Contacts of the helix formed by residues 406 - 412 (chain B) in PDB entry 1M7X
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 ALA 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B GLY* 6.3 0.4 - - - -
340B HIS* 4.1 13.7 - - + +
405B ASP* 1.3 82.8 - - - +
407B VAL* 1.3 63.6 + - - +
408B ALA* 3.1 4.5 - - - +
409B SER* 2.6 42.6 + - - +
410B MET* 3.5 5.0 + - + +
458B GLU* 2.8 24.8 + - - +
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Residues in contact with VAL 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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404B VAL* 3.8 24.9 - - + +
405B ASP 4.0 0.7 - - - -
406B ALA* 1.3 75.6 - - - +
408B ALA* 1.3 57.8 + - - +
410B MET* 2.8 25.0 + - - +
411B ILE* 2.9 21.3 + - + +
439B LEU* 3.6 25.4 - - + -
457B ALA* 3.8 24.5 - - + -
458B GLU 3.0 17.5 + - - +
459B GLU* 3.9 17.9 - - + -
466B VAL* 5.8 0.2 - - + -
475B LEU* 4.7 9.2 - - + -
477B PHE* 4.4 5.6 - - + -
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Residues in contact with ALA 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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406B ALA* 3.1 2.0 - - - -
407B VAL* 1.3 79.2 - - - +
409B SER* 1.3 56.8 + - - +
411B ILE* 3.8 4.9 - - - -
412B TYR* 3.1 34.5 + - - +
414B ASP* 5.0 0.3 - - - +
459B GLU* 2.8 29.5 + - - +
460B SER* 3.5 28.9 - - - +
461B THR* 3.7 12.3 - - + -
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Residues in contact with SER 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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339B GLY 4.7 7.3 + - - -
340B HIS* 5.8 0.3 - - - -
374B ILE* 6.0 1.7 - - - +
406B ALA* 2.6 33.7 + - - +
408B ALA* 1.3 78.4 - - - +
410B MET* 1.3 62.1 + - - +
412B TYR 3.3 15.5 - - - +
414B ASP* 4.7 10.6 - - - +
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Residues in contact with MET 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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338B PRO* 4.3 5.8 - - + +
339B GLY* 3.7 27.1 - - - +
377B TYR* 3.6 37.1 - - + +
404B VAL* 4.0 22.2 - - - -
405B ASP 4.6 0.9 - - - +
406B ALA 3.9 8.3 - - - +
407B VAL* 2.8 16.5 + - - +
409B SER* 1.3 82.2 - - - +
411B ILE* 1.3 65.7 + - + +
412B TYR 3.2 3.9 + - - +
432B ASN* 3.5 10.9 + - - +
435B ALA* 3.3 23.8 - - + +
438B PHE* 4.0 7.6 - - + -
439B LEU* 3.5 31.9 - - + -
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Residues in contact with ILE 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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407B VAL* 2.9 29.1 + - + +
408B ALA 3.6 1.8 - - - +
410B MET* 1.3 74.6 - - + +
412B TYR* 1.3 76.9 + - + +
431B GLU* 3.4 10.4 - - + +
432B ASN 2.9 22.9 + - - +
435B ALA* 4.5 2.7 - - - -
436B ILE* 3.8 31.6 - - + +
439B LEU* 4.0 14.6 - - + -
459B GLU* 3.5 31.2 - - + +
463B PHE* 3.6 33.2 - - + -
475B LEU* 5.1 7.0 - - + -
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Residues in contact with TYR 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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408B ALA 3.1 15.3 + - - +
409B SER 3.3 15.9 - - - +
410B MET 3.2 3.6 - - - +
411B ILE* 1.3 110.4 - - + +
413B ARG* 1.3 58.9 + - - +
414B ASP* 2.9 27.6 + - - +
430B ARG* 3.8 31.6 - - + -
431B GLU* 3.7 27.6 + - + -
432B ASN* 5.7 0.2 - - - -
461B THR* 3.7 33.3 + - + -
463B PHE* 4.0 17.0 - + - +
464B PRO* 5.6 1.2 - - - +
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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