Contacts of the helix formed by residues 265 - 273 (chain B) in PDB entry 2AJH
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 HIS 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B TYR* 4.9 2.2 - + - -
242B THR 4.9 4.5 - - - -
243B LEU* 3.3 29.4 - - + +
244B THR 5.7 0.6 + - - -
261B VAL* 3.8 18.8 - - + -
262B ALA 2.7 23.6 + - - +
263B ALA 3.4 1.0 - - - -
264B GLY* 1.3 71.6 - - - -
266B PRO* 1.3 86.9 - - + +
267B LEU* 3.1 24.8 + - + +
268B ALA* 2.7 18.2 + - - +
269B GLN* 2.9 11.5 + - - +
328B MET* 3.9 12.0 - - - +
332B THR 3.7 13.4 + - - -
333B GLY 3.4 28.2 - - - -
334B ALA* 4.8 0.8 - - - +
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Residues in contact with PRO 266 (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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239B TYR* 3.6 11.2 - - - +
264B GLY 3.6 6.2 - - - +
265B HIS* 1.3 99.0 - - + +
267B LEU* 1.3 50.9 + - - +
269B GLN* 3.1 16.0 + - + +
270B LYS* 2.7 34.5 + - - +
328B MET* 4.4 11.9 - - + -
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Residues in contact with LEU 267 (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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236B VAL* 4.1 24.0 - - + -
239B TYR* 3.1 31.0 + - + +
243B LEU* 4.0 28.5 - - + -
261B VAL* 4.3 5.4 - - + -
265B HIS* 2.9 19.3 + - + +
266B PRO* 1.3 75.2 - - - +
268B ALA* 1.3 66.7 + - - +
270B LYS* 3.4 2.3 + - - +
271B ALA* 3.0 20.8 + - - +
305B THR* 3.7 35.0 - - + +
307B PHE* 4.0 14.4 - - + -
320B VAL* 3.9 11.9 - - + -
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Residues in contact with ALA 268 (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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261B VAL* 4.2 10.5 - - + -
262B ALA 3.7 20.0 - - - +
263B ALA* 3.9 14.6 - - - +
265B HIS* 2.7 16.2 + - - +
267B LEU* 1.3 80.0 - - - +
269B GLN* 1.3 49.5 + - - +
271B ALA* 3.2 5.6 + - - -
272B ALA* 2.8 31.0 + - - +
278B LEU* 3.5 12.3 - - + +
282B ILE* 4.3 6.9 - - + +
305B THR* 4.8 1.1 - - - -
322B ALA* 4.7 9.9 - - + -
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Residues in contact with GLN 269 (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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263B ALA 4.3 2.8 - - - +
264B GLY* 3.4 33.3 + - - +
265B HIS 2.9 5.7 + - - +
266B PRO* 3.3 14.5 - - + +
268B ALA* 1.3 71.8 - - - +
270B LYS* 1.3 65.3 + - - +
271B ALA 3.1 1.3 - - - -
272B ALA* 3.0 22.8 + - + +
273B GLU* 3.5 12.4 + - - +
282B ILE* 4.6 9.9 - - + +
286B ARG* 4.4 10.4 + - - -
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Residues in contact with LYS 270 (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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238B ASP 6.0 2.0 - - - -
239B TYR* 3.9 29.6 - - + +
240B ASP* 6.5 0.4 - - + -
266B PRO 2.7 18.7 + - - +
267B LEU 3.8 5.2 - - - +
269B GLN* 1.3 72.1 - - - +
271B ALA* 1.3 58.3 + - - +
273B GLU* 2.7 57.5 + - - +
274B ASN* 4.9 0.3 + - - -
307B PHE* 4.4 10.8 - - + -
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Residues in contact with ALA 271 (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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267B LEU 3.0 17.3 + - - +
268B ALA 3.5 4.7 - - - +
270B LYS* 1.3 75.5 - - - +
272B ALA* 1.3 66.2 + - - +
273B GLU 3.3 0.8 + - - -
274B ASN 3.5 9.9 + - - +
275B ASN* 3.6 15.2 - - - +
278B LEU* 3.6 9.9 - - + -
305B THR* 3.5 28.8 - - - +
307B PHE* 3.6 17.9 - - + -
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Residues in contact with ALA 272 (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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268B ALA 2.8 12.9 + - - +
269B GLN* 3.0 14.1 + - + +
271B ALA* 1.3 74.7 - - - +
273B GLU* 1.3 67.8 + - - +
274B ASN 2.8 2.1 + - - -
275B ASN 2.9 23.8 + - - +
276B PRO* 5.0 0.5 - - - +
278B LEU* 4.0 7.6 - - + -
279B ALA* 4.8 14.1 - - + +
282B ILE* 4.0 21.1 - - + -
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Residues in contact with GLU 273 (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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269B GLN 3.5 7.9 + - - +
270B LYS* 2.7 53.7 + - - +
272B ALA* 1.3 77.3 - - - +
274B ASN* 1.3 76.4 + - - +
275B ASN 3.9 0.3 + - - -
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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