Contacts of the helix formed by residues 408 - 421 (chain B) in PDB entry 1M6X
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 408 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200B PRO 5.1 0.4 + - - -
201B LYS 5.7 2.0 + - - -
203B PHE* 3.6 25.3 + - - +
204B LYS* 5.6 0.2 - - - -
406B ILE 3.6 4.2 + - - -
407B ILE* 1.3 76.2 - - - +
409B GLN* 1.3 65.2 + - - +
410B GLU* 3.4 23.7 + - - +
411B VAL* 3.1 11.4 + - - +
412B LEU* 3.0 17.3 + - - +
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ALA* 3.4 32.6 - - - +
397B SER* 4.0 19.4 + - - -
407B ILE 3.3 4.1 + - - -
408B SER* 1.3 69.1 + - - +
410B GLU* 1.3 67.6 + - - +
411B VAL 2.9 0.3 + - - -
412B LEU* 3.0 10.7 + - + -
413B ASP* 2.8 42.7 + - - +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS* 5.3 1.6 - - - +
205B LEU* 3.4 41.8 + - + +
408B SER* 3.4 12.7 + - - +
409B GLN* 1.3 77.7 - - - +
411B VAL* 1.3 56.9 + - - +
413B ASP* 3.7 10.0 + - - +
414B TYR* 3.3 18.9 + - - +
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Residues in contact with VAL 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PHE* 3.8 24.0 - - + +
204B LYS* 3.9 16.6 - - - +
205B LEU* 4.0 11.9 - - + -
215B ILE* 4.2 31.6 - - + -
245B LEU* 6.1 0.7 - - + -
407B ILE* 4.0 16.2 - - + -
408B SER* 3.1 25.7 + - - +
409B GLN 2.9 0.8 - - - -
410B GLU* 1.3 75.4 - - + +
412B LEU* 1.3 69.0 + - + +
413B ASP 3.0 2.0 - - - -
414B TYR* 3.0 4.0 + - - +
415B LEU* 2.9 25.6 + - + +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 4.6 6.1 - - + -
396B GLY* 3.6 12.8 - - - -
397B SER* 4.7 5.4 - - - +
400B TYR* 3.6 42.3 - - + +
403B TRP* 3.9 15.5 - - + +
404B ASN* 4.2 18.4 - - - +
405B GLY 4.9 0.7 - - - +
407B ILE* 3.1 45.3 - - + +
408B SER 3.0 12.6 + - - +
409B GLN* 3.0 12.7 + - + +
411B VAL* 1.3 77.3 - - + +
413B ASP* 1.3 56.9 + - - +
415B LEU* 4.7 1.6 - - + +
416B SER* 2.9 30.7 + - - -
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Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER 4.1 8.4 - - - +
394B ALA* 3.9 9.2 - - - -
396B GLY* 3.4 22.3 + - - +
409B GLN* 2.8 46.4 + - - +
410B GLU* 3.7 7.8 - - - +
412B LEU* 1.3 75.1 - - - +
414B TYR* 1.3 58.1 + - - +
416B SER* 3.1 5.4 + - - -
417B SER* 2.7 41.6 + - - +
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Residues in contact with TYR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.7 27.8 - - + -
211B LEU 5.5 1.2 + - - -
213B VAL* 3.8 28.2 + - + +
214B ILE* 5.6 0.4 - - - -
215B ILE* 4.2 24.0 - - + -
234B SER* 4.9 3.1 + - - -
242B LEU* 4.0 26.1 - - + +
384B TRP* 3.8 31.0 - + + +
387B ILE* 4.0 27.1 - - + +
410B GLU 3.3 11.8 + - - +
411B VAL 3.0 6.8 + - - +
413B ASP* 1.3 79.8 - - - +
415B LEU* 1.3 60.9 + - - +
417B SER* 3.6 4.3 - - - -
418B TYR* 2.9 41.8 + + + +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ILE* 4.5 6.5 - - + -
242B LEU* 3.6 45.8 - - + +
245B LEU* 3.8 19.3 - - + -
246B ASP* 4.0 7.6 - - - -
249B LEU* 3.7 29.4 - - + -
400B TYR* 3.2 23.3 - - + +
411B VAL* 2.9 17.6 + - + +
412B LEU* 4.1 3.8 - - - +
414B TYR* 1.3 76.9 - - + +
416B SER* 1.3 68.7 + - - +
418B TYR* 3.2 4.7 + - + +
419B ILE* 2.9 33.2 + - + +
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Residues in contact with SER 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLU* 3.8 11.7 + - - +
396B GLY* 3.6 22.6 + - - -
399B ARG* 3.8 13.5 - - - +
400B TYR* 3.9 14.3 - - - -
412B LEU 2.9 22.6 + - - -
413B ASP* 3.4 3.8 - - - -
415B LEU* 1.3 77.0 - - - +
417B SER* 1.3 65.8 - - - +
419B ILE* 3.4 2.5 + - - +
420B ASN* 2.9 35.2 + - - -
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Residues in contact with SER 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ILE* 3.4 30.7 + - - +
390B LEU 5.2 3.8 + - - -
393B SER* 5.8 2.1 + - - -
413B ASP* 2.7 26.6 + - - +
414B TYR* 3.6 0.4 - - - -
416B SER* 1.3 74.2 - - - +
418B TYR* 1.3 66.6 + - - +
419B ILE 2.8 1.2 + - - -
420B ASN* 3.5 4.9 - - - +
421B ARG* 2.7 29.6 + - - +
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Residues in contact with TYR 418 (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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234B SER* 2.7 29.5 + - - -
235B ALA 4.7 0.2 + - - -
240B ASP* 2.4 31.2 + - - -
242B LEU* 3.5 38.4 - - + -
243B VAL* 4.9 1.1 - - + -
361B TYR* 4.6 1.4 + - - -
383B GLU* 4.1 16.8 - - - -
387B ILE* 3.6 27.2 - - + +
414B TYR* 2.9 33.0 + - + +
415B LEU* 3.5 6.3 - - + +
417B SER* 1.3 72.7 - - - +
419B ILE* 1.3 77.5 + - + +
421B ARG* 3.5 3.4 - - - +
422B ARG* 3.2 39.1 + - + +
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Residues in contact with ILE 419 (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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242B LEU 4.0 9.0 - - - +
243B VAL* 4.4 12.1 - - + -
246B ASP* 3.5 35.9 - - + +
399B ARG* 3.3 32.8 - - - +
400B TYR* 3.8 7.2 - - - +
415B LEU* 2.9 21.8 + - + +
416B SER 3.4 7.6 - - - +
417B SER 2.8 2.8 + - - -
418B TYR* 1.3 84.3 - - + +
420B ASN* 1.3 55.9 + - - +
422B ARG* 2.7 42.2 + - - +
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Residues in contact with ASN 420 (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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395B GLU* 4.3 16.4 + - - +
399B ARG* 4.0 20.0 + - - +
416B SER* 2.9 31.9 + - - -
417B SER* 2.9 8.5 + - - +
419B ILE* 1.3 72.5 - - - +
421B ARG* 1.3 54.0 + - - +
422B ARG 2.5 27.9 + - - +
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Residues in contact with ARG 421 (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 GLU* 3.2 43.2 + - - +
386B HIS* 2.7 45.8 + - - +
387B ILE* 3.9 16.6 - - + -
417B SER* 2.7 25.9 + - - +
418B TYR* 3.5 7.6 - - - +
420B ASN* 1.3 71.5 - - - +
422B ARG* 1.3 56.4 + - - +
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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