Contacts of the helix formed by residues 269 - 274 (chain D) in PDB entry 5MG3
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 ALA 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D THR* 3.0 18.8 + - + +
268D ARG* 1.4 81.1 - - + +
270D LYS* 1.4 56.1 + - - +
271D GLU 3.5 1.6 - - - -
272D ILE* 3.0 12.2 + - + -
273D LEU* 2.7 58.1 + - + +
382D GLY* 3.7 19.1 - - - +
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Residues in contact with LYS 270 (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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259D GLU* 2.7 37.7 + - - +
266D THR* 3.4 22.1 + - - +
267D ALA* 3.7 22.0 + - - +
268D ARG 3.6 1.2 - - - -
269D ALA* 1.4 73.1 - - - +
271D GLU* 1.3 59.7 + - + +
273D LEU* 3.7 6.0 - - + +
274D GLY* 2.9 24.4 + - - -
434D GLN* 4.4 27.6 - - + +
435D ILE* 2.7 39.4 + - + +
436D VAL* 4.2 2.8 - - - +
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Residues in contact with GLU 271 (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 ARG 5.3 0.6 + - - -
270D LYS* 1.3 75.6 - - + +
272D ILE* 1.3 65.0 + - + +
274D GLY* 3.6 4.7 - - - +
275D ALA* 3.1 22.5 + - - +
434D GLN* 4.0 29.3 + - - +
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Residues in contact with ILE 272 (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 ARG 3.9 15.5 + - - +
269D ALA* 3.0 11.4 + - + +
271D GLU* 1.3 77.4 - - + +
273D LEU* 1.3 70.2 + - + +
275D ALA* 3.2 5.9 + - - +
382D GLY 6.0 0.4 - - - +
383D ARG* 3.7 38.8 - - + +
384D ALA 3.2 27.6 - - - +
385D VAL* 4.0 24.0 - - + +
386D LEU* 3.1 36.2 - - + +
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Residues in contact with LEU 273 (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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234D LEU* 4.2 12.6 - - + +
237D ARG* 4.1 39.3 - - + +
238D VAL* 5.2 6.3 - - + -
241D LEU* 5.1 17.5 - - + -
259D GLU* 5.3 4.3 - - + +
266D THR* 5.3 7.4 - - + +
269D ALA* 2.7 41.9 + - + +
270D LYS* 3.9 4.5 - - + +
272D ILE* 1.3 79.4 - - + +
274D GLY* 1.3 58.7 + - - +
275D ALA 3.3 2.3 + - - +
372D TYR* 5.9 4.9 - - + -
386D LEU* 4.9 4.3 - - - +
433D ILE 4.7 0.7 - - - -
435D ILE* 3.7 34.3 - - + -
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Residues in contact with GLY 274 (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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234D LEU* 5.0 1.3 - - - -
270D LYS 2.9 15.0 + - - -
271D GLU* 3.5 5.6 + - - -
272D ILE 3.3 0.6 - - - -
273D LEU* 1.3 76.8 - - - +
275D ALA* 1.4 61.4 + - - +
276D THR* 4.2 1.2 - - - +
430D ILE* 6.1 0.5 - - - +
432D PRO* 3.5 29.1 - - - +
433D ILE 3.2 27.5 + - - -
434D GLN* 5.0 1.1 - - - -
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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