Contacts of the helix formed by residues 403 - 408 (chain B) in PDB entry 3MDL
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 403 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393B ASP 4.6 2.0 - - - -
394B THR* 4.4 13.1 - - - +
395B PHE* 4.6 0.4 - - - -
401B GLU 3.9 1.6 + - - -
402B TYR* 1.3 76.5 - - - +
404B PHE* 1.3 65.7 + - - +
405B LYS* 3.6 9.9 + - - +
406B GLN* 3.2 34.8 + - - +
407B PHE* 2.9 21.8 + - - +
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Residues in contact with PHE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B LEU* 3.9 22.0 - - + -
392B PRO 3.1 28.3 - - - -
393B ASP* 3.7 16.1 + - - -
395B PHE* 3.8 31.4 - + - -
403B SER* 1.3 73.1 - - - +
405B LYS* 1.3 57.7 + - - +
407B PHE 3.1 0.7 + - - -
408B LEU* 2.9 55.4 + - + +
441B PRO* 4.4 10.1 - - + -
443B ALA* 3.5 31.6 - - + -
444B VAL* 3.9 22.2 - - + -
615B COH 4.2 6.7 - - + -
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Residues in contact with LYS 405 (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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403B SER* 3.2 9.6 - - - +
404B PHE* 1.3 80.4 - - - +
406B GLN* 1.3 61.6 + - + +
408B LEU* 3.9 13.7 + - - +
681B NAG 4.2 6.9 - - - +
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Residues in contact with GLN 406 (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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401B GLU 3.7 6.8 - - - +
402B TYR* 3.5 24.0 - - + -
403B SER* 3.2 34.7 + - - +
405B LYS* 1.3 79.5 - - + +
407B PHE* 1.3 61.9 + - - +
408B LEU 4.4 0.2 - - - +
410B ASN* 2.9 30.5 + - - +
413B ILE* 3.6 3.3 - - - +
681B NAG 3.6 27.2 + - - +
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Residues in contact with PHE 407 (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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200B PHE* 3.7 10.8 - + - -
295B VAL* 3.6 28.7 - - + -
296B PRO* 3.2 43.1 - - + +
297B GLY 4.1 2.0 - - - -
395B PHE* 3.6 44.9 - + + -
397B ILE* 4.6 9.2 - - + -
402B TYR* 4.1 11.2 - - + +
403B SER 2.9 17.4 + - - +
404B PHE* 3.7 3.4 - - - +
406B GLN* 1.3 76.1 - - - +
408B LEU* 1.3 68.6 + - + +
410B ASN* 3.2 15.4 + - - +
413B ILE* 4.0 17.3 - - + -
422B PHE* 4.7 1.6 - + - -
426B PHE* 3.8 26.7 - + - -
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Residues in contact with LEU 408 (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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294B LEU* 3.6 18.8 - - + +
295B VAL* 4.6 8.3 - - + -
404B PHE* 2.9 41.2 + - + +
405B LYS* 3.9 11.1 + - - +
406B GLN 3.6 0.4 - - - -
407B PHE* 1.3 83.5 - - + +
409B TYR* 1.3 78.2 + - + +
410B ASN* 3.2 4.7 + - - +
615B COH 3.8 37.0 - - + -
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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