Contacts of the strand formed by residues 229 - 231 (chain H) in PDB entry 2POZ
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 PHE 229 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H TYR* 5.0 9.2 - + - -
157H LYS* 4.8 2.2 - - + -
202H LEU 3.9 0.2 + - - -
203H MSE 3.3 36.8 - - + -
204H VAL 3.1 20.5 + - - -
227H ILE* 3.3 11.2 - - - +
228H CYS* 1.3 84.3 - - - +
230H VAL* 1.3 66.0 + - - +
231H GLU* 4.4 10.3 - - + -
252H PRO* 3.3 24.0 - - + +
254H ALA* 3.7 14.4 - - + -
276H ILE* 3.3 29.2 - - + -
278H GLN* 3.8 27.8 - - - -
305H ALA* 5.0 3.8 - - + -
329H MSE 3.7 26.7 - - + -
330H ILE* 5.3 0.2 - - + -
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Residues in contact with VAL 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H VAL* 3.1 17.0 - - + +
206H LEU* 3.6 33.9 - - + -
219H CYS* 4.3 7.4 - - - -
222H ILE* 5.8 1.1 - - + -
227H ILE* 4.3 0.4 - - + +
229H PHE* 1.3 76.0 - - - +
231H GLU* 1.3 64.4 + - - +
232H GLU 4.0 0.3 + - - -
233H PRO* 4.4 9.2 - - + -
249H ILE* 4.2 14.6 - - + -
251H LEU* 4.3 17.5 - - + +
252H PRO 2.9 16.5 + - - +
253H ILE* 3.5 19.9 - - + +
254H ALA 3.0 20.3 + - - +
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Residues in contact with GLU 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H LYS* 2.8 23.3 + - + +
204H VAL 2.7 10.0 + - - +
205H ASP* 2.5 34.7 - - + +
206H LEU* 3.0 25.5 + - - +
229H PHE* 4.1 8.9 + - + -
230H VAL* 1.3 73.8 - - - +
232H GLU* 1.3 79.6 + - + +
233H PRO* 3.4 0.7 - - - +
254H ALA* 3.3 5.2 - - - +
257H GLU* 3.0 25.5 - - - +
278H GLN* 2.7 44.8 + - - +
307H HIS* 5.0 1.2 - - - -
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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
------------------------------------------------------------
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