + - + +
285B CYS* 3.0 6.4 + - - +
286B LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 4.2 11.4 - - + -
178B PHE* 4.3 5.6 - - + -
180B THR* 3.7 23.8 - - + -
184B HIS* 3.8 19.3 - - + +
185B SER* 3.7 15.5 - - - -
279B SER 3.0 13.4 + - - +
280B ALA* 4.1 4.9 - - - +
282B MET* 1.3 76.5 - - - +
284B HIS* 1.3 63.4 + - - +
286B LEU* 3.1 8.3 + - - +
287B ARG* 2.9 65.2 + - - +
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Residues in contact with HIS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.0 18.4 - - + +
61A GLY* 3.3 36.9 + - - -
64A ARG* 5.9 0.2 + - - -
3285A SO4 3.2 38.5 + - - -
280B ALA 3.2 17.3 + - - +
281B VAL* 3.7 6.7 - - + +
283B VAL* 1.3 79.8 - - - +
285B CYS* 1.3 59.4 + - - +
287B ARG* 3.3 5.3 + - - +
288B GLN* 2.9 46.2 + - + +
3284B SO4 3.0 40.9 + - - +
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Residues in contact with CYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLY 4.2 2.0 - - - -
274B CYS* 2.0 53.6 - - + -
275B LYS* 4.9 3.4 - - - +
281B VAL* 3.0 19.6 + - + +
282B MET 3.0 3.3 + - - +
284B HIS* 1.3 77.8 - - + +
286B LEU* 1.3 59.2 + - - +
288B GLN* 3.0 31.4 + - - +
289B LYS* 3.4 16.2 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 2.9 22.7 + - - -
65B PHE* 3.5 21.3 - - + -
174B ILE* 5.3 1.3 - - + -
178B PHE* 3.3 50.3 - - + -
268B ILE* 4.9 6.3 - - + +
269B ALA* 4.3 15.3 - - + -
272B ALA* 4.0 26.9 - - + -
274B CYS* 4.1 10.1 - - - -
282B MET 2.9 19.4 + - - +
283B VAL* 3.7 2.2 - - - +
285B CYS* 1.3 77.0 - - - +
287B ARG* 1.3 59.7 + - - +
288B GLN 3.3 0.5 + - - -
289B LYS* 3.4 11.1 + - + +
294B LEU* 4.3 15.0 - - + +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLY* 4.1 12.9 - - - +
62B PRO* 3.4 30.8 + - - -
64B ARG* 2.6 48.8 + - + +
65B PHE* 3.3 24.1 + - + -
66B THR* 3.5 8.7 - - - +
184B HIS 4.5 5.3 + - - -
283B VAL* 2.9 44.5 + - - +
284B HIS 3.5 10.1 - - - +
285B CYS 3.1 0.2 - - - -
286B LEU* 1.3 76.7 - - - +
288B GLN* 1.3 67.0 + - - +
289B LYS 3.4 1.3 - - - +
3284B SO4 2.9 31.5 + - - +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3285A SO4 5.0 5.2 + - - +
284B HIS* 2.9 53.6 + - + +
285B CYS* 3.0 19.9 + - - +
287B ARG* 1.3 80.6 + - - +
289B LYS* 1.3 66.5 + - + +
290B THR* 3.9 3.8 + - - +
293B GLU* 4.7 1.4 - - - +
3284B SO4 3.8 8.7 + - - -
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Residues in contact with LYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG* 2.7 26.7 + - - -
272B ALA* 3.2 29.2 + - + +
273B GLY 4.0 8.9 + - - -
274B CYS* 3.8 18.8 - - - -
285B CYS* 3.6 14.2 - - - +
286B LEU* 3.4 18.7 + - + +
287B ARG 3.9 1.0 - - - +
288B GLN* 1.3 84.1 - - + +
290B THR* 1.3 60.1 + - - +
293B GLU* 3.6 31.9 + - + +
294B LEU* 4.0 21.8 - - + -
3384B SO4 4.2 3.6 + - - -
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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