Contacts of the helix formed by residues 314 - 320 (chain E) in PDB entry 1MKD
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 314 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309E LEU* 2.7 51.0 + - - +
312E THR* 3.2 8.6 - - - -
313E ASN* 1.3 81.0 - - - +
315E GLU* 1.3 65.5 + - - +
316E LEU* 3.8 5.0 + - - +
317E ALA* 3.1 17.0 + - - +
318E LEU* 3.0 21.5 + - - +
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Residues in contact with GLU 315 (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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313E ASN 3.8 3.4 + - - +
314E SER* 1.3 73.6 - - - +
316E LEU* 1.3 58.1 + - - +
318E LEU* 3.3 23.7 + - - +
319E MET* 2.9 28.9 + - - +
336H LYS* 3.2 32.4 + - - +
339H GLN* 4.1 5.7 + - - +
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Residues in contact with LEU 316 (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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302E PRO* 5.5 4.5 - - + -
309E LEU* 4.5 16.6 - - + -
314E SER* 3.1 8.7 - - - +
315E GLU* 1.3 80.5 - - - +
317E ALA* 1.3 56.0 + - - +
319E MET* 3.3 7.8 - - + +
320E TYR* 3.0 44.1 + - + -
325E VAL* 3.5 19.5 - - + +
326E LEU* 4.7 6.7 - - + -
329E HIS* 3.7 50.0 - - + +
319H MET* 6.3 1.1 - - + -
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Residues in contact with ALA 317 (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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309E LEU 3.3 19.7 - - - +
310E ILE* 3.9 5.2 - - - +
313E ASN* 5.0 1.1 - - - -
314E SER* 3.1 24.2 + - - +
316E LEU* 1.3 74.1 - - - +
318E LEU* 1.3 64.2 + - - +
321E ASN 3.0 19.6 + - - -
322E ASP* 3.1 25.3 + - - +
325E VAL* 3.7 18.3 - - + +
358H ARG* 3.2 3.5 + - - -
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Residues in contact with LEU 318 (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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313E ASN 5.5 2.5 - - - +
314E SER 3.0 12.2 + - - +
315E GLU* 3.5 28.3 - - - +
317E ALA* 1.3 78.5 - - - +
319E MET* 1.3 65.0 + - - +
321E ASN* 3.5 15.1 + - - +
332H ALA* 3.5 35.0 - - + +
335H PHE* 4.2 12.1 - - + -
336H LYS* 3.9 24.5 - - + +
339H GLN* 3.5 25.4 - - - +
358H ARG* 3.7 14.5 + - - +
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Residues in contact with MET 319 (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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315E GLU 2.9 18.2 + - - +
316E LEU* 3.3 11.4 - - + +
318E LEU* 1.3 79.4 - - - +
320E TYR* 1.3 82.1 + - + +
321E ASN* 3.6 6.2 + - - -
316H LEU* 6.3 0.2 - - + -
319H MET* 3.1 31.6 - - - +
320H TYR* 2.7 59.0 + - + +
329H HIS* 5.4 4.7 - - + +
332H ALA* 4.1 13.6 - - + +
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Residues in contact with TYR 320 (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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316E LEU* 3.0 36.3 + - + +
319E MET* 1.3 89.1 - - + +
321E ASN* 1.3 74.5 + - - +
322E ASP 3.2 1.3 - - - -
323E SER* 2.9 28.0 + - - +
325E VAL* 3.7 23.6 - - + -
328E ASN* 3.5 31.4 + - + +
329E HIS* 4.0 17.1 - - - -
332E ALA* 3.7 11.4 - - - +
319H MET* 2.7 46.2 + - + +
320H TYR* 3.7 26.2 - + - -
328H ASN* 4.7 3.6 - - - +
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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