Contacts of the helix formed by residues 308 - 317 (chain M) in PDB entry 6NR8
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 ASP 308 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ASP* 6.1 0.2 - - - -
235M SER* 3.2 30.7 + - - +
236M HIS* 5.9 1.6 - - - +
306M PHE 4.8 2.4 - - - +
307M ASP* 1.3 78.0 - - - +
309M GLU* 1.3 52.8 + - - +
311M ASN* 3.7 13.9 + - - -
312M HIS* 2.4 38.6 + - - -
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Residues in contact with GLU 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274M TYR* 4.4 12.1 + - - -
278M GLN* 5.6 2.6 + - - -
281M GLU* 5.7 1.0 - - - +
306M PHE* 4.8 8.8 - - + -
307M ASP* 3.3 7.5 - - + +
308M ASP* 1.3 76.9 - - - +
310M ALA* 1.3 63.2 + - + +
311M ASN 3.1 0.2 - - - -
312M HIS* 3.0 30.2 + - + -
313M LEU* 3.3 21.0 + - + +
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Residues in contact with ALA 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256M GLU* 3.7 6.6 - - + +
257M PRO* 5.1 1.8 - - + -
285M PHE* 3.6 30.5 - - + -
306M PHE* 3.5 25.3 - - + -
309M GLU* 1.3 79.1 - - + +
311M ASN* 1.3 64.1 + - - +
312M HIS 3.5 0.2 - - - -
313M LEU* 3.7 12.3 - - + -
314M LEU* 3.1 28.8 + - + +
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Residues in contact with ASN 311 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233M ASP* 4.0 18.8 - - - +
234M PHE 5.1 0.4 - - - -
235M SER* 3.1 23.6 + - - +
256M GLU* 3.2 28.7 + - - +
306M PHE 5.6 0.2 + - - -
307M ASP 3.5 12.9 + - - +
308M ASP* 3.7 12.3 + - - -
309M GLU 3.1 0.8 - - - -
310M ALA* 1.3 78.4 - - - +
312M HIS* 1.3 59.2 + - - +
314M LEU* 3.2 6.4 + - - +
315M LEU* 3.0 32.9 + - - +
321M ALA* 3.8 15.2 - - - +
323M ARG* 3.9 16.7 - - - +
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Residues in contact with HIS 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M SER* 3.7 15.7 + - - -
236M HIS* 3.4 29.7 + + + +
239M MET* 3.7 34.8 - - + +
308M ASP 2.4 27.3 + - - -
309M GLU* 3.0 27.0 + - + -
311M ASN* 1.3 76.5 - - - +
313M LEU* 1.3 72.0 + - + +
315M LEU* 3.6 12.9 - - + +
316M GLN* 2.8 27.9 + - - +
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Residues in contact with LEU 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281M GLU* 4.8 8.7 - - - +
282M LYS* 3.4 23.8 - - - +
285M PHE* 3.8 20.9 - - + -
309M GLU* 3.3 27.3 + - + +
310M ALA* 3.6 17.7 - - + +
311M ASN 3.2 0.4 - - - -
312M HIS* 1.3 90.0 - - + +
314M LEU* 1.3 53.9 + - - +
316M GLN* 3.3 17.7 + - - +
317M ASN* 2.7 38.8 + - - -
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Residues in contact with LEU 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M PHE* 3.6 45.5 - - + +
256M GLU* 4.8 15.0 - - + +
285M PHE* 3.6 47.1 - - + +
289M ILE* 3.8 22.7 - - + -
310M ALA* 3.1 24.3 + - + +
311M ASN 3.2 7.2 + - - +
313M LEU* 1.3 73.5 - - - +
315M LEU* 1.3 65.4 + - + +
316M GLN 3.3 0.2 - - - -
317M ASN* 3.2 3.5 + - + +
318M ASN 3.2 14.6 + - - -
319M LEU 3.0 22.8 + - - +
321M ALA* 5.2 2.9 - - + -
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Residues in contact with LEU 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ASP 4.5 2.2 - - - +
234M PHE* 3.6 34.8 - - + -
235M SER 3.4 29.2 - - - +
236M HIS 4.6 0.7 - - - +
239M MET* 3.9 15.9 - - + -
240M PRO* 3.4 25.0 - - - +
242M LYS* 3.5 10.0 + - - +
311M ASN* 3.0 20.8 + - - +
312M HIS* 3.6 19.7 - - + +
313M LEU 3.3 0.2 - - - -
314M LEU* 1.3 77.2 - - - +
316M GLN* 1.3 62.0 + - - +
318M ASN 3.4 7.6 + - - -
319M LEU 4.3 2.5 - - - +
320M PRO* 3.7 26.0 - - + -
321M ALA* 4.3 6.1 - - + +
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Residues in contact with GLN 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239M MET* 3.7 31.5 - - - +
240M PRO* 4.5 4.6 - - + +
282M LYS* 4.8 4.2 + - - -
312M HIS 2.8 15.8 + - - +
313M LEU* 3.5 24.1 - - - +
314M LEU 3.3 0.2 - - - -
315M LEU* 1.3 76.5 - - - +
317M ASN* 1.3 62.0 + - - +
318M ASN* 3.1 16.7 + - - +
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Residues in contact with ASN 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282M LYS* 3.1 37.1 + - - +
285M PHE* 3.9 15.0 - - - +
286M GLU* 3.0 27.7 - - - +
289M ILE* 3.3 28.1 - - + +
313M LEU 2.7 25.8 + - - +
314M LEU* 3.2 8.2 + - - +
315M LEU 3.2 0.6 - - - -
316M GLN* 1.3 80.5 - - - +
318M ASN* 1.3 69.7 + - - +
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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