Contacts of the helix formed by residues 527 - 531 (chain G) in PDB entry 5MG3
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 527 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523G LEU 3.2 14.5 + - - +
524G ALA* 3.3 20.4 + - - +
525G THR 3.5 0.2 - - - -
526G LEU* 1.4 75.3 - - - +
528G PHE* 1.4 64.9 + + - +
530G ILE* 2.7 46.2 + - + +
531G SER* 3.0 33.6 + - - -
532G LEU* 5.3 6.5 - - + -
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Residues in contact with PHE 528 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524G ALA 3.7 21.3 - - - -
525G THR 4.1 9.0 - - - -
527G PHE* 1.4 82.0 - + + +
529G ILE* 1.4 60.4 + - + +
531G SER* 3.1 16.3 + - - -
532G LEU* 3.5 32.2 + - + +
533G VAL* 3.6 11.7 + - - +
42Y PRO* 5.0 3.3 - - + +
77Y ILE* 3.9 31.2 - - + -
78Y PHE* 6.1 1.3 - + - -
159Y THR* 6.3 0.2 - - + -
162Y VAL* 5.5 5.2 - - + -
163Y SER* 3.4 33.4 - - - -
166Y THR* 4.6 20.0 - - + -
167Y GLY* 5.8 0.9 - - - -
170Y PHE* 3.9 19.7 - + - -
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Residues in contact with ILE 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E VAL* 3.5 32.1 - - + -
525G THR 4.4 0.2 - - - +
526G LEU* 3.4 37.2 - - + +
527G PHE 3.0 0.4 + - - -
528G PHE* 1.4 73.0 - - - +
530G ILE* 1.3 62.0 + - + +
531G SER 3.4 2.0 + - - -
533G VAL* 3.7 14.0 - - - +
536G ASN* 3.6 20.3 + - - +
35Y ILE* 3.7 28.3 - - + +
36Y GLY* 5.0 0.9 - - - -
39Y ILE* 3.7 35.4 - - + -
77Y ILE* 4.0 22.0 - - + -
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Residues in contact with ILE 530 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E VAL* 4.5 21.3 - - + -
526G LEU 4.0 10.8 - - - +
527G PHE* 2.7 32.1 + - + +
529G ILE* 1.3 75.7 - - + +
531G SER* 1.4 57.0 + - - +
536G ASN* 5.9 0.2 - - - -
537G ILE* 3.8 31.2 - - + +
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Residues in contact with SER 531 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527G PHE* 3.0 48.5 + - - -
528G PHE* 3.1 13.9 + - - -
529G ILE 3.4 2.6 + - - -
530G ILE* 1.4 80.7 - - - +
532G LEU* 1.4 79.7 + - - +
533G VAL* 3.4 9.2 + - - +
534G LEU* 5.8 1.2 - - - +
537G ILE* 5.2 6.5 - - - +
538G ASN* 5.9 1.0 + - - -
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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