Contacts of the helix formed by residues 249 - 256 (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 ARG 249 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B THR* 3.0 7.7 + - - -
248B THR* 1.3 94.7 - - - +
250B PRO* 1.3 60.3 - - - +
251B ASP* 2.7 43.9 + - - -
252B THR* 2.9 35.0 + - - +
336B MET* 3.7 6.6 - - - +
341B HIS* 5.3 4.8 + - - +
360B ILE* 4.3 4.4 - - - +
376B THR 5.0 5.9 + - - -
377B GLU 3.9 13.1 + - - -
378B LYS* 3.7 43.1 - - - +
392B HIS* 3.6 12.9 - - - -
601B MET* 3.5 39.7 - - + +
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Residues in contact with PRO 250 (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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230B VAL* 3.9 30.1 - - + -
232B ILE* 5.4 0.4 - - + -
247B THR* 3.9 15.4 - - + +
248B THR* 3.3 11.7 - - - +
249B ARG* 1.3 88.3 - - - +
251B ASP* 1.3 62.5 + - - +
252B THR 3.1 0.2 - - - -
253B PHE* 3.0 25.9 + - + +
396B PHE* 3.5 37.9 - - + +
399B ILE* 3.2 25.9 - - + +
400B ALA 4.8 1.3 - - - +
403B LEU* 5.2 2.2 - - + -
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B THR 4.3 0.3 - - - +
249B ARG* 2.7 61.9 + - - -
250B PRO* 1.3 84.5 - - - +
252B THR* 1.3 60.6 + - - +
253B PHE 3.2 1.1 + - - -
254B MET* 4.9 1.0 + - - +
359B VAL* 5.1 0.3 - - - +
360B ILE* 5.0 2.9 - - - +
381B LEU* 3.3 24.8 - - + +
384B SER* 5.6 0.2 + - - -
392B HIS* 3.3 37.9 + - + +
395B ALA* 4.0 6.7 - - + -
396B PHE* 3.8 15.9 - - - +
399B ILE* 3.8 12.5 - - - +
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Residues in contact with THR 252 (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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249B ARG* 2.9 47.6 + - - +
251B ASP* 1.3 78.5 - - - +
253B PHE* 1.3 59.0 + - - +
254B MET 3.1 3.1 - - - -
255B GLY* 2.8 26.1 + - - -
336B MET* 3.6 3.8 - - - +
338B VAL* 3.6 18.4 - - - +
341B HIS* 4.6 0.4 - - + -
359B VAL* 3.8 8.4 - - - +
360B ILE* 3.5 19.3 - - + -
601B MET* 3.4 28.0 - - + +
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Residues in contact with PHE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.9 18.6 - - + -
234B PHE* 3.5 36.8 - + - -
250B PRO* 3.0 25.2 + - + +
251B ASP 3.2 1.8 + - - -
252B THR* 1.3 78.4 + - - +
254B MET* 1.3 61.3 + - - +
256B CYS* 3.1 17.9 + - + -
311B HIS* 3.0 50.5 + + - -
312B PRO* 3.8 17.0 - - + -
313B LEU* 3.9 14.8 - - + -
336B MET* 3.4 27.4 - - - -
399B ILE* 4.0 12.1 - - + +
403B LEU* 4.0 14.4 - - + -
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Residues in contact with MET 254 (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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251B ASP 4.9 0.4 + - - +
252B THR 3.0 1.0 + - - -
253B PHE* 1.3 77.5 - - - +
255B GLY* 1.3 59.0 + - - +
256B CYS 3.2 4.7 + - - +
311B HIS* 4.3 5.6 + - - -
313B LEU* 3.7 47.1 - - + +
314B THR* 3.7 24.7 + - - +
357B LYS* 3.1 25.6 + - - +
359B VAL* 3.8 5.2 - - + -
381B LEU* 5.7 0.2 - - + -
383B ASN 4.4 2.7 - - - +
384B SER* 3.6 52.9 - - - +
385B GLY* 4.8 2.2 - - - +
387B PHE* 4.2 14.4 - - + -
399B ILE* 4.3 8.3 - - + +
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Residues in contact with GLY 255 (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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252B THR 2.8 11.0 + - - -
254B MET* 1.3 77.4 - - - +
256B CYS* 1.3 60.7 + - - +
257B THR* 3.2 16.0 + - - +
338B VAL* 3.6 23.0 - - - +
339B PRO* 4.1 1.6 - - - +
357B LYS* 4.0 14.6 - - - +
359B VAL* 3.5 23.3 - - - +
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Residues in contact with CYS 256 (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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234B PHE* 5.0 0.2 - - - -
253B PHE* 3.1 30.0 + - + +
254B MET 3.2 3.1 - - - +
255B GLY* 1.3 75.8 - - - +
257B THR* 1.3 59.4 + - - +
258B TYR 3.5 15.5 - - - -
259B LEU* 4.1 3.4 - - - -
311B HIS* 3.6 17.1 - - + -
316B GLU* 5.7 0.9 - - - +
318B ILE* 3.9 22.4 - - - +
336B MET* 3.7 29.6 - - + -
337B ALA 3.4 18.4 - - - +
338B VAL* 3.8 3.5 - - + +
357B LYS* 6.0 0.2 - - - +
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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
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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