Contacts of the helix formed by residues 250 - 261 (chain C) in PDB entry 1YO5
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 HIS 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B A 3.6 46.1 + - - -
4B C 3.3 16.7 + - - +
247C GLN* 5.7 4.2 - - + +
248C PRO* 3.5 18.9 + - + +
249C ILE* 1.3 76.6 - - - +
251C LEU* 1.3 67.6 + - - +
252C TRP* 3.3 19.4 + - + -
253C GLN* 3.0 30.6 + - - +
254C PHE* 2.9 21.3 + - - +
291C TRP* 3.8 1.6 - - - -
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Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B C 2.9 14.9 + - - +
250C HIS* 1.3 72.5 - - - +
252C TRP* 1.3 58.0 + - - +
254C PHE* 3.2 5.0 + - + +
255C LEU* 2.9 51.9 + - + +
291C TRP* 3.6 45.2 - - + +
305C LEU* 3.6 42.0 - - + +
308C SER* 3.8 15.7 - - - -
309C ILE* 3.7 20.4 - - + +
312C TYR* 3.3 13.8 + - + +
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Residues in contact with TRP 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B C 4.6 0.9 - - - -
250C HIS* 4.1 20.5 + - + +
251C LEU* 1.3 75.4 - - - +
253C GLN* 1.3 90.6 + - + +
255C LEU* 3.5 6.6 + - - +
256C LYS* 3.1 60.1 + - + +
312C TYR* 3.1 44.2 + + + +
317C ILE* 3.9 32.9 - - + +
318C ILE* 4.2 1.3 - - + -
331C PHE* 3.7 17.8 - + + -
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Residues in contact with GLN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C PRO 4.9 0.3 - - - +
249C ILE* 3.6 23.2 - - + +
250C HIS* 3.0 40.5 + - - +
252C TRP* 1.3 116.1 - - + +
254C PHE* 1.3 61.6 + - - +
256C LYS* 3.2 5.8 + - - +
257C GLU* 2.9 29.2 + - - +
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ILE* 3.9 8.6 - - + +
250C HIS 2.9 6.9 + - - +
251C LEU* 3.4 16.4 - - + +
253C GLN* 1.3 76.1 - - - +
255C LEU* 1.3 66.8 + - + +
257C GLU* 3.2 9.4 - - - +
258C LEU* 3.1 55.9 + - + +
287C VAL* 4.1 9.2 - - + -
290C LEU* 3.7 19.7 - - + -
291C TRP* 3.4 63.0 - + + -
294C ARG* 3.9 39.5 - - + -
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Residues in contact with LEU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C LEU* 2.9 39.8 + - + +
252C TRP* 3.7 4.9 - - - +
254C PHE* 1.3 84.7 - - + +
256C LYS* 1.3 60.9 + - - +
258C LEU* 3.4 7.1 + - + +
259C LEU* 3.1 29.8 + - + +
269C ILE* 4.0 23.5 - - + +
279C PHE* 4.3 10.5 - - + -
281C ILE* 5.2 2.7 - - + -
287C VAL* 4.0 22.0 - - + -
305C LEU* 5.0 4.0 - - + -
309C ILE* 4.2 20.9 - - + -
318C ILE* 4.2 19.7 - - + -
331C PHE* 4.2 8.3 - - + -
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C TRP* 3.1 39.4 + - + +
253C GLN* 3.2 8.5 + - - +
255C LEU* 1.3 75.4 - - - +
257C GLU* 1.3 56.2 + - - +
259C LEU* 3.2 9.1 + - - +
260C LEU* 3.0 29.6 + - - +
271C TRP* 5.2 8.1 - - + -
331C PHE* 3.4 46.7 - - + -
333C HIS* 5.1 2.2 - - - +
334C PRO* 4.0 35.4 + - - +
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Residues in contact with GLU 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C ILE* 4.5 11.1 - - - +
253C GLN 2.9 11.7 + - - +
254C PHE* 3.2 12.3 - - - +
256C LYS* 1.3 76.1 - - - +
258C LEU* 1.3 66.2 + - + +
260C LEU* 3.3 23.8 + - + +
261C LYS* 3.8 17.2 + - + +
265C TYR* 4.5 10.3 + - + -
294C ARG* 2.6 47.4 + - - -
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Residues in contact with LEU 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PHE* 3.1 51.3 + - + +
255C LEU* 3.8 8.3 - - + +
256C LYS 3.4 0.2 - - - -
257C GLU* 1.3 82.1 - - - +
259C LEU* 1.3 61.4 + - - +
260C LEU 3.4 0.7 + - - -
261C LYS 3.4 11.8 + - - +
262C PRO* 4.2 1.2 - - - +
265C TYR* 3.4 57.7 - - + +
268C PHE* 5.9 0.4 - - + -
269C ILE* 3.6 26.0 - - + +
287C VAL* 4.2 17.5 - - + -
290C LEU* 4.0 16.2 - - + -
294C ARG* 5.6 0.9 - - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C LEU 3.1 22.1 + - - +
256C LYS* 3.2 5.1 + - - +
258C LEU* 1.3 75.5 - - - +
260C LEU* 1.3 62.9 + - - +
261C LYS 3.3 0.6 + - - -
262C PRO* 3.5 13.0 - - - +
269C ILE* 3.9 14.6 - - + -
270C ARG* 3.4 43.5 - - - +
271C TRP* 3.6 45.4 + - + +
279C PHE* 3.7 27.6 - - + -
331C PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS 3.0 12.9 + - - +
257C GLU* 3.5 17.0 - - + +
258C LEU 3.2 0.4 - - - -
259C LEU* 1.3 79.3 - - - +
261C LYS* 1.3 75.9 + - + +
262C PRO* 3.3 8.2 - - - +
271C TRP* 5.4 0.9 - - - +
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Residues in contact with LYS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C GLU* 3.8 11.5 + - + +
258C LEU 3.4 6.6 + - - +
259C LEU 3.3 0.4 - - - -
260C LEU* 1.3 103.1 - - + +
262C PRO* 1.3 60.6 - - - +
263C HIS* 3.2 4.0 - - + +
264C SER* 3.1 19.1 + - - +
265C TYR* 2.9 42.0 + - + -
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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
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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