Contacts of the helix formed by residues 399 - 414 (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 CYS 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ILE* 3.9 6.1 - - + -
360B PRO 3.3 25.8 - - - +
361B LEU* 3.5 25.6 - - - -
362B ASP* 3.5 7.0 - - - -
394B VAL* 3.6 35.9 - - + -
395B SER 3.0 15.4 + - - +
397B LYS 2.8 1.6 + - - -
398B ALA* 1.3 74.7 - - - +
400B ARG* 1.3 60.7 + - - +
401B GLN 3.3 2.9 - - - -
402B ASN* 3.1 3.5 + - - -
403B ILE* 2.7 30.0 + - + +
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU 4.2 4.2 + - - -
333B LEU* 2.9 52.4 + - + +
334B ASP* 2.7 45.1 + - - +
362B ASP* 3.4 1.0 + - - +
396B LEU* 3.4 24.7 + - + +
397B LYS* 3.0 11.0 + - - +
399B CYS* 1.3 76.6 - - - +
401B GLN* 1.3 73.9 + - - +
403B ILE* 3.0 8.8 + - - +
404B GLU* 2.7 49.3 + - + +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ASP* 2.9 34.3 - - + +
399B CYS 3.3 0.4 - - - -
400B ARG* 1.3 85.9 - - + +
402B ASN* 1.3 60.4 + - - +
404B GLU* 3.3 17.7 + - - +
405B THR* 3.0 23.7 + - - -
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Residues in contact with ASN 402 (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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359B ILE* 3.8 10.5 - - + -
360B PRO* 2.5 37.7 + - + +
361B LEU 2.6 20.6 + - - +
362B ASP* 3.0 16.9 + - - +
373B ILE* 3.4 17.7 - - + +
399B CYS 3.1 4.2 + - - +
401B GLN* 1.3 75.4 - - - +
403B ILE* 1.3 61.3 + - - +
405B THR* 3.0 12.2 + - - -
406B LEU* 2.8 26.5 + - - +
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Residues in contact with ILE 403 (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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333B LEU* 4.9 8.5 - - + -
345B ILE* 3.5 38.8 - - + -
347B ILE* 4.7 14.1 - - + -
359B ILE* 4.0 17.5 - - + -
394B VAL* 3.9 7.6 - - + -
396B LEU* 3.9 21.1 - - + -
399B CYS* 2.7 43.1 + - + +
400B ARG* 3.5 6.5 - - - +
402B ASN* 1.3 71.8 - - - +
404B GLU* 1.3 62.8 + - - +
406B LEU* 3.3 7.2 + - - +
407B LEU* 2.9 45.2 + - + +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.1 26.5 - - + +
333B LEU* 3.4 18.1 - - + +
400B ARG* 2.7 54.4 + - + +
401B GLN* 3.6 16.5 + - - +
403B ILE* 1.3 71.6 - - - +
405B THR* 1.3 62.4 + - - +
407B LEU* 3.2 4.5 + - - +
408B THR* 2.8 29.2 + - - +
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Residues in contact with THR 405 (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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373B ILE* 3.7 17.5 - - + -
401B GLN 3.0 13.6 + - - -
402B ASN* 3.0 12.5 + - - -
404B GLU* 1.3 79.1 - - - +
406B LEU* 1.3 63.2 + - - +
408B THR* 2.9 25.5 + - - -
409B LYS* 3.1 25.0 + - + +
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Residues in contact with LEU 406 (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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176A ILE* 4.8 4.7 - - + -
347B ILE* 4.4 12.3 - - + -
357B PHE* 3.4 50.3 - - + -
359B ILE* 3.4 33.2 - - + -
373B ILE* 3.8 24.0 - - + +
402B ASN 2.8 18.4 + - - +
403B ILE 3.6 4.3 - - - +
405B THR* 1.3 73.1 - - - +
407B LEU* 1.3 62.7 + - - +
409B LYS* 3.1 7.2 + - + +
410B ILE* 3.1 42.4 + - + +
413B ILE* 5.0 3.8 - - + -
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Residues in contact with LEU 407 (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 ILE* 6.2 0.2 - - + -
326B ILE* 3.0 41.1 - - + +
329B LEU* 4.0 17.9 - - + -
330B LEU* 3.9 31.6 - - + +
333B LEU* 3.8 28.9 - - + -
347B ILE* 3.7 25.4 - - + -
403B ILE* 2.9 28.0 + - + +
404B GLU* 3.4 7.4 - - - +
405B THR 3.2 0.2 - - - -
406B LEU* 1.3 76.7 - - - +
