Contacts of the helix formed by residues 378 - 387 (chain B) 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 LYS 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B TYR* 3.7 25.4 - - - +
288B ASN* 2.8 16.0 + - - +
336B HIS* 3.2 30.6 + - + +
337B PHE* 3.3 32.3 - - + -
347B MET* 4.3 11.7 - - - -
377B ASP* 1.3 82.5 + - - +
379B ALA* 1.3 65.2 + - - +
380B LEU 3.4 2.2 - - - -
381B ALA* 3.2 15.1 + - + +
382B LEU* 3.0 26.5 + - + +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ASN* 3.1 17.6 + - - +
291B ALA* 3.9 17.9 - - + +
292B ALA* 3.3 28.6 - - - +
376B ALA* 3.4 17.5 + - + +
377B ASP 3.6 0.4 - - - -
378B LYS* 1.3 76.4 - - - +
380B LEU* 1.3 68.4 + - + +
382B LEU 3.2 2.1 + - - -
383B ALA* 2.9 26.4 + - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ALA 6.0 0.4 - - - +
376B ALA 5.6 1.1 - - - +
377B ASP 5.5 0.6 - - - -
378B LYS 3.4 0.4 - - - -
379B ALA* 1.3 88.7 - - + +
381B ALA* 1.3 57.2 + - - +
383B ALA* 3.4 6.4 + - - +
384B GLU* 2.9 30.5 + - - +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B HIS* 3.7 23.4 - - + +
377B ASP 5.8 0.2 - - - +
378B LYS* 3.2 17.9 + - + +
380B LEU* 1.3 80.3 - - - +
382B LEU* 1.3 56.4 + - - +
384B GLU* 3.5 7.3 + - - +
385B ALA* 3.0 28.1 + - - +
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Residues in contact with LEU 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ASN* 3.9 38.4 - - + +
289B ILE* 4.2 12.3 - - + +
292B ALA* 3.9 8.3 - - + -
294B LEU* 4.2 13.8 - - + +
329B ILE* 6.4 0.7 - - + -
332B LEU* 4.2 24.0 - - + +
333B VAL* 5.1 2.5 - - + +
336B HIS* 4.2 25.6 - - + -
337B PHE* 3.9 20.0 - - + -
378B LYS* 3.0 13.6 + - + +
379B ALA 3.6 6.5 - - - +
381B ALA* 1.3 74.5 - - - +
383B ALA* 1.3 64.7 + - - +
385B ALA* 3.3 3.9 + - - +
386B ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ALA* 3.4 27.0 - - - +
294B LEU* 4.4 9.6 - - - +
379B ALA 2.9 15.1 + - - +
380B LEU* 3.7 8.1 - - + +
382B LEU* 1.3 76.6 - - - +
384B GLU* 1.3 61.4 + - - +
386B ALA* 3.5 1.4 + - - +
387B GLY 3.1 28.2 + - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LEU 2.9 18.7 + - - +
381B ALA* 3.6 8.3 - - - +
382B LEU 3.2 0.2 - - - -
383B ALA* 1.3 78.4 - - - +
385B ALA* 1.3 61.9 + - - +
386B ALA 3.5 0.2 + - - -
387B GLY* 3.6 10.4 + - - -
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B LEU* 3.7 21.9 - - + +
335B GLU* 6.0 0.2 - - - +
336B HIS* 3.7 22.2 - - + +
381B ALA 3.0 17.5 + - - +
382B LEU* 3.3 3.8 + - - +
384B GLU* 1.3 78.6 - - - +
386B ALA* 1.3 61.9 + - - +
387B GLY 3.6 0.2 + - - -
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LEU* 3.4 32.8 - - + -
324B VAL* 3.9 28.8 - - + +
328B THR* 6.1 1.3 - - - -
332B LEU* 4.2 18.3 - - + +
382B LEU 3.1 10.5 + - - +
383B ALA 3.9 2.7 - - - +
384B GLU 3.3 0.4 - - - -
385B ALA* 1.3 78.0 - - - +
387B GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ALA 3.1 17.5 + - - +
384B GLU* 3.6 7.1 + - - -
385B ALA 3.4 2.8 - - - -
386B ALA* 1.3 81.6 - - - +
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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