Contacts of the helix formed by residues 334 - 342 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A SER* 3.4 20.4 - - - +
80A PHE* 4.5 3.8 - - - +
81A THR 5.1 0.2 - - - +
308A ILE* 5.0 3.2 - - + +
332A TRP 3.7 4.2 + - - -
333A LYS* 1.3 75.0 - - - +
335A MET* 1.3 67.0 + - - +
336A HIS* 3.6 12.6 - - + +
337A THR* 2.7 29.7 + - + -
338A GLN* 3.5 3.8 - - - +
352A SER* 3.4 36.2 + - - +
353A GLU* 5.2 1.6 - - + +
356A PHE* 5.8 0.4 - - - +
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Residues in contact with MET 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 2.8 20.2 + - - +
81A THR* 3.5 34.3 - - + +
83A ILE* 3.8 32.8 - - + +
86A VAL* 4.0 2.7 - - + -
98A PHE* 3.6 35.0 - - + -
303A ILE* 4.7 0.9 - - - -
333A LYS 3.5 20.8 + - - +
334A ALA* 1.3 70.1 - - - +
336A HIS* 1.3 58.0 + - - +
337A THR 3.1 0.4 - - - -
338A GLN* 3.1 38.8 + - + +
341A PHE* 3.5 34.6 - - + +
219B TYR* 6.2 1.6 - - + -
221B HIS* 4.7 4.3 - - + +
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Residues in contact with HIS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 2.7 29.9 + - - +
98A PHE* 4.8 0.6 - - + -
100A ASP* 4.2 7.4 - - - -
301A ILE* 4.1 9.1 - - + +
303A ILE* 3.5 29.4 - - + +
304A SER 3.8 5.2 - - - +
306A LYS* 5.5 1.8 - - + +
334A ALA* 3.1 10.2 - - + +
335A MET* 1.3 76.1 - - - +
337A THR* 1.3 60.4 + - + +
338A GLN 3.5 0.2 - - - -
346A ALA* 3.6 27.6 - - + -
348A LEU* 3.5 31.6 - - + +
352A SER* 3.3 24.5 - - - -
353A GLU* 2.7 34.3 + - + +
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Residues in contact with THR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A SER 4.2 5.4 - - - -
305A GLN* 3.3 7.3 - - - +
306A LYS* 3.0 44.1 + - + -
308A ILE* 4.1 15.9 - - + -
333A LYS* 2.9 35.9 + - - +
334A ALA* 2.7 21.3 + - + +
336A HIS* 1.3 104.0 - - + +
338A GLN* 1.3 58.1 + - - +
353A GLU* 4.0 6.3 - - + +
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.7 14.2 - - - +
305A GLN* 4.3 2.7 - - - -
333A LYS* 3.1 31.1 + - - +
334A ALA 3.5 12.8 - - - +
335A MET* 3.1 26.7 + - + +
336A HIS 3.5 0.8 - - - -
337A THR* 1.3 78.1 - - - +
339A GLU* 1.3 65.9 - - - +
340A VAL* 3.8 19.3 - - + -
341A PHE* 3.0 13.3 + - + +
219B TYR* 2.9 25.7 + - - +
220B GLU* 3.2 15.8 - - - +
221B HIS* 2.9 35.2 + - + +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A GLN* 3.4 37.7 + - + +
338A GLN* 1.3 72.6 - - - +
340A VAL* 1.3 64.6 + - - +
341A PHE 3.0 1.4 + - - -
342A LYS* 3.0 47.4 + - - +
220B GLU* 4.8 0.2 + - - -
221B HIS 3.5 4.1 + - - +
222B LEU* 3.7 39.7 - - + +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 3.8 3.8 - - + -
338A GLN* 3.8 7.0 - - + -
339A GLU* 1.3 76.1 - - - +
341A PHE* 1.3 88.4 + - + +
342A LYS 3.3 2.0 + - - +
403A BME 3.1 33.2 + - - +
221B HIS* 3.2 28.3 + - + +
222B LEU 3.8 8.7 + - - -
223B ASP* 3.4 38.6 - - - +
224B TYR* 3.5 12.8 - - + +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.1 12.1 - - + -
86A VAL* 3.7 22.0 - - + -
87A ALA* 5.5 0.2 - - - -
90A CYS* 3.8 29.8 - - - -
96A PRO* 4.0 11.2 - - + -
98A PHE* 3.6 35.4 - + + -
303A ILE* 3.3 19.3 - - + +
335A MET* 3.5 41.7 - - + +
338A GLN* 3.0 8.3 + - + +
340A VAL* 1.3 98.3 - - + +
342A LYS* 1.3 67.6 + - - +
343A GLY 3.2 0.2 + - - -
344A ALA* 2.9 19.4 + - + +
403A BME 3.9 13.7 - - - -
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ILE* 3.4 16.2 - - - +
304A SER* 4.8 9.9 - - - +
338A GLN 3.7 2.8 + - - -
339A GLU* 3.0 42.7 + - - +
340A VAL 3.3 2.7 - - - +
341A PHE* 1.3 78.9 - - - +
343A GLY* 1.3 62.2 + - - +
344A ALA* 3.4 2.1 + - - +
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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