Contacts of the helix formed by residues 351 - 358 (chain H) 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 ASP 351 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243H GLN* 3.1 23.3 - - - +
246H ILE* 3.9 3.6 - - - -
349H ARG 3.3 3.9 + - - +
350H ALA* 1.3 72.0 - - - +
352H LEU* 1.3 63.9 - - - +
353H LYS* 2.9 16.1 + - - +
354H GLN* 2.8 58.2 + - - +
355H LEU* 3.1 25.3 + - - +
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Residues in contact with LEU 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H ILE* 3.7 29.3 - - + +
177H LEU* 3.9 25.8 - - + -
178H THR* 4.1 17.7 - - - +
181H ARG* 3.1 40.6 - - - +
242H VAL* 3.8 23.3 - - + -
243H GLN* 4.5 0.4 + - - -
246H ILE* 3.9 17.9 - - + +
351H ASP* 1.3 73.7 - - - +
353H LYS* 1.3 65.7 + - - +
355H LEU* 2.9 17.7 + - + +
356H MET* 3.1 13.5 + - - +
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Residues in contact with LYS 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H ARG* 4.6 18.3 - - - +
182H GLU* 5.0 7.8 + - - -
351H ASP* 2.9 11.6 + - - +
352H LEU* 1.3 78.8 - - - +
354H GLN* 1.3 64.4 + - + +
355H LEU 3.3 0.2 + - - -
356H MET* 3.3 14.7 + - + +
357H VAL* 3.4 19.3 - - + +
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Residues in contact with GLN 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349H ARG 4.7 3.3 + - - +
350H ALA* 3.7 19.3 - - + +
351H ASP* 2.8 46.9 + - - +
353H LYS* 1.3 73.4 - - + +
355H LEU* 1.3 58.5 + - - +
357H VAL* 3.2 13.0 - - + +
358H HIS* 3.1 24.9 + - - +
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Residues in contact with LEU 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174H ILE* 3.8 19.5 - - + -
246H ILE* 3.8 34.3 - - + -
249H MET* 4.2 15.5 - - + -
337H PHE* 3.2 25.4 - - + -
340H LYS* 4.7 4.3 - - + -
341H CYS* 4.2 7.9 - - - -
350H ALA* 3.4 22.9 - - + +
351H ASP 3.1 16.1 + - - +
352H LEU* 2.9 9.4 + - + +
354H GLN* 1.3 73.6 - - - +
356H MET* 1.3 66.2 + - - +
357H VAL 3.1 1.8 - - - -
358H HIS* 3.2 13.3 + - + +
361H ILE* 3.1 25.5 - - - +
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Residues in contact with MET 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H ILE* 4.3 10.1 - - + -
174H ILE* 4.0 21.3 - - - +
175H LYS* 3.8 38.6 - - + -
178H THR* 5.7 1.1 - - - -
352H LEU 3.1 10.2 + - - +
353H LYS* 3.3 14.3 + - + +
355H LEU* 1.3 76.6 - - - +
357H VAL* 1.3 62.5 + - + +
358H HIS 4.4 0.2 - - - +
361H ILE* 3.1 49.7 - - + +
362H LYS* 4.7 1.7 + - - +
365H ASP* 4.3 11.7 - - - +
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Residues in contact with VAL 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353H LYS* 3.4 14.8 - - + +
354H GLN* 3.2 19.7 - - + +
355H LEU 3.1 0.4 - - - -
356H MET* 1.3 79.3 - - + +
358H HIS* 1.3 69.3 + - - +
359H ALA* 3.6 1.9 + - - -
362H LYS* 5.0 8.4 - - - +
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Residues in contact with HIS 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333H GLU* 3.1 30.3 - - - -
336H ASP* 3.4 24.6 + - - -
337H PHE* 3.5 27.8 + + + -
340H LYS* 4.3 15.7 - - + -
354H GLN 3.1 14.3 + - - +
355H LEU* 3.2 20.8 + - + +
357H VAL* 1.3 81.8 - - - +
359H ALA* 1.3 81.4 + - + +
360H PHE* 3.0 21.2 + - - +
361H ILE* 3.0 13.9 + - + +
362H LYS* 3.3 8.7 + - - +
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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