Contacts of the helix formed by residues 549 - 553 (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 PHE 549 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547M ILE 3.7 0.4 + - - -
548M PRO* 1.3 78.9 - - + +
550M LEU* 1.3 59.1 + - - +
551M GLU* 3.1 19.6 + - - -
552M HIS* 2.9 47.4 + + + +
553M ASP* 3.8 3.3 + - - -
579M VAL* 4.1 16.2 - - + -
883M GLY* 3.7 19.5 - - - -
886M LEU* 3.7 22.0 - - + -
887M GLU* 3.6 33.2 - - + -
890M LEU* 4.0 20.2 - - + -
903M SER* 4.1 20.9 + - - -
904M PRO 5.2 1.6 + - - -
905M ILE* 5.0 1.6 - - - +
909M ALA* 3.8 21.1 - - + -
914M ILE* 4.1 7.9 - - + -
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Residues in contact with LEU 550 (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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540M PHE* 3.9 12.3 - - + -
544M THR* 3.8 32.1 - - + +
547M ILE* 3.4 30.7 + - + +
548M PRO 3.1 3.3 - - - -
549M PHE* 1.3 76.9 - - - +
551M GLU* 1.3 62.6 + - - +
552M HIS 3.0 0.2 - - - -
553M ASP* 3.1 16.2 + - + +
558M ALA* 3.8 19.3 - - + -
905M ILE* 3.8 22.6 - - + +
906M PHE* 3.7 23.1 - - + -
1070N TYR* 3.2 31.6 - - + +
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Residues in contact with GLU 551 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M PHE* 3.3 10.7 + - - -
550M LEU* 1.3 82.4 + - - +
552M HIS* 1.3 85.7 + - + +
553M ASP 3.4 0.7 - - - -
904M PRO 4.8 3.0 - - - +
905M ILE* 4.1 0.9 - - - -
906M PHE* 3.2 52.4 + - + -
907M ASP 4.9 0.2 + - - -
908M GLY* 5.1 6.4 + - - -
909M ALA 5.4 2.4 - - - +
910M LYS* 5.3 5.6 + - - +
1061N PHE* 4.3 1.9 - - - -
1064N GLY* 3.4 11.5 - - - -
1065N LEU* 2.9 53.7 + - - +
1070N TYR* 4.2 4.7 - - - -
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Residues in contact with HIS 552 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549M PHE* 2.9 29.6 + + + +
551M GLU* 1.3 98.7 + - + +
553M ASP* 1.3 57.5 + - - +
880M MET 3.6 2.1 - - - +
882M LEU* 3.2 20.4 + - + +
883M GLY 3.9 13.5 - - - +
886M LEU* 3.3 30.7 - - + +
909M ALA 5.2 3.6 + - - -
911M GLU* 6.4 0.4 - - + -
951N ILE* 5.7 0.2 - - - +
1061N PHE* 2.8 43.8 + - - +
1062N ARG 3.3 19.3 + - - -
1063N GLU 3.3 17.5 - - - -
1064N GLY* 3.6 5.6 - - - -
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Residues in contact with ASP 553 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547M ILE* 3.9 10.7 - - - +
549M PHE 4.0 3.9 - - - +
550M LEU* 3.1 8.1 + - + +
551M GLU 3.4 0.4 - - - -
552M HIS* 1.3 77.7 - - - +
554M ASP* 1.3 61.9 + - - +
558M ALA* 4.6 12.6 - - + +
843M HIS* 2.6 36.7 + - - +
880M MET 3.9 2.0 - - - -
881M ASN* 3.2 14.7 - - + +
882M LEU 3.1 6.1 + - - -
883M GLY* 2.6 31.7 + - - -
1061N PHE* 3.6 3.1 - - - -
1070N TYR* 2.7 35.7 + - - -
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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
------------------------------------------------------------
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