Contacts of the helix formed by residues 351 - 357 (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 ASP 351 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E GLN* 3.3 20.2 - - - +
246E ILE* 3.6 6.3 - - - -
349E ARG 3.8 1.3 + - - +
350E ALA* 1.3 73.3 - - - +
352E LEU* 1.3 54.2 + - - +
353E LYS* 3.2 17.0 - - - +
354E GLN* 3.0 37.1 + - - +
355E LEU* 2.8 35.5 + - - +
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Residues in contact with LEU 352 (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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174E ILE* 4.2 22.1 - - + +
177E LEU* 4.0 24.2 - - + +
178E THR* 3.6 37.7 - - - +
181E ARG* 3.9 28.3 - - - +
242E VAL* 4.1 13.9 - - + -
246E ILE* 3.8 24.7 - - + +
351E ASP* 1.3 73.6 - - - +
353E LYS* 1.3 60.9 + - - +
355E LEU* 3.1 8.8 + - + +
356E MET* 2.8 31.0 + - - +
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Residues in contact with LYS 353 (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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181E ARG* 5.7 3.7 - - - +
351E ASP* 3.2 17.0 - - - +
352E LEU* 1.3 78.3 - - - +
354E GLN* 1.3 66.4 + - + +
356E MET* 3.4 14.0 + - - +
357E VAL* 3.6 18.0 + - - +
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Residues in contact with GLN 354 (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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340E LYS* 5.7 5.1 - - - +
348E GLU 5.6 2.0 + - - -
349E ARG 4.9 2.5 + - - +
350E ALA* 3.7 22.0 - - + +
351E ASP* 3.0 39.2 + - - +
353E LYS* 1.3 79.8 - - + +
355E LEU* 1.3 61.6 + - - +
357E VAL* 3.3 23.0 + - - +
358E HIS* 3.4 8.3 + - - +
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Residues in contact with LEU 355 (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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174E ILE* 3.7 22.9 - - + -
246E ILE* 3.9 36.6 - - + -
249E MET* 4.3 11.0 - - + -
337E PHE* 3.4 26.7 - - + +
340E LYS* 4.8 3.1 - - + -
341E CYS* 4.1 9.6 - - - -
350E ALA* 3.6 21.8 - - + -
351E ASP 2.8 24.1 + - - +
352E LEU* 3.7 7.2 - - + +
354E GLN* 1.3 73.3 - - - +
356E MET* 1.3 63.5 + - - +
358E HIS* 3.3 15.8 + - + +
361E ILE* 3.2 22.5 - - - +
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Residues in contact with MET 356 (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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171E ILE* 5.5 2.9 - - - -
174E ILE* 3.6 31.8 - - + +
175E LYS* 3.7 39.5 - - + +
178E THR* 4.8 7.6 - - + +
352E LEU 2.8 16.6 + - - +
353E LYS* 3.6 10.8 - - - +
354E GLN 3.2 0.6 - - - -
355E LEU* 1.3 78.2 - - - +
357E VAL* 1.3 62.1 + - + +
358E HIS 3.4 0.6 - - - +
361E ILE* 3.4 28.9 - - - +
362E LYS* 4.7 3.8 + - - +
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Residues in contact with VAL 357 (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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353E LYS 3.7 12.6 - - - +
354E GLN* 3.3 16.8 - - + +
356E MET* 1.3 83.6 - - + +
358E HIS* 1.3 65.1 + - - +
359E ALA 3.7 0.3 + - - -
362E LYS* 3.2 36.2 - - - +
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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