Contacts of the helix formed by residues 294 - 298 (chain B) in PDB entry 1M7X
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 PHE 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B HIS* 3.1 19.2 - - - +
293B PRO* 1.3 109.8 - - + +
295B ASP* 1.3 64.9 + - - +
296B GLY* 4.4 5.8 - - - +
297B SER* 3.1 16.5 + - - +
301B GLN* 5.5 5.2 - - - +
311B ARG* 3.6 3.6 - - - -
344B ASP* 3.9 22.9 - - + -
345B ASP* 5.8 2.5 - - - -
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Residues in contact with ASP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B HIS* 4.5 7.7 + - + -
255B ARG* 5.1 2.9 + - - -
262B TRP* 3.1 24.9 + - - -
292B HIS* 4.7 2.0 + - - -
293B PRO 4.5 2.4 - - - +
294B PHE* 1.3 72.5 - - - +
296B GLY* 1.3 53.7 + - - +
298B TRP* 2.6 37.4 + - - -
311B ARG* 2.2 35.7 + - - +
580B HIS* 3.8 21.2 + - + +
581B ASP* 4.6 9.4 - - - +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE* 3.3 4.1 - - - +
295B ASP* 1.3 78.3 - - - +
297B SER* 1.3 55.6 + - - +
298B TRP* 3.1 21.9 + - - -
580B HIS* 3.4 24.4 - - - -
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B HIS* 3.5 5.7 - - - -
294B PHE* 3.1 20.9 + - - +
295B ASP 2.9 3.2 + - - -
296B GLY* 1.3 72.9 - - - +
298B TRP* 1.3 67.5 + - - +
299B GLY* 2.9 19.5 + - - -
300B TYR* 3.2 20.8 + - - +
301B GLN* 3.4 45.9 + - - +
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Residues in contact with TRP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B HIS* 3.7 19.4 - - - +
287B LEU* 3.9 15.9 - - + +
288B PRO* 3.8 17.8 - - - +
292B HIS* 3.8 6.3 + - - -
295B ASP 2.6 19.4 + - - -
296B GLY 3.2 15.0 + - - -
297B SER* 1.3 82.0 + - - +
299B GLY* 1.3 56.4 + - - +
300B TYR* 3.6 8.3 - + + -
525B HIS* 3.7 31.6 - + - -
526B ASP* 4.0 12.6 - - - -
529B VAL* 3.9 18.6 - - + -
530B HIS* 3.9 30.7 - + - -
578B TRP* 3.5 21.8 - + - -
580B HIS* 3.1 40.8 - + + +
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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
------------------------------------------------------------
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