Contacts of the helix formed by residues 334 - 342 (chain B) in PDB entry 1O69
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 ALA 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B SER* 3.3 26.7 - - - +
80B PHE* 4.3 4.7 - - + +
308B ILE* 5.6 2.4 - - + +
332B TRP 3.8 4.0 + - - -
333B LYS* 1.3 75.2 - - - +
335B MET* 1.3 65.1 + - - +
336B HIS* 3.5 21.3 - - + -
337B THR* 2.7 32.3 + - + +
338B GLN* 3.5 3.1 - - - +
352B SER* 3.6 21.2 + - - +
353B GLU* 5.5 0.4 - - + -
356B PHE* 5.7 0.8 - - - +
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Residues in contact with MET 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A TYR* 6.2 1.3 - - + -
221A HIS* 4.7 4.0 - - + +
79B SER* 2.8 19.9 + - - +
81B THR* 3.5 29.2 - - + +
82B PHE* 4.7 0.2 - - - -
83B ILE* 3.8 33.9 - - + +
86B VAL* 3.9 2.2 - - + -
98B PHE* 3.6 37.5 - - + -
303B ILE* 4.8 1.3 - - - -
332B TRP* 6.3 0.2 - - + -
333B LYS 3.4 26.0 - - - +
334B ALA* 1.3 70.6 - - - +
336B HIS* 1.3 56.8 + - - +
337B THR 3.0 5.6 + - - -
338B GLN* 3.1 34.7 + - + +
341B PHE* 3.7 30.9 - - + +
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Residues in contact with HIS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 2.6 27.7 + - - +
98B PHE* 4.8 1.0 - - + -
100B ASP* 4.4 2.2 + - - -
301B ILE* 4.0 9.9 - - + +
303B ILE* 3.4 28.9 - - + +
304B SER 3.8 4.7 - - - +
306B LYS* 5.5 1.9 - - + +
334B ALA* 3.5 10.7 - - + +
335B MET* 1.3 75.3 - - - +
337B THR* 1.3 62.1 + - + +
338B GLN 3.5 0.7 - - - -
346B ALA* 3.4 28.5 - - + -
348B LEU* 3.5 36.1 - - + +
352B SER* 3.3 26.0 - - - -
353B GLU* 2.7 35.5 + - + +
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Residues in contact with THR 337 (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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304B SER 4.0 7.6 - - - -
305B GLN* 3.4 4.5 - - - +
306B LYS* 2.9 39.8 + - + +
308B ILE* 4.0 20.6 - - + -
333B LYS* 2.8 41.3 + - - +
334B ALA* 2.7 22.4 + - + +
336B HIS* 1.3 103.6 - - + +
338B GLN* 1.3 54.7 + - - +
353B GLU* 4.2 7.6 - - + +
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Residues in contact with GLN 338 (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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219A TYR* 3.0 24.5 + - - +
220A GLU* 3.4 12.5 - - - +
221A HIS* 2.8 40.0 + - + +
303B ILE* 3.6 13.9 - - - +
305B GLN* 4.3 2.2 - - - -
333B LYS* 3.1 30.4 + - - +
334B ALA 3.5 11.9 - - - +
335B MET* 3.1 25.5 + - + +
336B HIS 3.5 1.2 - - - -
337B THR* 1.3 78.3 - - - +
339B GLU* 1.3 65.6 + - - +
340B VAL* 3.9 18.8 - - + -
341B PHE* 3.0 14.3 + - + -
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Residues in contact with GLU 339 (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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220A GLU* 5.1 0.4 + - - -
221A HIS 3.4 2.6 + - - +
222A LEU* 3.7 40.2 - - + +
305B GLN* 3.4 37.7 + - + +
338B GLN* 1.3 70.7 - - - +
340B VAL* 1.3 64.4 + - - +
341B PHE 2.9 1.2 + - - -
342B LYS* 2.9 43.5 + - - +
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Residues in contact with VAL 340 (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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221A HIS* 3.1 19.6 + - + +
222A LEU 3.8 8.2 + - - -
223A ASP* 3.5 32.3 - - - +
224A TYR* 3.6 13.5 - - + +
83B ILE* 3.8 14.4 - - + -
338B GLN* 3.9 7.4 - - + -
339B GLU* 1.3 76.7 - - - +
341B PHE* 1.3 87.6 + - + +
342B LYS* 3.3 2.0 + - - +
403B BME 2.9 44.5 + - - +
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Residues in contact with PHE 341 (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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83B ILE* 4.1 9.6 - - + -
86B VAL* 3.8 22.2 - - + -
87B ALA* 5.4 0.2 - - - -
90B CYS* 3.6 30.3 - - - -
96B PRO* 4.0 12.8 - - + -
98B PHE* 3.6 36.1 - + + -
303B ILE* 3.4 12.7 - - + +
335B MET* 3.7 45.3 - - + +
338B GLN* 3.0 10.0 + - + +
340B VAL* 1.3 99.9 - - + +
342B LYS* 1.3 68.8 + - - +
343B GLY 3.2 0.3 + - - -
344B ALA* 3.0 21.4 + - + +
403B BME 3.7 15.0 - - - -
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Residues in contact with LYS 342 (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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303B ILE* 3.2 16.2 - - - +
304B SER* 4.9 16.8 - - - +
338B GLN 3.7 2.4 + - - -
339B GLU* 2.9 39.4 + - - +
340B VAL 3.3 2.6 - - - +
341B PHE* 1.3 79.3 - - - +
343B GLY* 1.3 62.7 + - - +
344B ALA 3.4 1.7 + - - -
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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