Contacts of the helix formed by residues 314 - 320 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309B LEU* 2.6 50.6 + - - +
312B THR* 3.2 8.7 + - - -
313B ASN* 1.3 80.6 - - - +
315B GLU* 1.3 64.6 + - - +
316B LEU* 3.8 4.4 + - - +
317B ALA* 3.1 17.3 + - - +
318B LEU* 3.1 20.3 + - - +
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Residues in contact with GLU 315 (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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336A LYS* 2.7 38.4 + - - +
339A GLN* 3.6 9.7 + - - +
313B ASN 3.8 2.5 + - - +
314B SER* 1.3 74.1 - - - +
316B LEU* 1.3 58.0 + - - +
318B LEU* 3.3 23.1 + - - +
319B MET* 2.9 29.3 + - - +
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Residues in contact with LEU 316 (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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302B PRO* 5.5 4.5 - - + -
309B LEU* 4.5 16.8 - - + -
314B SER* 3.1 8.7 - - - +
315B GLU* 1.3 81.2 - - - +
317B ALA* 1.3 56.3 + - - +
319B MET* 3.3 7.9 - - + +
320B TYR* 3.0 43.4 + - + -
325B VAL* 3.5 18.9 - - + +
326B LEU* 4.7 6.1 - - + -
329B HIS* 3.7 50.3 - - + +
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Residues in contact with ALA 317 (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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358A ARG* 3.1 5.8 + - - +
309B LEU 3.3 19.1 - - - +
310B ILE* 3.9 6.1 - - - +
313B ASN* 5.0 1.3 - - - -
314B SER* 3.1 24.2 + - - +
316B LEU* 1.3 73.4 - - - +
318B LEU* 1.3 61.4 + - - +
321B ASN 2.9 24.3 + - - -
322B ASP* 3.1 23.7 + - - +
325B VAL* 3.7 18.8 - - + +
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Residues in contact with LEU 318 (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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332A ALA* 3.3 32.7 - - + +
335A PHE* 3.9 15.9 - - + -
336A LYS* 3.9 26.2 - - + +
339A GLN* 3.3 27.6 - - - +
358A ARG* 3.5 13.6 + - - +
313B ASN 5.5 2.2 - - - +
314B SER 3.1 12.2 + - - +
315B GLU* 3.5 24.7 - - - +
316B LEU 3.3 0.2 - - - -
317B ALA* 1.3 78.3 - - - +
319B MET* 1.3 64.1 + - - +
321B ASN* 3.5 14.9 + - - +
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Residues in contact with MET 319 (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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316A LEU* 6.5 0.4 - - + -
319A MET* 3.4 29.2 - - - +
320A TYR* 2.9 50.4 + - + +
329A HIS* 5.4 4.7 - - + +
332A ALA* 4.0 15.1 - - + +
315B GLU 2.9 18.0 + - - +
316B LEU* 3.3 10.8 - - + +
318B LEU* 1.3 79.7 - - - +
320B TYR* 1.3 83.5 + - + +
321B ASN* 3.4 6.2 + - - -
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Residues in contact with TYR 320 (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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319A MET* 2.8 53.9 + - + +
320A TYR* 3.7 25.4 - + - -
328A ASN* 4.5 3.9 - - - +
316B LEU* 3.0 36.2 + - + +
319B MET* 1.3 84.3 - - + +
321B ASN* 1.3 73.9 + - - +
322B ASP 3.2 2.0 - - - -
323B SER* 3.0 21.4 + - - +
325B VAL* 3.7 30.5 - - + -
328B ASN* 3.5 30.2 + - + +
329B HIS* 4.0 17.6 + - - -
332B ALA* 3.7 9.9 - - - +
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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