Contacts of the helix formed by residues 231 - 236 (chain E) in PDB entry 4MNE
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 SER 231 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E TYR 3.7 1.6 + - - -
230E MET* 1.3 78.8 - - - +
232E PRO* 1.3 75.2 - - - +
233E GLU* 2.7 23.6 + - - -
234E ARG* 3.0 19.8 + - - +
235E LEU* 3.1 12.4 + - - +
244E SER* 2.5 34.9 + - - -
247E TRP* 3.5 19.3 - - - -
248E SER* 4.7 1.8 + - - -
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Residues in contact with PRO 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E MET 3.7 0.8 - - - -
231E SER* 1.3 88.1 - - - +
233E GLU* 1.3 68.8 + - - +
235E LEU* 3.1 20.9 + - + +
236E GLN* 3.5 19.1 + - - +
247E TRP* 3.6 29.8 - - + -
317E ILE* 4.0 25.6 - - + +
318E VAL* 4.3 9.5 - - + +
344E LYS* 3.9 34.1 - - + +
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Residues in contact with GLU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E SER* 2.7 24.6 + - - +
232E PRO* 1.3 82.9 - - - +
234E ARG* 1.3 58.9 + - - +
235E LEU 3.3 0.2 - - - -
236E GLN* 3.5 7.9 + - - -
237E GLY 3.5 2.4 + - - -
238E THR* 3.1 45.5 + - - +
239E HIS* 3.6 22.5 - - + +
240E TYR* 5.9 0.2 - - - -
243E GLN* 4.9 0.5 - - - +
244E SER* 2.9 11.8 + - - +
344E LYS 3.8 1.6 + - - +
346E PRO* 3.5 28.5 - - + +
349E ARG* 2.5 34.9 + - - -
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Residues in contact with ARG 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E MET* 4.5 1.8 - - - +
189E ARG* 2.8 48.8 + - - +
216E ILE* 5.9 1.6 - - - +
230E MET* 3.3 29.9 - - + +
231E SER* 3.0 17.3 + - - +
233E GLU* 1.3 75.1 - - - +
235E LEU* 1.3 62.2 + - - +
236E GLN 3.0 6.5 + - - -
237E GLY* 3.3 9.0 + - - +
239E HIS 4.5 4.5 - - - +
240E TYR* 3.3 46.7 + - + -
244E SER* 3.4 30.5 - - - +
245E ASP* 5.1 0.6 + - - -
660F ASN* 5.5 2.6 + - - -
661F ASN* 3.0 31.9 + - - +
664F GLN* 3.4 18.4 - - - +
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E MET* 3.5 29.2 - - + +
231E SER 3.1 11.4 + - - +
232E PRO* 3.1 8.9 + - + +
234E ARG* 1.3 77.3 - - - +
236E GLN* 1.3 58.9 + - - +
237E GLY 3.5 0.2 - - - -
314E LEU* 3.9 27.1 - - + +
317E ILE* 3.9 23.1 - - + -
318E VAL* 3.7 27.1 - - + -
663F ASP* 3.8 29.8 - - + +
664F GLN* 3.5 18.5 - - - +
667F PHE* 3.2 20.9 - - + -
668F MET* 3.7 2.6 - - - +
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Residues in contact with GLN 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E PRO* 3.5 19.8 + - - +
233E GLU* 3.5 5.9 + - - +
234E ARG 3.0 0.8 - - - -
235E LEU* 1.3 84.2 - - + +
237E GLY* 1.3 64.1 + - - +
238E THR* 3.2 22.8 + - + +
318E VAL* 3.4 27.5 - - + +
667F PHE* 3.9 16.2 - - + -
668F MET* 4.2 18.8 - - - +
673F TYR* 5.2 9.1 - - + -
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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