Contacts of the strand formed by residues 230 - 238 (chain C) in PDB entry 2Y05
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 MET 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210C GLY* 5.1 0.4 - - - -
211C TYR* 3.4 29.2 - - - +
212C ASP 3.8 6.7 - - - +
213C CYS 4.0 1.3 - - - +
214C TYR* 3.7 22.0 - - + +
226C VAL* 3.3 18.6 + - - +
227C ILE* 3.3 19.3 + - - +
228C GLY 5.2 1.2 - - - +
229C GLN* 1.3 79.7 - - - +
231C LYS* 1.3 60.0 + - - +
234C GLY 3.7 4.3 - - - -
235C ARG 3.6 40.4 - - - +
236C ILE* 4.3 7.2 - - + -
263C GLN* 3.0 23.3 + - + +
265C LEU* 3.7 25.4 - - + -
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Residues in contact with LYS 231 (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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142C GLY 5.8 0.8 + - - -
144C THR* 4.9 4.5 + - - -
209C ASP* 3.5 48.7 + - - +
210C GLY* 3.6 13.2 - - - -
211C TYR 2.8 23.3 + - - +
212C ASP* 3.1 40.3 + - - +
229C GLN 3.6 0.2 + - - -
230C MET* 1.3 78.5 - - - +
232C LYS* 1.3 64.8 + - - +
233C PHE 3.5 0.3 + - - -
234C GLY* 3.0 20.2 + - - -
263C GLN* 3.5 2.9 + - - +
265C LEU* 3.6 7.8 - - - +
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Residues in contact with LYS 232 (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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231C LYS* 1.3 78.1 - - - +
233C PHE* 1.3 101.8 + - + +
234C GLY* 3.1 0.9 + - - -
262C TYR 4.5 7.9 - - - +
263C GLN* 3.3 34.4 - - - +
264C GLU* 3.3 23.5 + - - -
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Residues in contact with PHE 233 (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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232C LYS* 1.3 110.2 - - + +
234C GLY* 1.3 65.6 + - - +
235C ARG* 3.7 17.0 + - - +
263C GLN 2.8 13.9 + - - -
264C GLU* 3.4 47.8 - - + -
266C ARG* 5.0 2.1 + - - +
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Residues in contact with GLY 234 (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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211C TYR 4.4 0.7 - - - -
212C ASP* 3.4 14.8 - - - -
230C MET* 3.7 14.4 - - - -
231C LYS* 3.0 21.4 + - - -
232C LYS 3.1 1.4 - - - -
233C PHE* 1.3 80.8 - - - +
235C ARG* 1.3 60.4 + - - +
236C ILE* 5.0 0.4 - - - +
265C LEU* 3.6 10.0 - - - +
266C ARG 3.1 21.5 + - - +
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Residues in contact with ARG 235 (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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136C ILE 4.8 0.2 - - - +
137C CYS* 2.8 43.9 + - - +
138C GLY 3.5 16.0 + - - -
143C GLU* 3.7 17.2 + - - +
212C ASP* 2.9 29.8 + - - +
213C CYS* 3.3 28.0 - - - +
214C TYR 2.9 24.9 + - - +
230C MET* 3.6 1.3 - - - +
233C PHE 3.7 12.0 + - - +
234C GLY* 1.3 76.5 - - - +
236C ILE* 1.3 62.4 + - - +
237C ALA 4.1 0.4 + - - -
266C ARG* 3.4 37.0 - - + +
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Residues in contact with ILE 236 (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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136C ILE* 4.6 2.3 - - - +
137C CYS* 4.8 1.1 - - - -
214C TYR* 3.3 37.5 - - + +
216C ASP* 4.2 8.3 - - + +
227C ILE* 3.9 17.0 - - + -
230C MET* 4.3 9.9 - - + -
234C GLY 5.0 0.7 - - - +
235C ARG* 1.3 77.4 - - - +
237C ALA* 1.3 70.2 + - - +
238C ILE* 3.6 11.2 + - + -
265C LEU* 4.4 7.6 - - + -
266C ARG* 2.7 17.3 + - - +
267C MET* 3.2 39.0 - - + -
268C GLU* 3.0 27.0 + - - +
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Residues in contact with ALA 237 (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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132C GLY 3.6 14.8 - - - +
136C ILE* 4.1 8.1 - - + -
137C CYS* 3.5 25.1 - - - -
214C TYR 2.9 9.3 + - - +
215C PHE* 4.2 9.4 - - + -
216C ASP* 3.0 25.8 + - - +
236C ILE* 1.3 69.5 - - - +
238C ILE* 1.3 61.0 + - - +
239C CYS* 3.2 3.8 + - - +
268C GLU 3.5 5.2 - - - -
270C PHE* 4.0 15.0 - - + -
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Residues in contact with ILE 238 (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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216C ASP* 4.3 9.4 - - - +
236C ILE* 4.2 14.8 - - + -
237C ALA* 1.3 67.5 - - - +
239C CYS* 1.3 60.6 + - - +
240C GLY* 4.7 13.5 - - - +
241C ALA* 6.2 1.8 - - + -
267C MET* 4.1 31.2 - - + +
268C GLU 2.8 12.8 + - - +
269C ALA* 3.3 37.4 - - + +
270C PHE* 3.5 10.8 + - - +
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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