Contacts of the helix formed by residues 369 - 373 (chain M) in PDB entry 5D4D
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 PRO 369 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66M LEU* 4.1 25.8 - - + -
111M ASP* 4.0 32.3 - - + +
113M VAL* 4.2 13.2 - - + +
368M THR* 1.3 84.0 - - + +
370M ALA* 1.3 58.9 + - - +
372M LEU* 3.7 9.6 - - + -
373M VAL* 3.0 34.8 + - + +
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Residues in contact with ALA 370 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111M ASP* 3.8 18.2 + - - +
113M VAL* 3.7 11.4 - - + -
368M THR* 3.1 8.0 - - - +
369M PRO* 1.3 82.5 - - - +
371M LYS* 1.3 64.1 + - + +
372M LEU 3.5 0.2 + - - -
373M VAL 3.5 10.0 - - - +
277P GLN* 6.2 1.8 - - - +
280P GLN* 2.4 37.7 + - - +
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Residues in contact with LYS 371 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358M ARG* 3.4 18.9 - - - +
368M THR* 3.4 22.3 + - - +
370M ALA* 1.3 80.7 - - + +
372M LEU* 1.3 64.7 + - - +
373M VAL 5.0 0.8 - - - +
277P GLN* 4.8 20.4 - - - +
280P GLN* 4.7 0.7 - - - +
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Residues in contact with LEU 372 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63M GLY 6.1 2.9 - - - +
66M LEU* 3.7 38.6 - - + -
355M VAL* 3.6 38.0 - - + +
358M ARG* 3.1 40.6 + - + +
359M MET* 4.0 22.9 - - + -
368M THR 3.2 21.0 + - - +
369M PRO* 3.6 6.7 - - + +
370M ALA 3.2 0.2 - - - -
371M LYS* 1.3 78.7 - - - +
373M VAL* 1.3 58.9 + - - +
374M ASN 3.6 0.5 + - - -
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Residues in contact with VAL 373 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52M PHE* 5.8 3.8 - - + -
66M LEU* 4.1 15.7 - - + -
113M VAL* 4.8 16.7 - - + +
114M PHE 5.9 0.9 - - - +
115M LEU* 4.1 20.4 - - + -
351M LEU* 3.8 28.5 - - + -
355M VAL* 3.8 19.1 - - + -
369M PRO* 3.0 20.3 + - + +
370M ALA 3.5 12.9 - - - +
371M LYS 5.0 0.8 - - - -
372M LEU* 1.3 75.5 - - - +
374M ASN* 1.3 64.9 + - - +
375M SER* 4.1 2.5 + - - +
276P ARG* 5.9 0.3 - - - -
280P GLN* 4.3 9.2 + - - +
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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