Contacts of the helix formed by residues 410 - 417 (chain E) in PDB entry 6N0M
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 TYR 410 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283E MET* 5.1 6.2 + - - +
286E ARG* 4.3 9.9 - - + +
287E PHE* 3.6 55.4 - + + +
290E GLU* 4.0 13.9 - - + +
395E ASN* 3.7 25.5 + - + +
399E CYS* 4.1 6.7 - - + -
403E ILE 2.9 22.5 + - - -
404E ARG* 4.0 4.0 - - + -
405E TYR* 3.3 45.7 + - - -
408E TYR* 2.8 47.2 + + + -
409E ASP* 1.3 70.9 + - - +
411E GLY* 1.3 60.4 + - - +
412E GLU 3.2 0.4 - - - -
413E VAL* 3.3 32.1 + - + +
414E ASN* 4.2 0.3 + - - -
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Residues in contact with GLY 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ARG* 4.3 21.2 - - - +
409E ASP* 2.9 12.7 + - - -
410E TYR* 1.3 74.9 - - - +
412E GLU* 1.3 65.5 + - - +
413E VAL 3.1 1.8 + - - -
414E ASN* 3.1 22.9 + - - +
415E GLN* 3.5 19.6 + - - +
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Residues in contact with GLU 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E LEU* 3.7 39.5 - - + +
388E VAL* 4.3 4.9 - - - +
391E ARG* 3.3 17.3 + - - -
408E TYR* 3.1 41.0 + - - +
409E ASP* 2.9 34.5 + - - +
411E GLY* 1.3 74.5 - - - +
413E VAL* 1.3 61.4 + - - +
415E GLN* 3.1 12.5 + - - +
416E LEU* 3.0 30.0 + - + +
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Residues in contact with VAL 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E GLU* 3.5 25.8 - - + +
392E ALA* 4.0 18.8 - - - +
396E TYR* 3.7 19.7 - - + +
408E TYR* 3.8 21.8 - - + -
410E TYR* 3.3 26.9 - - + +
411E GLY 3.1 0.6 - - - -
412E GLU* 1.3 76.2 - - - +
414E ASN* 1.3 58.4 + - - +
417E LEU* 3.0 52.0 + - + +
422E LYS* 4.5 2.4 - - - +
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Residues in contact with ASN 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B SER 5.3 1.0 - - - +
383B GLY 4.9 10.1 + - - +
286E ARG 5.5 1.6 + - - -
289E LEU* 6.3 0.8 - - - +
290E GLU* 2.7 24.2 + - - +
293E GLU* 3.7 7.3 - - - +
410E TYR 4.5 2.8 + - - -
411E GLY* 3.1 16.1 + - - +
413E VAL* 1.3 78.1 - - - +
415E GLN* 1.3 61.3 + - + +
417E LEU 3.9 10.1 - - - +
418E GLU* 5.5 0.7 - - - -
422E LYS* 2.7 30.8 + - - +
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Residues in contact with GLN 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LEU* 4.8 2.4 - - - +
264E ARG* 4.5 21.7 - - + +
267E GLN* 5.5 2.9 - - - +
268E LEU* 4.1 20.0 - - + +
409E ASP* 5.0 4.0 + - - -
411E GLY 3.5 17.0 + - - +
412E GLU* 3.1 18.0 + - - +
414E ASN* 1.3 80.4 - - + +
416E LEU* 1.3 70.8 + - + +
417E LEU 5.2 0.2 - - - -
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Residues in contact with LEU 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E LEU* 3.5 24.2 - - + +
264E ARG* 4.1 4.9 - - + -
265E MET* 3.8 32.5 - - + +
268E LEU* 3.7 31.6 - - + -
388E VAL* 3.5 35.2 - - + +
389E LEU* 4.0 18.6 - - + +
392E ALA* 3.8 9.9 - - + -
412E GLU* 3.0 17.7 + - - +
415E GLN* 1.3 81.9 - - + +
417E LEU* 1.3 65.6 + - + +
418E GLU* 3.3 8.5 + - - +
444E TRP* 5.2 3.1 + - - -
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Residues in contact with LEU 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389E LEU* 3.5 27.8 - - + -
392E ALA* 3.3 38.6 - - + +
393E ILE* 3.6 20.4 - - + +
396E TYR* 3.8 12.8 - - + -
413E VAL* 3.0 35.7 + - + +
414E ASN* 3.9 9.7 - - - +
415E GLN 5.3 0.4 - - - -
416E LEU* 1.3 74.2 - - - +
418E GLU* 1.3 65.9 + - - +
421E LEU* 4.0 17.7 - - + -
422E LYS* 3.4 25.3 + - + +
425E ILE* 4.8 2.5 - - + -
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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