Contacts of the strand formed by residues 227 - 232 (chain C) in PDB entry 5PAO
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 GLN 227 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C CYS* 3.1 19.5 + - + +
225C PRO 4.6 1.0 - - - +
226C TRP* 1.3 82.6 - - + +
228C VAL* 1.3 79.6 + - - +
239C GLY* 3.9 11.7 - - - -
240C GLY 3.8 9.1 + - - +
267C VAL 4.2 3.3 - - - +
268C LEU* 3.7 14.6 - - - +
269C GLY 4.5 4.2 + - - -
270C GLU 5.3 2.5 + - - +
342C SER* 2.7 41.3 + - - +
343C GLY* 4.2 4.0 - - - -
344C TRP* 3.4 31.6 - - + -
357C LEU* 3.7 21.5 - - + -
406C GLY* 4.4 0.4 - - - -
407C PRO* 3.4 14.9 - - + +
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Residues in contact with VAL 228 (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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226C TRP 3.7 0.9 - - - +
227C GLN* 1.3 89.7 + - - +
229C LEU* 1.3 71.6 + - - +
230C LEU* 3.9 12.3 - - + -
239C GLY* 3.3 2.9 - - - -
240C GLY* 2.9 39.2 + - - +
241C THR 3.9 1.3 - - - +
242C LEU 3.6 27.4 - - - +
248C VAL* 3.9 13.2 - - + -
266C ALA* 3.9 21.8 - - + -
267C VAL 3.5 8.5 - - - +
268C LEU* 3.9 19.5 - - + -
344C TRP* 3.8 2.8 - - - -
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Residues in contact with LEU 229 (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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227C GLN 4.4 0.2 + - - -
228C VAL* 1.3 73.2 - - - +
230C LEU* 1.3 71.8 + - - +
231C LEU* 3.9 25.1 - - + -
236C GLN* 4.1 23.3 - - + +
238C CYS 4.0 7.0 - - - +
265C ILE 3.7 0.7 - - - +
266C ALA* 3.5 3.1 - - - -
267C VAL* 2.8 51.2 + - + +
270C GLU* 4.1 9.9 - - + +
273C LEU* 3.7 31.6 - - + -
344C TRP* 3.7 28.4 - - + -
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Residues in contact with LEU 230 (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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228C VAL* 3.9 9.6 - - + -
229C LEU* 1.3 74.3 - - - +
231C LEU* 1.3 60.9 + - - +
236C GLN* 3.9 0.7 - - - -
237C LEU* 2.8 37.9 + - + -
238C CYS* 2.9 27.6 + - + +
239C GLY 3.6 11.9 - - - +
240C GLY* 5.1 0.4 - - - -
248C VAL* 4.9 1.6 - - + -
250C SER* 3.5 26.0 - - - +
255C PHE* 3.9 23.8 - - + -
264C LEU* 4.6 3.6 - - + -
265C ILE 3.3 4.0 - - - +
266C ALA* 3.9 27.4 - - + -
285C VAL* 4.8 2.5 - - + -
306C LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 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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229C LEU* 3.9 23.1 - - + -
230C LEU* 1.3 79.4 - - - +
232C VAL* 1.3 60.4 + - - +
233C ASN 4.3 0.2 - - - -
234C GLY* 3.8 24.0 - - - +
235C ALA 3.2 21.5 - - - +
236C GLN* 3.9 5.2 - - + +
237C LEU* 4.6 1.1 - - - -
263C ASN 3.6 1.0 - - - +
264C LEU* 3.5 9.3 - - - +
265C ILE* 2.8 45.4 + - + +
267C VAL* 3.8 29.4 - - + -
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Residues in contact with VAL 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 LEU* 1.3 74.8 - - - +
233C ASN* 1.3 77.4 + - - +
234C GLY 3.2 0.2 - - - -
235C ALA* 2.9 35.6 + - + +
236C GLN 5.5 0.4 - - - +
237C LEU* 4.1 24.2 - - + -
258C ILE* 4.1 24.2 - - + -
259C LYS 6.2 0.2 - - - +
260C ASN 4.9 7.6 - - - +
263C ASN* 3.5 14.1 - - + +
264C LEU* 4.7 6.3 - - + +
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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