Contacts of the helix formed by residues 428 - 433 (chain F) in PDB entry 6M04
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 GLN 428 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424F ASP* 3.0 29.8 + - - +
427F ASP* 1.3 74.6 - - - +
429F LEU* 1.3 61.3 + - - +
430F TYR 3.2 1.8 - - - -
431F SER* 3.0 12.5 + - - -
432F LYS* 3.0 35.9 + - + +
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Residues in contact with LEU 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E LYS* 6.5 0.4 - - + -
296E ALA* 5.6 3.4 - - + +
297E HIS* 3.4 44.9 - - + +
204F PHE* 3.6 26.9 - - + -
427F ASP* 4.6 2.1 - - + +
428F GLN* 1.3 78.5 - - - +
430F TYR* 1.3 60.0 + - + +
432F LYS* 4.2 19.5 - - + +
433F ARG* 2.9 40.4 + - + +
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Residues in contact with TYR 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E SER* 5.7 0.7 + - - -
297E HIS* 5.4 9.2 + + - -
19F ILE* 3.9 33.5 - - + +
200F LEU* 3.5 38.0 - - + +
204F PHE* 3.4 52.6 - + + -
420F LEU* 5.2 1.9 - - - +
423F VAL* 4.7 9.9 - - + +
426F TYR* 4.6 0.7 - + - -
427F ASP* 4.0 32.5 - - + +
428F GLN* 3.2 1.0 - - - +
429F LEU* 1.3 78.0 - - + +
431F SER* 1.3 58.4 + - - +
433F ARG* 3.9 9.7 + - - +
434F PHE* 3.6 17.3 - - - +
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Residues in contact with SER 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F LYS* 2.5 35.6 + - - +
403F GLU* 2.9 21.7 + - - +
420F LEU* 4.8 9.1 - - - +
423F VAL* 5.7 1.1 - - - +
424F ASP* 3.9 16.9 + - - +
427F ASP 4.6 1.4 + - - -
428F GLN* 3.0 21.0 + - - -
430F TYR* 1.3 79.1 - - - +
432F LYS* 1.3 61.2 + - - +
433F ARG 3.3 0.2 - - - -
434F PHE* 3.2 15.0 + - - +
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Residues in contact with LYS 432 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F LEU* 5.5 6.3 - - + +
403F GLU* 2.8 32.2 - - + +
406F PHE* 3.5 36.6 - - + -
407F SER* 5.4 8.6 + - - -
428F GLN* 3.0 30.1 + - + +
429F LEU* 3.3 18.8 + - + +
431F SER* 1.3 78.0 - - - +
433F ARG* 1.3 59.3 + - - +
435F GLY 4.0 0.7 + - - -
436F VAL* 4.5 10.6 - - - +
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Residues in contact with ARG 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F LEU* 3.7 26.3 + - - +
203F CYS* 2.7 53.9 + - - -
204F PHE* 3.3 48.1 - - + +
209F THR* 4.2 22.7 - - - +
210F THR* 6.3 0.7 - - - -
213F LEU* 4.8 18.6 - - + +
429F LEU* 2.9 24.5 + - + +
430F TYR* 3.9 11.1 + - - +
432F LYS* 1.3 76.8 - - - +
434F PHE* 1.3 80.4 + - - +
435F GLY 3.5 0.3 + - - -
436F VAL* 3.8 5.9 + - - +
437F PHE* 3.8 12.6 + - - +
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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