Contacts of the helix formed by residues 333 - 343 (chain A) in PDB entry 3HA6
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 THR 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 5.4 1.8 - - - -
331A ALA* 3.2 3.0 - - - +
332A ASN* 1.3 87.9 - - + +
334A TYR* 1.3 63.4 + - - +
335A GLN* 3.5 18.7 + - - +
336A GLU* 3.2 31.5 + - - +
337A THR* 3.1 23.6 + - - -
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Residues in contact with TYR 334 (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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293A LEU* 3.6 31.3 - - + +
333A THR* 1.3 70.8 - - - +
335A GLN* 1.3 105.4 + - + +
337A THR* 3.4 0.9 + - - -
338A TYR* 3.0 57.8 + + + +
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Residues in contact with GLN 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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333A THR* 3.5 21.2 - - - +
334A TYR* 1.3 124.1 + - + +
336A GLU* 1.3 63.4 + - + +
338A TYR* 3.4 8.0 + - - +
339A LYS* 3.2 32.1 + - - +
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ALA* 3.8 11.9 - - + +
332A ASN* 4.2 22.2 + - - +
333A THR* 3.2 22.2 + - - +
335A GLN* 1.3 75.0 - - + +
337A THR* 1.3 67.0 + - - +
339A LYS* 3.1 17.4 + - + +
340A ARG* 3.0 46.5 + - - +
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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
----------------------------------------------------------
293A LEU* 3.8 24.2 - - + +
294A ASP* 3.8 17.5 + - - +
329A PHE* 3.3 29.9 + - + +
331A ALA* 3.7 13.9 + - - +
333A THR 3.1 13.1 + - - -
334A TYR 3.4 7.2 + - - -
336A GLU* 1.3 75.8 - - - +
338A TYR* 1.3 58.7 + - - +
340A ARG* 3.1 4.5 + - - +
341A ILE* 2.9 52.3 + - + +
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 5.3 8.8 - - + +
293A LEU* 3.9 18.9 - - + +
296A LEU* 3.7 31.1 - - + +
301A ILE* 3.7 40.3 - - + +
334A TYR* 3.0 48.4 + + + +
335A GLN* 3.4 9.0 - - - +
336A GLU 3.2 0.2 - - - -
337A THR* 1.3 78.3 - - - +
339A LYS* 1.3 61.4 + - + +
341A ILE* 3.6 2.2 + - + -
342A SER* 3.0 25.5 + - - -
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Residues in contact with LYS 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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335A GLN* 3.2 18.8 + - - +
336A GLU* 3.1 19.1 + - + +
338A TYR* 1.3 78.7 - - + +
340A ARG* 1.3 57.4 + - + +
342A SER* 3.3 7.8 + - - -
343A ARG* 2.9 70.8 + - - +
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Residues in contact with ARG 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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328A PRO 5.2 3.6 + - - -
329A PHE* 3.9 26.6 - - + +
330A GLU 3.3 18.2 + - - -
331A ALA* 4.0 17.6 - - - +
336A GLU* 3.0 37.5 + - - +
337A THR 3.1 6.3 + - - +
339A LYS* 1.3 75.4 - - + +
341A ILE* 1.3 58.2 + - - +
343A ARG 3.2 1.2 + - - -
344A VAL 2.8 8.7 + - - -
345A GLU* 2.7 71.6 + - + +
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Residues in contact with ILE 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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293A LEU 3.6 23.3 - - - +
294A ASP 4.6 2.9 - - - +
296A LEU* 3.3 26.7 - - + +
298A PRO* 3.7 15.6 - - - +
301A ILE* 3.5 28.9 - - + -
313A TRP* 3.5 18.5 - - + -
329A PHE* 3.6 30.1 - - + -
337A THR* 2.9 31.8 + - + +
338A TYR* 4.6 1.3 - - + -
340A ARG* 1.3 69.3 - - - +
342A SER* 1.3 66.3 + - - +
344A VAL* 3.0 19.8 + - - +
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Residues in contact with SER 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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298A PRO* 4.3 3.8 - - - -
301A ILE* 4.6 8.7 - - - +
302A GLU* 2.8 31.6 + - - +
338A TYR 3.0 20.4 + - - -
339A LYS* 3.3 8.3 - - - -
341A ILE* 1.3 75.8 - - - +
343A ARG* 1.3 61.6 + - - +
366A HIS* 3.1 26.3 + - - -
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Residues in contact with ARG 343 (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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339A LYS* 2.9 57.1 + - - +
340A ARG 3.8 3.1 - - - +
341A ILE 3.2 0.2 - - - -
342A SER* 1.3 78.4 - - - +
344A VAL* 1.3 70.2 + - - +
345A GLU* 3.2 30.8 + - + +
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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