Contacts of the helix formed by residues 411 - 417 (chain D) 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 GLY 411 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ARG* 3.7 21.6 - - - +
409D ASP* 2.8 16.3 + - - -
410D TYR* 1.3 73.3 - - - +
412D GLU* 1.3 63.8 + - - -
413D VAL 3.1 2.5 - - - -
414D ASN* 3.0 24.5 + - - +
415D GLN* 3.4 19.2 + - - +
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Residues in contact with GLU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D LEU* 3.7 36.7 - - + +
388D VAL* 5.0 3.6 - - - +
391D ARG* 4.4 11.6 + - - -
408D TYR* 3.6 32.3 + - - +
409D ASP* 2.8 47.8 + - + +
411D GLY* 1.3 70.9 - - - -
413D VAL* 1.3 61.9 + - - +
414D ASN 3.3 0.2 + - - -
415D GLN* 3.3 11.6 + - - +
416D LEU* 3.0 31.8 + - + +
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Residues in contact with VAL 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D GLU* 3.8 16.8 - - + +
392D ALA* 4.2 17.9 - - - +
396D TYR* 3.6 27.4 - - + +
408D TYR* 3.8 22.0 - - + +
410D TYR* 3.5 28.5 - - + +
411D GLY 3.0 0.2 + - - -
412D GLU* 1.3 77.5 - - - +
414D ASN* 1.3 53.6 + - - +
417D LEU* 2.8 53.6 + - + +
422D LYS* 4.2 5.6 - - + +
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Residues in contact with ASN 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C GLY 5.3 7.8 + - - +
290D GLU* 2.7 24.6 + - - +
293D GLU* 4.2 4.2 - - - +
410D TYR 4.1 3.6 + - - -
411D GLY* 3.0 15.3 + - - +
413D VAL* 1.3 72.0 - - - +
415D GLN* 1.3 68.2 + - + +
416D LEU 3.2 1.7 + - - -
417D LEU 4.1 10.2 - - - +
418D GLU* 5.6 0.7 - - - -
422D LYS* 2.6 31.2 + - - +
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Residues in contact with GLN 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D LEU* 4.8 0.9 - - - +
264D ARG* 3.4 54.0 + - + +
267D GLN* 4.7 3.6 - - - +
268D LEU* 3.6 26.3 - - + +
286D ARG* 5.6 1.4 - - - +
409D ASP* 4.2 9.1 + - - -
411D GLY* 3.4 22.1 + - - +
412D GLU* 3.6 13.6 - - - +
414D ASN* 1.3 81.7 - - + +
416D LEU* 1.3 64.5 + - + +
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Residues in contact with LEU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D LEU* 3.5 28.4 - - + +
264D ARG* 4.5 4.0 - - + +
265D MET* 3.7 35.0 - - + +
268D LEU* 3.9 27.6 - - + -
388D VAL* 3.6 30.7 - - + +
389D LEU* 4.1 9.7 - - + +
392D ALA* 3.9 7.9 - - + -
408D TYR* 4.7 0.2 - - - +
412D GLU* 3.0 23.2 + - + +
415D GLN* 1.3 83.3 - - + +
417D LEU* 1.3 75.9 + - + +
418D GLU* 3.3 4.6 + - - +
444D TRP* 5.2 3.5 + - - -
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D LEU* 3.7 20.9 - - + -
392D ALA* 3.5 45.8 - - + +
393D ILE* 3.8 15.5 - - + +
396D TYR* 3.6 15.9 - - + -
413D VAL* 2.8 38.8 + - + +
414D ASN* 4.1 8.1 - - - +
416D LEU* 1.3 70.3 - - - +
418D GLU* 1.3 67.4 + - - +
419D ARG* 4.6 0.2 - - - -
421D LEU* 3.5 21.1 - - + -
422D LYS* 3.5 23.4 - - + +
425D ILE* 4.7 1.8 - - + -
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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