Contacts of the strand formed by residues 247 - 251 (chain C) in PDB entry 2INU
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 ASN 247 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 2.8 25.1 + - - +
225C HIS* 3.5 21.6 + - - +
226C ALA 2.9 23.8 + - - -
245C CYS* 3.4 8.5 - - - +
246C GLY* 1.3 81.8 - - - +
248C CYS* 1.3 63.7 + - - +
250C GLU* 3.2 25.1 + - - +
267C ALA* 4.4 0.2 - - - -
270C ASP 4.6 2.6 + - - +
271C GLY* 3.3 8.5 - - - -
272C VAL* 3.0 42.3 - - + +
294C ARG* 5.6 1.6 - - - +
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Residues in contact with CYS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ALA* 3.3 3.5 - - - +
227C LEU* 2.9 29.0 + - - +
242C ILE* 3.7 31.1 - - + +
245C CYS* 4.4 3.1 - - - -
247C ASN* 1.3 74.1 - - - +
249C VAL* 1.3 66.4 + - - +
250C GLU* 5.7 0.2 - - - -
265C MSE 4.0 12.6 - - - -
266C GLY 3.2 40.4 - - - -
267C ALA* 3.6 11.4 - - - -
272C VAL 3.0 9.7 + - - -
273C THR* 3.2 12.6 - - - +
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Residues in contact with VAL 249 (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 LEU* 3.5 22.7 - - + -
237C VAL* 4.4 11.0 - - + -
242C ILE* 3.6 26.7 - - + -
248C CYS* 1.3 78.5 - - - +
250C GLU* 1.3 66.3 + - - +
251C LEU* 3.7 23.3 - - + -
260C VAL* 5.2 1.6 - - + -
265C MSE 3.9 15.0 - - + -
272C VAL* 4.7 0.2 - - - +
273C THR 2.7 14.1 + - - +
274C LEU* 3.7 23.8 - - + -
275C LEU 2.9 26.7 + - - +
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Residues in contact with GLU 250 (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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225C HIS* 2.8 36.3 + - - +
226C ALA 5.5 0.2 + - - -
227C LEU 2.9 13.0 + - - +
228C ILE* 3.4 19.5 - - + +
229C VAL 2.8 26.9 + - - -
247C ASN* 3.2 22.5 + - + +
248C CYS 5.6 0.2 - - - +
249C VAL* 1.3 75.4 - - - +
251C LEU* 1.3 63.9 + - - +
252C THR* 3.4 18.3 + - + +
272C VAL* 3.8 18.8 - - + -
275C LEU* 3.8 16.6 - - + +
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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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229C VAL* 3.2 17.7 - - + +
232C ALA* 5.1 1.3 - - + -
235C LEU* 3.9 23.3 - - + -
237C VAL* 5.3 0.4 - - + -
249C VAL* 3.7 21.3 - - + -
250C GLU* 1.3 73.0 - - - +
252C THR* 1.3 59.6 + - - +
258C THR* 4.3 8.5 - - + -
260C VAL* 4.3 22.2 - - + -
274C LEU* 4.3 9.0 - - + -
275C LEU 2.8 16.5 + - - +
276C ALA* 3.4 1.8 - - + -
277C GLU* 2.8 32.7 + - - +
279C HIS* 3.3 33.0 + - + +
282C LEU* 4.4 11.2 - - + -
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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