Contacts of the helix formed by residues 296 - 301 (chain B) in PDB entry 1XO2
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 SER 296 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292B TYR* 4.4 7.3 + - - -
293B SER* 2.9 17.4 + - - -
295B LEU* 1.3 78.9 - - - +
297B HIS* 1.3 66.2 + - - +
298B PRO* 3.6 3.5 - - - +
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Residues in contact with HIS 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.1 30.6 + - + -
275B ASP* 2.9 26.6 + - - -
276B LEU* 3.6 27.8 - - + +
279B LYS* 4.8 6.7 - - + -
289B ILE* 4.7 10.3 - - + -
293B SER 3.1 7.5 + - - +
294B ALA* 3.4 21.2 + - - +
296B SER* 1.3 79.4 - - - +
298B PRO* 1.3 84.8 - - + +
299B TYR* 2.7 36.0 + - + +
300B PHE* 3.1 21.5 + - + +
301B GLN 4.2 1.2 + - - -
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Residues in contact with PRO 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.9 31.7 - - + +
296B SER 3.6 3.8 - - - +
297B HIS* 1.3 96.7 - - + +
299B TYR* 1.3 55.8 + - - +
300B PHE 2.8 12.9 + - - -
301B GLN* 3.0 26.5 + - + +
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR 3.9 5.6 + - - -
122B ILE* 4.1 3.8 - - - +
123B LYS* 3.1 75.7 + - + +
126B MET* 4.8 1.3 - - + -
209B PHE* 4.0 25.3 - + - -
213B PHE* 4.4 3.5 - + - -
270B ASP* 4.5 18.4 - - + -
272B LEU* 3.9 13.9 - - + +
273B GLY* 3.3 29.6 - - - -
276B LEU* 3.9 11.9 - - + -
297B HIS* 2.7 30.8 + - + +
298B PRO* 1.3 70.5 - - - +
300B PHE* 1.3 81.4 + + + +
301B GLN 3.7 0.2 - - - -
302B ASP 5.4 0.4 + - - -
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Residues in contact with PHE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LYS* 3.7 31.6 - - + -
126B MET* 4.2 6.5 - - + -
127B PHE* 3.7 37.2 - + + -
130B LEU* 3.7 25.1 - - + -
276B LEU* 4.0 14.8 - - + -
294B ALA 2.9 29.4 - - - -
295B LEU* 4.3 7.4 - - - +
297B HIS* 3.1 17.4 + - + +
298B PRO 2.9 0.8 - - - -
299B TYR* 1.3 105.3 - + - +
301B GLN* 1.3 65.7 + - - +
302B ASP* 2.8 8.7 + - - -
303B LEU* 3.7 13.2 + - + +
305B ARG* 5.5 3.6 - - - +
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Residues in contact with GLN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B HIS 4.2 1.6 + - - -
298B PRO* 3.0 23.5 + - + +
299B TYR 3.7 0.2 - - - -
300B PHE* 1.3 75.3 - - - +
302B ASP* 1.3 62.8 + - + +
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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