Contacts of the helix formed by residues 321 - 325 (chain D) in PDB entry 1I2M
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 321 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D GLY 3.6 0.8 + - - -
320D ARG* 1.3 75.9 - - - +
322D GLU* 1.3 73.8 + - - +
324D GLY* 3.1 16.8 + - - -
325D ARG* 3.8 1.1 + - - -
326D LEU* 3.7 15.7 + - + -
332D ALA* 3.6 28.8 - - + +
333D GLU* 3.6 22.7 - - - -
334D GLU* 3.8 4.1 - - - +
386D TRP* 3.4 9.8 - - - -
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Residues in contact with GLU 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ARG* 5.7 1.0 - - - -
77C ASP* 5.0 2.1 - - - +
110C ARG* 3.9 29.3 + - - +
269D TYR* 4.4 9.2 + - - -
320D ARG* 2.7 52.7 + - - +
321D ALA* 1.3 81.3 + - - +
323D TYR* 1.3 73.6 + - + +
324D GLY 3.2 0.5 + - - -
325D ARG* 2.9 31.5 + - - +
334D GLU* 5.7 1.0 - - - +
386D TRP* 4.4 4.7 - - - -
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Residues in contact with TYR 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 5.2 3.6 - - + -
106C ARG* 3.3 58.1 + - + -
107C ASP* 2.6 31.6 + - - -
110C ARG* 2.9 31.2 + - + -
320D ARG* 4.4 0.7 - - - -
321D ALA 3.4 0.2 + - - -
322D GLU* 1.3 71.5 - - + +
324D GLY* 1.3 55.7 + - - +
325D ARG* 3.3 27.1 - - - +
355D SER* 5.3 0.2 - - - -
370D GLY 3.0 24.8 - - - +
371D MET* 3.9 34.1 - - + +
384D ASP* 3.4 19.2 - - - +
385D ALA 4.3 0.2 - - - +
386D TRP* 3.7 18.9 - + - -
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Residues in contact with GLY 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D ALA 3.1 8.2 + - - -
323D TYR* 1.3 78.7 - - - +
325D ARG* 1.3 58.6 + - - +
326D LEU 3.1 4.0 - - - -
327D GLY* 3.0 19.5 + - - -
332D ALA* 6.2 0.4 - - - -
369D TRP* 3.4 7.6 - - - -
370D GLY* 3.5 7.7 + - - -
385D ALA 3.5 3.8 - - - +
386D TRP* 3.4 39.9 - - - +
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Residues in contact with ARG 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D GLN* 5.4 2.4 + - - -
304D HIS* 4.0 12.3 + - - +
305D HIS* 3.3 45.7 + - + +
307D VAL* 4.7 0.5 - - - +
320D ARG* 3.0 75.1 + - - +
321D ALA 3.8 0.8 + - - -
322D GLU* 2.9 24.3 + - - +
323D TYR* 3.3 25.9 - - - -
324D GLY* 1.3 75.7 - - - +
326D LEU* 1.3 56.6 + - - +
327D GLY 3.3 0.2 - - - -
354D ALA 4.3 4.8 + - - -
355D SER* 3.6 44.3 + - - +
356D VAL* 5.1 0.4 - - - +
357D GLY 4.6 0.2 + - - -
369D TRP* 2.9 18.9 + - - -
370D GLY* 3.8 9.9 - - - -
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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