Contacts of the helix formed by residues 325 - 337 (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 SER 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B VAL* 1.3 77.5 - - - +
326B ASP* 1.3 64.6 + - - +
327B GLU* 3.6 19.6 - - - +
328B THR* 3.0 29.6 + - - -
329B ILE* 3.0 18.0 + - - +
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Residues in contact with ASP 326 (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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316B VAL* 3.4 23.2 - - - +
317B ASN* 3.5 8.8 - - - +
318B THR* 2.7 50.5 + - - +
319B PHE 4.6 0.5 + - - -
320B GLY 5.4 1.2 + - - -
322B GLY* 5.0 0.2 - - - -
324B VAL 3.5 1.1 + - - +
325B SER* 1.3 72.0 - - - +
327B GLU* 1.3 66.5 + - - +
329B ILE* 3.4 9.4 + - - +
330B THR* 2.8 33.1 + - - -
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Residues in contact with GLU 327 (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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2A ALA 4.4 9.4 - - - +
3A ASN* 4.0 6.5 - - - +
4A ASP* 3.1 46.1 + - + +
5A TYR* 5.4 0.5 - - - +
325B SER* 3.6 21.9 - - - +
326B ASP* 1.3 87.5 + - - +
328B THR* 1.3 56.6 + - - +
330B THR* 3.4 8.8 + - - -
331B LYS* 2.9 35.9 + - + +
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Residues in contact with THR 328 (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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324B VAL* 4.3 15.9 - - + -
325B SER* 3.0 27.4 + - - -
327B GLU* 1.3 75.5 - - - +
329B ILE* 1.3 59.9 + - - +
331B LYS* 3.2 12.4 + - + +
332B LEU* 2.9 43.3 + - + +
386B ALA* 6.1 1.1 - - - -
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Residues in contact with ILE 329 (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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289B ILE* 3.7 35.9 - - + -
294B LEU* 4.3 20.4 - - + -
316B VAL* 3.7 11.2 - - + -
318B THR* 3.6 28.3 - - + -
322B GLY* 4.7 6.1 - - - -
324B VAL* 3.4 36.6 - - + +
325B SER 3.0 12.5 + - - +
326B ASP* 3.5 10.1 - - - +
328B THR* 1.3 72.2 - - - +
330B THR* 1.3 62.1 + - - +
332B LEU* 3.1 11.1 + - + +
333B VAL* 2.8 28.6 + - + +
382B LEU* 6.4 0.7 - - + -
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Residues in contact with THR 330 (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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314B VAL* 3.8 36.8 - - + +
315B MET* 4.1 1.4 - - - -
316B VAL* 3.2 29.5 + - - +
326B ASP 2.8 22.8 + - - -
327B GLU* 3.4 13.5 - - - +
328B THR 3.3 0.2 - - - -
329B ILE* 1.3 76.7 - - - +
331B LYS* 1.3 63.0 + - + +
333B VAL* 3.3 13.2 + - - +
334B ARG* 3.3 18.4 + - + +
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Residues in contact with LYS 331 (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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327B GLU* 2.9 21.4 + - - +
328B THR* 3.2 15.5 + - + +
330B THR* 1.3 78.8 - - + +
332B LEU* 1.3 61.6 - - + +
334B ARG* 3.2 19.8 + - - +
335B GLU* 3.3 22.5 + - - +
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Residues in contact with LEU 332 (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* 4.7 9.4 - - + -
324B VAL* 4.9 1.8 - - + -
328B THR* 2.9 37.2 + - + +
329B ILE* 3.1 12.1 + - + +
331B LYS* 1.3 70.4 - - + +
333B VAL* 1.3 65.7 + - - +
335B GLU* 3.1 17.5 + - - +
336B HIS* 3.0 37.3 + - + +
382B LEU* 4.2 17.0 - - + +
385B ALA* 3.7 28.5 - - + +
386B ALA* 4.2 28.0 - - + +
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Residues in contact with VAL 333 (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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285B VAL* 3.6 27.1 - - + -
289B ILE* 4.1 11.2 - - + -
300B ILE* 4.0 19.7 - - + -
314B VAL* 4.6 5.4 - - + -
316B VAL* 4.1 15.7 - - + -
329B ILE* 2.8 19.7 + - + +
330B THR* 3.4 10.3 - - - +
331B LYS 3.2 0.2 - - - -
332B LEU* 1.3 75.9 - - + +
334B ARG* 1.3 57.8 + - - +
337B PHE* 3.0 45.4 + - + +
339B LEU* 4.1 19.6 - - + +
382B LEU* 5.1 2.0 - - + +
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Residues in contact with ARG 334 (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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310B GLU* 4.0 20.2 + - - +
311B PRO* 3.9 36.7 + - - +
313B SER* 5.2 0.4 - - - +
314B VAL* 3.6 40.8 - - - +
330B THR* 3.6 16.1 - - + +
331B LYS* 3.2 12.4 + - - +
333B VAL* 1.3 78.1 - - - +
335B GLU* 1.3 61.6 + - + +
337B PHE 3.2 16.3 - - - +
339B LEU* 4.7 12.7 - - - +
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Residues in contact with GLU 335 (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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331B LYS* 3.3 20.9 + - - +
332B LEU* 3.1 23.1 + - - +
334B ARG* 1.3 79.4 - - + +
336B HIS* 1.3 72.1 + - + +
337B PHE 4.9 0.2 - - - -
385B ALA* 6.0 0.2 - - - +
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Residues in contact with HIS 336 (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* 3.0 34.5 + - + +
335B GLU* 1.3 91.9 + - + +
337B PHE* 1.3 75.3 + - + +
347B MET* 4.9 0.2 - - - +
378B LYS* 3.2 34.6 + - + +
381B ALA* 3.7 39.4 - - + +
382B LEU* 4.2 13.5 + - + +
385B ALA* 3.7 18.8 - - + +
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Residues in contact with PHE 337 (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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284B TYR* 3.7 30.3 - + - -
285B VAL* 3.7 44.0 - - + -
288B ASN* 4.1 5.6 - - + -
333B VAL* 3.0 29.3 + - + +
334B ARG* 3.2 19.1 - - - +
335B GLU 3.7 0.6 - - - -
336B HIS* 1.3 92.1 - - + +
338B ASP* 1.3 59.7 + - - +
339B LEU* 3.6 13.9 + - + +
347B MET* 3.9 11.7 - - + -
378B LYS* 3.3 28.9 - - + -
382B LEU* 3.9 27.4 - - + -
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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