Contacts of the helix formed by residues 405 - 416 (chain B) in PDB entry 5M64
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 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B ILE* 4.1 30.5 - - - +
204B ARG 4.4 8.3 - - - -
206B LEU* 5.5 0.7 - - - -
403B LEU* 2.9 9.6 + - - +
404B LEU* 1.3 76.0 - - - +
406B GLY* 1.3 57.6 + - - -
407B PHE 3.2 2.7 - - - +
408B LEU* 3.2 15.5 + - - +
409B TYR* 2.9 26.5 + - - +
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Residues in contact with GLY 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B SER* 3.7 19.4 + - - +
49B PHE* 4.7 13.2 - - - -
52B LEU* 5.1 6.9 - - - +
164B MET* 5.6 4.5 - - - -
203B ILE* 4.7 4.8 - - - +
404B LEU 3.1 8.1 + - - -
405B GLY* 1.3 75.8 - - - +
407B PHE* 1.3 60.5 + - - +
409B TYR* 3.2 10.6 + - - +
410B GLY* 3.0 22.2 + - - -
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Residues in contact with PHE 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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48B SER* 3.3 30.2 - - - -
51B ALA* 3.9 11.2 - - + -
60B LEU* 4.9 9.9 - - + -
243B GLN* 3.1 42.3 - - - +
403B LEU* 5.2 2.5 - - + -
404B LEU* 3.7 38.6 - - + +
405B GLY 3.2 1.4 - - - +
406B GLY* 1.3 74.4 - - - +
408B LEU* 1.3 60.0 + - - +
410B GLY* 3.2 3.4 + - - +
411B MET* 2.9 34.6 + - - +
553B THR* 3.2 25.4 - - - -
646B HIS* 3.3 32.3 - + + -
647B SER 5.2 0.4 - - - -
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Residues in contact with LEU 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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203B ILE* 5.2 14.1 - - + -
204B ARG 5.5 2.2 - - - +
206B LEU* 4.8 21.3 - - + -
403B LEU* 5.3 15.0 - - + +
405B GLY* 3.2 19.1 + - - +
407B PHE* 1.3 77.7 - - - +
409B TYR* 1.3 57.8 + - - +
411B MET* 3.3 14.7 + - + +
412B ILE* 2.9 53.3 + - + +
464B PHE* 5.4 1.6 - - + -
470B LEU* 5.3 7.4 - - + -
476B LEU* 4.3 29.2 - - + -
478B LEU* 5.7 2.9 - - + -
484B TYR* 5.2 16.2 - - + -
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Residues in contact with TYR 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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49B PHE* 4.1 22.4 - + + -
52B LEU* 5.7 2.2 - - + -
161B LEU* 3.3 38.5 - - + +
162B PRO* 3.3 19.6 - - - +
194B PHE* 4.1 21.8 - + + -
203B ILE* 6.1 3.8 - - + -
405B GLY 2.9 13.8 + - - +
406B GLY* 3.4 12.6 - - - +
407B PHE 3.2 0.4 - - - -
408B LEU* 1.3 78.7 - - - +
410B GLY* 1.3 58.1 + - - +
412B ILE* 3.3 8.8 + - + +
413B LEU* 3.0 54.8 + - + +
461B MET* 3.9 11.6 - - - +
464B PHE* 4.8 9.9 - + - -
465B LEU* 3.8 28.9 - - + -
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Residues in contact with GLY 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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52B LEU* 5.2 11.9 - - - +
60B LEU* 6.2 4.7 - - - -
61B LEU* 5.7 7.6 - - - +
242B ASP 5.6 1.8 - - - -
406B GLY 3.0 13.1 + - - -
407B PHE* 3.2 4.2 + - - -
409B TYR* 1.3 76.9 - - - +
411B MET* 1.3 60.0 + - - +
413B LEU* 3.3 8.3 + - - +
