Contacts of the helix formed by residues 331 - 336 (chain A) in PDB entry 4I2C
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 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A THR 3.6 11.0 - - - +
330A MET* 1.3 83.6 - - - +
332A GLY* 1.3 70.4 + - - +
334A PHE* 4.0 4.7 + - - +
335A ARG* 3.5 16.1 + - - +
345A ASP* 2.8 38.1 + - - +
346A PHE 3.9 1.7 + - - -
347A LEU* 4.0 16.4 - - + +
447A LEU* 3.7 27.8 - - + -
450A TRP* 3.5 28.4 + - + +
451A THR* 4.3 1.1 - - - -
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Residues in contact with GLY 332 (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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331A THR* 1.3 82.9 + - - +
333A GLY* 1.3 63.9 + - - -
335A ARG* 3.1 9.5 + - - +
336A ARG* 3.4 13.3 + - - +
345A ASP* 3.7 10.1 - - - -
450A TRP 2.9 17.5 + - - -
451A THR* 3.5 13.0 - - - +
602A APC 3.3 14.8 - - - -
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Residues in contact with GLY 333 (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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332A GLY* 1.3 69.2 - - - -
334A PHE* 1.3 57.1 + - - +
336A ARG* 3.0 32.5 + - - +
337A GLY 3.3 0.3 + - - -
338A LYS* 3.1 43.9 + - - +
602A APC 2.8 23.6 + - - -
604A MN 4.4 1.0 + - - -
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Residues in contact with PHE 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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303A VAL* 3.3 25.1 - - + -
304A ASN 4.0 16.6 - - - -
305A ARG* 4.0 10.1 - - + -
308A ALA* 3.9 18.6 - - + -
330A MET* 3.5 25.8 - - + -
331A THR 4.0 2.7 + - - +
332A GLY 3.3 1.0 - - - -
333A GLY* 1.3 75.3 - - - +
335A ARG* 1.4 61.3 + - - +
337A GLY* 3.1 14.6 + - - -
338A LYS 3.4 16.8 - - - +
339A MET 3.8 20.9 - - - -
340A THR 3.8 6.3 - - - -
341A GLY* 3.5 13.2 - - - -
343A ASP 3.3 26.9 - - - -
344A VAL* 4.2 13.0 - - + -
345A ASP 5.7 0.2 - - - -
602A APC 5.0 1.8 - - - -
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Residues in contact with ARG 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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329A THR* 4.3 7.0 - - - +
330A MET* 3.4 29.1 + - - +
331A THR* 3.5 8.0 + - - +
332A GLY 3.1 11.8 + - - +
334A PHE* 1.4 77.8 - - - +
336A ARG* 1.3 57.2 + - - +
337A GLY 3.3 3.1 + - - -
447A LEU* 3.6 26.9 - - - +
451A THR* 2.9 30.6 + - + +
491A GLU* 3.1 33.5 + - - -
502A TYR* 5.0 1.4 + - - -
505A PRO* 3.6 37.8 - - + +
506A TRP* 4.4 4.3 + - - +
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Residues in contact with ARG 336 (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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161A LEU* 3.8 3.8 - - - +
332A GLY* 3.4 1.7 + - - +
333A GLY* 3.0 30.1 + - - +
335A ARG* 1.3 74.3 - - - +
337A GLY* 1.3 58.7 + - - +
338A LYS* 3.5 13.9 - - - +
451A THR* 2.8 48.4 + - + +
452A GLY* 3.7 3.9 - - - -
453A SER* 3.5 39.8 - - - +
505A PRO 3.4 18.8 - - - +
506A TRP* 3.3 14.2 - - - +
508A ARG 3.5 13.5 - - - -
509A ASN* 3.0 40.0 + - - +
602A APC 3.2 29.3 + - - -
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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