Contacts of the strand formed by residues 226 - 231 (chain C) in PDB entry 6XAV
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 226 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C ALA* 5.3 14.5 - - + +
72C TYR* 3.3 12.9 + - - -
204C LEU* 3.7 17.9 + - - +
205C MET* 3.7 16.9 - - + +
206C VAL* 3.5 18.5 + - - +
225C GLY* 1.3 71.6 - - - -
227C VAL* 1.3 64.6 + - - +
228C VAL* 3.4 22.3 + - + +
249C LYS* 3.0 32.8 + - - +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 4.6 1.6 + - - -
206C VAL* 3.5 29.2 - - + +
208C LEU* 4.8 2.9 - - + -
216C VAL 5.1 0.7 - - - +
219C MET* 3.8 27.4 - - + +
220C GLN* 3.5 41.9 + - + +
223C VAL* 3.7 30.5 - - + -
225C GLY 3.9 4.4 + - - +
226C GLU* 1.3 79.1 - - - +
228C VAL* 1.3 64.4 + - - +
229C ALA* 4.7 7.6 - - + -
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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
----------------------------------------------------------
68C ALA* 5.5 5.8 - - - +
71C SER* 3.9 28.7 - - - +
72C TYR* 4.2 21.5 - - + -
206C VAL 3.1 18.7 + - - +
207C LEU* 3.4 9.2 - - + +
208C LEU 3.3 10.2 + - - -
226C GLU* 3.4 30.4 + - + +
227C VAL* 1.3 74.1 - - - +
229C ALA* 1.3 61.1 + - - +
242C VAL* 3.8 25.8 - - + -
246C VAL* 4.4 12.8 - - + -
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Residues in contact with ALA 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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71C SER* 3.2 27.7 + - - +
207C LEU* 5.3 0.2 - - - -
208C LEU* 3.2 25.1 - - + -
216C VAL* 3.7 40.2 - - + -
220C GLN* 4.7 1.3 - - - +
227C VAL* 3.9 6.8 + - + -
228C VAL* 1.3 76.8 - - - +
230C SER* 1.3 63.8 + - - +
231C THR* 5.9 0.2 - - - -
238C ARG* 4.6 1.6 + - - -
242C VAL* 5.1 1.9 - - - +
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Residues in contact with SER 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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208C LEU 2.8 7.7 + - - +
209C ILE* 3.5 22.4 - - - -
210C ASP 2.7 32.6 + - - -
211C GLU* 3.8 1.7 + - - -
216C VAL* 5.4 0.9 - - - -
229C ALA* 1.3 78.2 - - - +
231C THR* 1.3 58.8 + - - +
234C GLU* 4.1 4.9 - - - +
238C ARG* 3.5 19.2 - - - +
239C HIS* 3.1 21.6 + - - -
242C VAL* 4.4 12.6 - - - -
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Residues in contact with THR 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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210C ASP* 4.1 1.6 - - - -
211C GLU 3.4 13.9 - - - +
213C PRO* 3.8 30.5 - - + -
216C VAL* 3.7 28.3 - - + -
229C ALA 5.9 0.2 - - - -
230C SER* 1.3 79.5 + - - +
232C PHE* 1.3 63.9 + - - +
233C ASP* 3.1 23.6 + - - +
234C GLU* 3.5 10.6 + - - +
239C HIS* 3.2 14.0 - - - -
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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
------------------------------------------------------------
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