Contacts of the helix formed by residues 355 - 360 (chain D) in PDB entry 3IML
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 TYR 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D ASP* 3.5 12.3 - - + +
29D LEU* 3.8 27.4 - - + -
30D ASP* 2.8 15.5 + - - +
33D LEU* 3.9 11.0 - - + -
271D PRO* 3.4 13.9 - - + +
276D ARG* 3.5 31.0 - - - +
280D TYR* 3.8 25.8 - + - -
350D LEU* 2.5 46.5 + - - +
352D ARG 3.2 27.1 - - - -
354D ILE* 1.3 90.6 - - + +
356D GLU* 1.3 64.9 + - - +
357D LYS 3.2 1.8 - - - -
358D THR* 2.8 27.3 + - + -
359D ALA 3.5 0.3 + - - -
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Residues in contact with GLU 356 (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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23D GLN* 3.9 16.9 - - + +
26D ASP* 3.6 12.9 - - - +
27D ALA* 3.4 27.4 - - - +
30D ASP* 2.9 19.0 + - - +
73D THR* 3.5 15.0 + - - +
76D ARG* 3.0 41.1 + - - +
355D TYR* 1.3 75.0 - - - +
357D LYS* 1.3 57.5 + - - +
359D ALA* 3.0 25.5 + - - +
360D ALA 4.4 0.3 + - - -
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Residues in contact with LYS 357 (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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354D ILE* 3.8 13.0 - - - +
355D TYR 4.5 0.2 - - - +
356D GLU* 1.3 80.5 - - + +
358D THR* 1.3 58.8 + - - +
359D ALA 3.3 0.7 + - - -
360D ALA* 3.6 4.7 + - - +
366D ARG* 2.9 30.6 + - - +
368D GLU* 4.7 18.5 + - + +
369D PRO* 6.3 1.2 - - - +
370D GLU* 5.0 13.5 - - - +
371D PHE* 3.7 21.5 - - + -
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Residues in contact with THR 358 (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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26D ASP* 3.8 0.2 + - - -
253D ASP* 4.7 0.2 - - - +
276D ARG* 3.0 8.5 + - - -
280D TYR* 3.8 11.2 - - - +
354D ILE 3.6 18.2 - - - +
355D TYR* 2.8 18.6 + - + +
357D LYS* 1.3 76.3 - - - +
359D ALA* 1.3 55.8 + - - +
360D ALA* 3.1 8.0 + - - -
362D GLY 3.8 3.4 + - - +
363D HIS* 3.0 50.2 + - - -
366D ARG* 3.6 13.9 + - - +
371D PHE* 3.7 17.9 - - + -
373D TRP* 3.9 15.9 - - + -
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Residues in contact with ALA 359 (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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19D LYS* 2.6 35.8 + - - +
22D ASP* 3.9 5.0 - - - +
23D GLN* 3.4 31.9 - - + +
26D ASP* 3.8 17.5 - - + +
267D SER* 4.2 3.1 - - - +
356D GLU 3.0 17.7 + - - +
358D THR* 1.3 79.6 + - - +
360D ALA* 1.3 54.8 + - - +
363D HIS* 4.3 6.5 - - - -
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Residues in contact with ALA 360 (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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14D GLU* 3.8 24.9 - - + +
19D LYS* 4.1 11.2 - - + +
23D GLN* 3.8 22.0 - - - +
356D GLU 4.4 1.0 + - - -
357D LYS 3.6 4.3 + - - +
358D THR 3.1 0.8 + - - -
359D ALA* 1.3 79.2 - - - +
361D TYR* 1.3 73.6 + - + +
362D GLY 3.3 3.1 - - - +
366D ARG* 2.7 30.5 + - - -
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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