Contacts of the helix formed by residues 246 - 250 (chain M) in PDB entry 2DFS
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 LYS 246 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M LEU* 2.9 29.5 + - + +
245M GLU* 1.3 71.5 - - - +
247M SER* 1.3 63.3 + - - +
249M VAL* 3.3 18.4 + - - +
405M LYS* 3.3 50.5 + - + +
406M HIS* 5.0 4.0 - - - +
409M ALA* 4.3 15.4 - - + +
570M ASP* 2.6 32.4 + - - +
636M VAL* 4.5 21.0 - - + +
639M GLN* 2.7 31.8 + - + +
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Residues in contact with SER 247 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245M GLU* 4.5 6.2 - - - +
246M LYS* 1.3 74.7 + - - +
248M ARG* 1.3 62.6 + - - +
249M VAL 3.2 1.0 + - - -
250M VAL* 3.2 8.8 + - - +
251M PHE* 3.1 26.8 + - - +
405M LYS* 4.3 8.3 - - - +
449M PHE* 4.8 6.9 - - - -
450M GLU* 2.7 37.3 + - - +
567M LYS* 4.5 27.4 - - - -
636M VAL* 5.2 4.4 - - - +
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Residues in contact with ARG 248 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209M ALA* 3.5 23.6 - - - -
210M LYS 3.5 10.1 + - - -
211M THR* 3.8 15.1 - - - +
219M ARG* 3.9 8.1 - - - +
245M GLU* 2.6 51.2 + - - +
246M LYS 3.3 0.4 - - - -
247M SER* 1.3 79.8 + - - +
249M VAL* 1.4 61.2 + - - +
250M VAL 3.3 0.2 - - - -
251M PHE* 3.1 22.7 + - - +
252M GLN* 3.2 13.0 + - - +
256M GLU* 2.7 34.6 + - - +
257M ARG 3.1 24.9 + - - +
258M ASN* 3.3 10.4 - - - +
259M TYR* 4.0 15.9 - - + -
450M GLU* 5.3 5.2 - - + +
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Residues in contact with VAL 249 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244M LEU* 6.3 0.2 - - + -
245M GLU 4.5 0.7 - - - +
246M LYS* 3.5 19.7 - - - +
247M SER 3.2 0.8 + - - -
248M ARG* 1.4 76.8 - - - +
250M VAL* 1.3 64.6 + - + +
258M ASN* 2.8 24.3 + - - +
259M TYR* 3.9 16.4 - - + -
262M PHE* 4.7 5.8 - - + -
287M TYR* 3.7 11.1 - - - +
332M ILE* 4.5 13.2 - - + -
404M ALA 4.2 21.5 - - - +
405M LYS* 4.2 7.2 - - + +
408M TYR* 3.7 38.4 - - + -
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Residues in contact with VAL 250 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M SER* 3.2 8.7 + - - +
249M VAL* 1.3 83.0 - - + +
251M PHE* 1.3 58.9 + - + +
252M GLN* 4.2 1.3 - - - -
286M HIS* 4.7 3.6 + - - -
287M TYR* 3.5 38.3 - - + -
290M GLN* 2.8 27.1 + - - +
400M ARG* 5.6 0.2 + - - -
401M ASP* 4.0 36.2 - - + +
404M ALA* 3.9 17.0 - - + -
405M LYS* 4.1 17.5 - - + -
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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
------------------------------------------------------------
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