Contacts of the helix formed by residues 287 - 298 (chain B) in PDB entry 1YNW
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 CYS 287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B THR 4.9 1.6 - - - -
271B CYS* 4.0 4.9 - - - -
272B ARG* 4.7 5.4 - - + +
277B CYS* 4.1 9.9 - - + -
279B ILE* 4.7 4.5 - - + +
284B ARG 4.7 1.4 + - - -
285B ASN 3.3 2.6 - - - -
286B ARG* 1.3 82.3 - - + +
288B GLN* 1.3 64.7 + - - +
289B TYR* 3.4 13.2 - - - -
290B CYS* 3.1 23.1 - - + +
291B ARG* 3.0 20.5 + - - +
351B ZN 2.2 37.5 - - - -
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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
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258B PHE* 3.6 6.8 - - + -
267B LEU* 6.0 0.8 - - - +
269B TYR* 2.7 58.3 + - + -
284B ARG 5.7 0.2 - - - -
285B ASN* 4.5 9.4 + - - +
286B ARG 4.2 0.8 - - - -
287B CYS* 1.3 71.2 - - - +
289B TYR* 1.3 65.8 + - - +
291B ARG* 3.2 7.4 + - - +
292B TYR* 3.0 19.2 + - - +
420D T 3.5 11.9 + - - -
421D T 2.7 37.0 + - - +
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Residues in contact with TYR 289 (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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269B TYR* 3.2 33.6 - + + +
270B THR* 3.7 5.5 + - - -
271B CYS* 3.1 39.0 - - + +
275B LYS* 3.5 44.9 - - + +
287B CYS* 3.3 5.7 - - - -
288B GLN* 1.3 79.6 - - - +
290B CYS* 1.3 57.0 + - - +
292B TYR* 3.5 3.3 + + - +
293B GLN* 2.7 70.0 + - + +
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Residues in contact with CYS 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B CYS* 3.1 15.9 - - - -
275B LYS* 3.6 16.8 - - - -
276B ASP* 5.4 0.4 - - - -
277B CYS* 3.0 30.5 - - + +
279B ILE* 4.3 7.3 - - + +
287B CYS* 3.1 8.5 - - - +
289B TYR* 1.3 80.0 - - - +
291B ARG* 1.3 69.1 + - - +
293B GLN* 3.7 7.7 - - - +
294B LYS* 3.0 20.6 + - - +
351B ZN 2.8 30.5 - - - -
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Residues in contact with ARG 291 (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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237B ILE* 4.7 6.0 - - + +
255B CYS* 3.0 44.2 - - - +
258B PHE* 3.1 46.6 - - + +
279B ILE* 4.0 15.4 - - + +
284B ARG* 3.2 48.1 + - - +
285B ASN* 3.4 16.3 + - - +
287B CYS 3.0 14.2 + - - +
288B GLN* 3.2 10.1 + - - +
290B CYS* 1.3 71.9 - - - +
292B TYR* 1.3 69.2 + - - +
294B LYS* 2.7 17.4 + - - +
295B CYS* 3.1 12.9 + - - -
421D T 4.7 4.3 + - - -
422D G 2.8 22.0 + - - -
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Residues in contact with TYR 292 (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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258B PHE* 3.0 26.0 - + + -
259B PHE* 3.5 28.7 - + - -
262B THR* 3.1 38.6 - - + -
263B VAL* 4.6 4.8 - - + +
269B TYR* 3.8 10.5 - + + -
288B GLN 3.0 8.3 + - - +
289B TYR* 3.8 3.6 - + - +
291B ARG* 1.3 78.1 - - - +
293B GLN* 1.3 77.9 + - - +
295B CYS* 2.8 23.9 + - - +
296B LEU* 3.1 44.4 + - + +
302B ARG* 4.2 15.9 - - - +
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Residues in contact with GLN 293 (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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289B TYR* 2.7 63.4 + - + +
290B CYS* 3.7 9.4 - - - +
291B ARG 3.0 0.2 + - - -
292B TYR* 1.3 83.7 - - + +
294B LYS* 1.3 63.3 + - - +
296B LEU* 3.3 26.4 + - - +
297B ALA* 3.0 20.5 + - - +
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Residues in contact with LYS 294 (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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236B ALA 3.9 11.9 + - - -
237B ILE* 3.0 30.6 + - + +
279B ILE* 3.1 44.8 + - + +
290B CYS 3.0 12.6 + - - +
291B ARG* 2.7 15.7 + - - +
293B GLN* 1.3 68.5 - - - +
295B CYS* 1.3 66.5 + - - +
297B ALA* 2.7 11.9 + - + +
298B MET* 2.6 38.9 + - + +
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Residues in contact with CYS 295 (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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237B ILE* 3.9 27.8 - - - +
255B CYS* 4.5 5.4 - - - -
258B PHE* 4.4 14.6 - - - -
259B PHE* 3.8 27.1 - - + -
291B ARG* 3.1 15.2 + - - -
292B TYR* 2.8 22.8 + - - +
294B LYS* 1.3 72.6 - - - +
296B LEU* 1.3 61.0 + - - +
298B MET* 3.2 5.9 + - - +
299B GLY 3.3 0.5 + - - -
300B MET* 2.9 42.0 + - - +
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Residues in contact with LEU 296 (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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259B PHE* 4.1 10.3 - - + -
292B TYR* 3.1 52.1 + - + +
293B GLN* 3.5 24.9 - - - +
295B CYS* 1.3 75.4 - - - +
297B ALA* 1.3 55.9 + - - +
299B GLY* 2.7 28.6 + - - -
300B MET 3.5 18.8 + - - +
302B ARG* 4.4 12.1 - - + -
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Residues in contact with ALA 297 (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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293B GLN 3.0 11.5 + - - +
294B LYS* 2.7 23.9 + - + +
296B LEU* 1.3 75.2 - - - +
298B MET* 1.3 60.5 + - + +
299B GLY 3.1 3.2 + - - -
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Residues in contact with MET 298 (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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236B ALA* 3.4 36.1 - - + +
237B ILE* 3.2 35.2 - - + -
249B VAL* 3.1 21.2 - - + +
294B LYS* 2.6 28.4 + - + +
295B CYS 3.8 1.8 - - - +
297B ALA* 1.3 75.5 - - - +
299B GLY* 1.3 57.3 + - - +
300B MET 3.7 0.4 - - - -
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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