Contacts of the helix formed by residues 253 - 255 (chain B) in PDB entry 4IXU
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 ASP 253 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ASP* 2.9 7.8 - - - +
144B ALA* 3.3 7.8 + - - +
145B HIS* 3.1 7.1 - - - -
199B ARG* 2.7 25.5 + - - -
251B ASP* 3.0 18.0 + - - +
252B ILE* 1.3 76.9 - - - +
254B ALA* 1.3 60.2 + - - +
255B PHE 3.1 5.1 - - - +
260B ALA* 5.3 1.1 - - - -
263B THR* 3.9 27.6 + - + +
265B THR* 3.0 27.3 + - - +
266B PRO* 4.7 2.9 - - + -
267B VAL 5.1 0.5 + - - -
296B GLU* 5.1 0.2 - - - +
402B MN 2.2 36.5 + - - -
406B 38I 3.2 4.2 + - - -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.6 19.1 - - + -
143B ASP 3.6 23.3 - - - +
144B ALA 3.8 9.9 - - - +
196B ILE 4.9 0.7 - - - +
197B GLY* 5.4 0.7 - - - -
199B ARG* 2.9 20.1 + - - +
250B PHE* 4.3 3.4 - - + -
251B ASP 2.9 16.2 + - - +
253B ASP* 1.3 81.3 + - - +
255B PHE* 1.3 56.7 + - - +
271B LEU* 3.0 28.1 + - + +
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Residues in contact with PHE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 3.2 13.0 + - - -
250B PHE* 3.5 18.4 - + - -
252B ILE* 3.0 27.1 + - + +
253B ASP* 3.3 6.8 - - - +
254B ALA* 1.3 79.5 - - - +
256B ASP* 1.3 67.8 + - - +
257B PRO* 3.4 2.8 - - - +
259B LEU* 4.2 5.8 - - + -
260B ALA* 3.9 14.2 - - + +
271B LEU* 3.7 12.6 - - + +
272B THR 3.5 27.8 - - - -
273B TYR* 4.1 9.2 - - - -
276B GLY* 3.6 24.9 - - - -
277B MET* 4.2 2.5 - - + -
314B LEU* 3.4 34.8 - - + -
318B VAL* 3.5 31.9 - - + -
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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