Contacts of the helix formed by residues 320 - 332 (chain B) in PDB entry 1M2V
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 GLY 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B SER 3.6 1.0 + - - -
317B ILE 3.2 13.2 + - - -
318B LYS 3.2 4.2 - - - -
319B SER* 1.3 79.9 + - - +
321B LEU* 1.3 65.8 + - - +
322B LEU* 3.0 4.6 + - - -
323B ALA* 3.2 11.0 + - - +
324B THR* 3.1 27.2 + - - -
529B PHE* 4.2 1.1 - - - -
531B GLY* 5.3 2.2 - - - -
537B ILE* 6.4 1.1 - - - -
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 6.4 0.2 - - + -
311B ASP* 5.5 0.4 - - + +
316B SER* 3.4 14.1 + - - +
319B SER* 3.0 18.8 + - - +
320B GLY* 1.3 78.6 - - - +
322B LEU* 1.3 57.6 + - - +
324B THR* 3.6 1.9 - - - -
325B THR* 2.9 32.1 + - - -
445B VAL* 3.9 10.5 - - + -
446B SER* 3.4 13.2 - - - +
447B GLY* 3.3 38.1 - - - +
502B ALA* 3.5 28.0 - - + +
529B PHE* 3.5 17.2 - - + -
540B PHE* 3.8 25.6 - - + -
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Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.8 22.9 - - + -
311B ASP 5.2 0.2 - - - -
312B VAL* 4.2 20.6 - - + -
316B SER* 3.3 21.2 + - - +
317B ILE* 3.2 29.8 - - + -
320B GLY 3.0 2.4 + - - -
321B LEU* 1.3 75.1 - - - +
323B ALA* 1.3 68.0 + - - +
324B THR 3.0 1.3 - - - -
325B THR* 3.0 4.6 + - - -
326B ILE* 2.8 53.5 + - + +
410B ILE* 4.5 8.1 - - + +
411B PRO* 4.7 16.2 - - + +
414B PHE* 4.6 6.5 - - + -
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Residues in contact with ALA 323 (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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320B GLY* 3.2 12.5 + - - +
322B LEU* 1.3 79.2 - - - +
324B THR* 1.3 58.3 + - - +
326B ILE* 3.8 5.3 - - - +
327B ASN* 2.8 44.5 + - - +
411B PRO* 4.9 14.4 - - + -
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLY 3.1 14.7 + - - -
321B LEU* 3.6 9.9 - - - -
322B LEU 3.0 0.6 - - - -
323B ALA* 1.3 77.2 - - - +
325B THR* 1.3 53.8 + - - +
327B ASN* 3.0 6.2 + - - +
328B THR* 2.8 39.1 + - - +
529B PHE* 4.1 4.6 - - + -
537B ILE* 3.9 34.7 - - + +
540B PHE* 3.9 17.9 - - + -
541B SER* 3.7 28.9 - - - -
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 5.9 0.4 - - + -
310B ILE* 4.0 26.2 - - + -
321B LEU 2.9 18.5 + - - -
322B LEU* 3.0 6.6 + - - -
324B THR* 1.3 78.2 - - - +
326B ILE* 1.3 62.6 + - - +
328B THR* 3.9 5.1 - - - -
329B LEU* 3.2 26.1 + - + +
445B VAL* 3.1 43.1 - - + +
540B PHE* 3.7 12.1 - - - -
544B PHE* 4.2 14.1 - - + -
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 3.7 29.2 - - + -
322B LEU* 2.8 41.5 + - + +
323B ALA 4.0 2.7 - - - +
325B THR* 1.3 72.4 - - + +
327B ASN* 1.3 59.9 + - - +
329B LEU* 4.0 4.1 - - + +
330B LEU* 3.0 32.6 + - + +
407B LEU* 3.0 46.0 - - + +
410B ILE* 4.0 19.7 - - + -
411B PRO* 3.8 21.3 - - + -
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Residues in contact with ASN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA* 2.8 32.8 + - - +
324B THR* 3.4 5.6 - - - +
326B ILE* 1.3 75.6 - - - +
328B THR* 1.3 66.6 + - - +
330B LEU* 3.1 15.6 + - - +
331B GLN* 2.8 48.7 + - - +
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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
----------------------------------------------------------
324B THR* 2.8 22.7 + - - +
325B THR* 3.9 4.2 - - - -
327B ASN* 1.3 74.0 - - - +
329B LEU* 1.3 52.0 + - - +
331B GLN* 3.1 3.2 + - - +
332B ASN* 2.8 59.1 + - + +
540B PHE* 5.3 0.3 - - - -
541B SER* 2.9 49.0 + - - +
544B PHE* 3.7 23.5 - - + -
545B ALA* 3.9 4.7 - - + -
548B ILE* 5.3 0.4 - - + -
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Residues in contact with LEU 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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308B PHE* 3.5 55.4 - - + -
310B ILE* 5.1 9.2 - - + -
325B THR* 3.2 17.7 + - + +
326B ILE* 4.0 3.6 - - - +
328B THR* 1.3 79.7 - - - +
330B LEU* 1.3 61.5 + - - +
332B ASN 3.2 1.2 + - - -
333B LEU* 2.9 41.9 + - + +
336B ILE* 3.8 20.2 - - + -
345B ILE* 4.8 4.0 - - + -
347B ILE* 5.0 6.1 - - + -
407B LEU* 4.0 24.0 - - + -
544B PHE* 4.5 5.1 - - + -
548B ILE* 4.1 11.9 - - + -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B ILE* 3.0 24.2 + - + +
327B ASN* 3.3 17.3 - - - +
329B LEU* 1.3 79.1 - - - +
331B GLN* 1.3 62.7 + - + +
332B ASN 3.5 0.2 + - - -
333B LEU* 3.6 11.0 + - - +
400B ARG* 4.2 6.4 + - - -
404B GLU* 4.1 33.4 - - + +
407B LEU* 3.9 33.8 - - + +
408B THR* 4.6 16.8 - - - +
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ASN* 2.8 45.9 + - - +
328B THR* 3.8 4.2 - - - +
330B LEU* 1.3 79.0 - - + +
332B ASN* 1.3 66.5 + - - +
333B LEU 3.6 1.0 + - - -
334B ASP* 4.3 10.9 - - - +
335B SER* 5.0 0.5 + - - -
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Residues in contact with ASN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR* 2.8 45.2 + - - +
329B LEU 3.2 3.3 + - - -
331B GLN* 1.3 86.9 - - - +
333B LEU* 1.3 64.3 + - - +
334B ASP 3.0 2.9 - - - +
335B SER* 2.9 33.4 + - - +
336B ILE* 3.3 14.4 + - - +
545B ALA* 3.4 19.8 - - - +
548B ILE* 3.8 16.4 - - + -
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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
------------------------------------------------------------
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