408B THR* 1.3 63.5 + - - +
410B ILE* 3.6 8.9 + - + +
411B PRO* 3.1 10.4 - - - +
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Residues in contact with THR 408 (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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330B LEU* 4.6 14.3 - - + +
404B GLU* 2.8 20.8 + - - +
405B THR* 3.0 15.6 - - - -
407B LEU* 1.3 78.4 - - - +
409B LYS* 1.3 60.3 + - + +
411B PRO* 3.6 9.0 - - - +
412B GLN* 4.0 14.1 - - - +
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Residues in contact with LYS 409 (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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175A THR* 3.0 33.7 + - + +
176A ILE* 4.1 25.7 - - + +
372B GLN* 5.3 7.3 + - - +
373B ILE* 5.2 9.9 + - + +
405B THR* 3.1 26.5 + - + +
406B LEU* 3.1 12.2 + - + +
408B THR* 1.3 77.5 - - + +
410B ILE* 1.3 54.7 + - - +
411B PRO 3.2 2.7 - - - -
412B GLN* 2.5 48.0 + - - +
413B ILE* 3.0 19.7 + - + -
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Residues in contact with ILE 410 (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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322B LEU* 4.5 8.6 - - + +
326B ILE* 4.0 27.4 - - + -
347B ILE* 4.1 17.9 - - + -
349B CYS* 3.6 34.1 - - - -
357B PHE* 4.6 4.5 - - + -
406B LEU* 3.1 36.8 - - + +
407B LEU* 3.9 10.8 - - + +
409B LYS* 1.3 74.9 - - - +
411B PRO* 1.3 70.8 - - + +
412B GLN 3.1 1.2 + - - -
413B ILE* 3.3 10.4 + - + +
414B PHE* 3.2 29.4 + - + +
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Residues in contact with PRO 411 (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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317B ILE* 5.9 0.3 - - - +
322B LEU* 4.7 11.9 - - + +
323B ALA* 4.9 15.9 - - + -
326B ILE* 3.8 26.2 - - + -
327B ASN* 6.4 0.2 - - - +
407B LEU 3.1 16.2 - - - +
408B THR 3.6 7.4 - - - +
409B LYS 3.3 4.3 - - - -
410B ILE* 1.3 93.6 - - + +
412B GLN* 1.3 57.1 + - + +
414B PHE 3.8 0.7 - - - -
415B GLN* 2.9 28.1 + - - +
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Residues in contact with GLN 412 (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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175A THR* 4.0 18.1 + - + +
408B THR* 4.0 13.8 - - - +
409B LYS* 2.5 36.2 + - - +
411B PRO* 1.3 70.8 - - + +
413B ILE* 1.3 67.8 + - - +
414B PHE 2.8 3.7 + - - -
415B GLN* 2.8 34.4 + - - +
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Residues in contact with ILE 413 (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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175A THR* 3.5 26.9 - - + +
176A ILE* 3.4 32.3 - - + -
178A ARG* 4.0 21.1 + - - +
357B PHE* 4.6 5.4 - - + -
375B MET* 3.2 33.4 - - + -
406B LEU* 5.0 0.9 - - + -
409B LYS* 3.0 21.3 + - + +
410B ILE* 3.7 15.7 - - + +
412B GLN* 1.3 76.8 - - - +
414B PHE* 1.3 68.0 + - + +
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Residues in contact with PHE 414 (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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178A ARG* 5.3 3.4 - - - -
312B VAL* 3.0 33.2 - - + +
317B ILE* 4.0 14.9 - - + +
322B LEU* 4.6 2.2 - - + -
349B CYS* 4.1 19.3 - - + -
351B ASP* 3.8 7.6 - - - -
355B HIS* 3.4 45.5 - + - -
375B MET* 3.4 26.9 - - + -
410B ILE* 3.2 25.3 + - + +
411B PRO 3.8 1.8 - - - -
412B GLN 2.9 0.6 - - - -
413B ILE* 1.3 84.5 - - + +
415B GLN* 1.3 53.8 + - - +
416B SER* 2.6 23.8 + - - -
417B ASN* 3.4 26.7 + - + +
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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