414B LYS* 3.0 28.1 + - - +
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Residues in contact with MET 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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242B ASP 4.0 9.2 - - - +
243B GLN* 3.2 47.3 - - + +
244B THR* 3.7 16.1 - - - +
245B SER 4.5 2.9 - - - +
403B LEU* 5.2 12.1 - - + -
407B PHE 2.9 21.6 + - - +
408B LEU* 3.3 18.6 + - + +
410B GLY* 1.3 72.4 - - - +
412B ILE* 1.3 61.8 + - + +
414B LYS* 3.4 8.1 + - - +
415B GLU* 2.9 30.0 + - - +
476B LEU* 3.7 37.7 - - + -
477B ASP* 4.9 3.6 - - - +
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Residues in contact with ILE 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 LEU* 2.9 39.4 + - + +
409B TYR* 3.6 8.1 - - + +
410B GLY 3.3 0.2 - - - -
411B MET* 1.3 72.8 - - + +
413B LEU* 1.3 60.8 + - - +
415B GLU* 4.4 4.9 - - - -
416B LYS* 2.8 53.3 + - + +
461B MET* 4.2 16.4 - - + -
464B PHE* 3.5 45.3 - - + -
470B LEU* 4.4 17.3 - - + -
472B SER* 5.5 4.3 - - - +
476B LEU* 6.3 1.8 - - + -
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Residues in contact with LEU 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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61B LEU* 5.8 12.8 - - + -
137B LEU* 6.0 5.2 - - + -
161B LEU* 4.1 19.3 - - + -
409B TYR* 3.0 50.1 + - + +
410B GLY* 3.3 11.6 + - - +
412B ILE* 1.3 77.2 - - - +
414B LYS* 1.3 62.0 + - - +
416B LYS* 3.7 2.0 - - + -
417B ILE* 3.0 47.0 + - + +
457B ILE* 4.8 10.5 - - + -
461B MET* 3.6 25.6 - - + -
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Residues in contact with LYS 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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61B LEU* 6.0 6.4 - - - +
64B GLY* 4.9 7.9 - - - -
65B VAL* 5.5 6.1 - - + +
67B ASP 5.4 2.5 - - - -
68B ILE* 3.7 30.8 - - + +
240B ARG* 4.4 10.2 - - - +
242B ASP* 3.6 30.1 - - + +
244B THR* 3.4 33.2 + - + +
356B ARG* 5.8 3.6 - - - +
410B GLY 3.0 16.5 + - - +
411B MET* 3.8 6.3 - - - +
412B ILE 3.4 0.2 - - - -
413B LEU* 1.3 76.7 - - - +
415B GLU* 1.3 74.7 + - + +
417B ILE* 3.8 9.0 + - - +
418B ASP* 3.5 20.5 + - - +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B MET 2.9 17.5 + - - +
412B ILE* 3.8 6.3 - - - +
414B LYS* 1.3 93.2 + - + +
416B LYS* 1.3 66.4 + - + +
417B ILE 3.2 3.8 + - - -
418B ASP* 3.6 19.1 + - - +
419B GLU* 4.3 2.4 + - - +
472B SER* 5.0 14.1 - - - +
473B GLN* 4.2 12.3 + - - +
474B SER* 2.9 42.0 + - - +
475B GLY 5.8 0.9 - - - +
476B LEU* 6.4 1.8 - - + -
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ILE* 2.8 35.2 + - + +
413B LEU* 3.7 3.4 - - - +
415B GLU* 1.3 80.3 - - + +
417B ILE* 1.3 62.4 + - - +
419B GLU* 3.2 33.8 - - + +
457B ILE* 4.8 7.0 - - - +
460B LYS* 3.6 36.1 - - + +
461B MET* 3.7 22.0 - - + -
464B PHE* 6.2 2.5 - - + -
470B LEU* 6.2 0.9 - - + -
471B VAL* 2.4 50.4 + - + +
472B SER* 4.8 2.2 - - - +
473B GLN* 5.1 4.2 - - - +
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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