Contacts of the helix formed by residues 253 - 265 (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 GLU 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B SER* 3.1 30.3 + - - +
246B HIS* 4.7 0.2 + - - -
252B CYS* 1.3 74.5 - - - +
254B GLY* 1.3 64.2 + - - +
256B LYS* 2.9 38.9 + - - +
257B GLY* 3.0 12.5 + - - -
422D G 4.2 3.9 - - + +
423D A 3.8 41.0 + - + +
424D C 2.8 34.1 + - + -
425D C 5.0 3.1 + - - -
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Residues in contact with GLY 254 (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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252B CYS* 3.2 8.9 - - - +
253B GLU* 1.3 74.5 - - - +
255B CYS* 1.3 55.5 + - - +
256B LYS 2.9 10.4 + - - -
257B GLY* 3.1 2.1 + - - -
258B PHE* 2.9 26.2 + - - +
261B ARG* 4.3 1.0 + - - -
284B ARG* 4.4 2.2 - - - -
291B ARG* 3.7 6.1 - - - -
422D G 3.7 39.5 + - - +
423D A 4.4 1.0 + - - -
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Residues in contact with CYS 255 (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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235B CYS* 4.0 8.1 - - - -
237B ILE* 3.7 23.3 - - + -
238B CYS* 3.8 4.9 - - - -
251B SER* 4.3 5.2 - - - -
252B CYS* 3.0 10.9 - - - +
254B GLY* 1.3 73.7 - - - +
256B LYS* 1.3 59.3 + - - +
258B PHE* 4.1 3.8 - - - -
259B PHE* 3.3 21.3 + - - +
291B ARG* 3.0 33.0 - - - +
295B CYS* 4.5 4.4 - - - -
300B MET* 4.0 8.6 - - + +
350B ZN 2.2 37.2 - - - -
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Residues in contact with LYS 256 (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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246B HIS* 3.2 41.8 - - + +
247B TYR* 4.0 30.6 - - + +
251B SER* 4.8 2.9 - - - +
252B CYS 3.4 11.8 + - - +
253B GLU* 2.9 36.8 + - - +
254B GLY 2.9 1.0 + - - -
255B CYS* 1.3 77.4 - - - +
257B GLY* 1.3 67.4 + - - +
259B PHE* 3.0 5.2 + - - +
260B LYS* 2.9 25.9 + - + +
300B MET* 5.0 1.1 - - - -
412C A 5.2 4.9 + - - +
413C G 3.5 34.9 + - - -
414C G 5.0 6.3 - - - -
424D C 4.4 2.2 - - - +
425D C 4.5 2.2 - - - +
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Residues in contact with GLY 257 (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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253B GLU 3.0 12.9 + - - -
254B GLY 3.7 0.7 - - - -
256B LYS* 1.3 81.0 - - - +
258B PHE* 1.3 56.7 + - - +
260B LYS* 3.0 10.7 + - - -
261B ARG* 2.8 58.4 + - - +
422D G 4.7 3.8 - - - -
423D A 6.3 0.4 - - - -
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Residues in contact with PHE 258 (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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254B GLY 2.9 16.6 + - - +
255B CYS* 4.4 2.5 - - - -
257B GLY* 1.3 74.9 - - - +
259B PHE* 1.3 54.8 + - - +
261B ARG* 3.1 15.2 - - + +
262B THR* 2.5 41.1 + - - -
269B TYR* 3.3 26.9 - + - -
288B GLN* 3.6 20.6 - - + -
291B ARG* 3.1 41.1 - - + +
292B TYR* 3.0 52.5 - + + -
295B CYS* 4.4 9.4 - - - -
421D T 3.8 23.8 - - - +
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Residues in contact with PHE 259 (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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247B TYR* 3.7 21.3 - + + -
255B CYS 3.3 18.3 + - - +
256B LYS* 3.0 5.2 + - - +
258B PHE* 1.3 78.9 - - - +
260B LYS* 1.3 68.5 + - - +
262B THR* 3.8 2.4 - - - -
263B VAL* 3.3 30.9 + - + +
292B TYR* 3.5 30.3 - + - -
295B CYS* 3.8 22.4 - - + -
296B LEU* 4.1 10.1 - - + -
300B MET* 3.5 46.7 - - + -
301B LYS 3.2 28.5 - - - -
302B ARG* 4.3 1.6 - - + -
305B VAL* 4.8 3.4 - - + -
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Residues in contact with LYS 260 (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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247B TYR* 3.8 20.6 - - - +
256B LYS* 2.9 16.8 + - + +
257B GLY* 3.6 13.7 - - - +
259B PHE* 1.3 73.1 - - - +
261B ARG* 1.3 79.0 + - - +
263B VAL* 2.7 17.0 + - - +
264B ARG* 3.0 53.3 + - + +
305B VAL* 4.3 12.8 - - + -
413C G 4.0 9.9 + - + +
414C G 3.3 42.4 + - - -
415C T 4.7 9.0 + - - +
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Residues in contact with ARG 261 (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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254B GLY 4.3 1.0 + - - -
257B GLY* 2.8 23.3 + - - +
258B PHE* 3.1 28.4 - - - +
260B LYS* 1.3 83.9 - - + +
262B THR* 1.3 66.0 + - - +
264B ARG* 3.5 5.3 + - - -
265B LYS* 3.1 29.5 + - + +
267B LEU* 4.5 8.5 - - + -
420D T 4.5 2.9 - - - -
421D T 3.3 54.2 + - - +
422D G 2.9 52.0 + - - -
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Residues in contact with THR 262 (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* 2.5 32.7 + - - -
259B PHE 3.8 4.5 - - - -
260B LYS 2.8 3.4 + - - -
261B ARG* 1.3 75.4 - - - +
263B VAL* 1.3 58.8 + - - +
266B ASP* 2.9 22.7 + - - -
267B LEU* 3.1 24.3 + - - +
269B TYR* 2.6 31.5 + - + +
292B TYR* 3.1 41.9 - - + -
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B PHE* 3.3 38.8 - - + +
260B LYS 2.7 11.0 + - - +
262B THR* 1.3 68.9 - - - +
264B ARG* 1.3 54.9 + - - +
265B LYS 2.6 6.2 + - - -
266B ASP* 2.5 29.1 + - - +
292B TYR* 4.6 7.9 - - + +
302B ARG* 4.2 32.8 - - + +
305B VAL* 4.2 20.6 - - + -
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Residues in contact with ARG 264 (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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260B LYS* 3.0 43.4 + - + +
261B ARG* 4.1 4.7 - - - +
263B VAL* 1.3 73.6 - - - +
265B LYS* 1.3 74.6 + - + +
266B ASP* 5.4 0.2 - - - -
305B VAL* 3.4 14.0 - - + +
306B GLN 3.1 26.0 - - - -
413C G 2.4 43.2 + - - -
414C G 2.7 31.4 + - - -
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Residues in contact with LYS 265 (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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261B ARG* 3.1 20.4 + - + +
263B VAL 2.6 4.9 + - - -
264B ARG* 1.3 94.2 + - + +
266B ASP* 1.3 70.1 + - - +
267B LEU* 2.8 31.6 + - + +
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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