Contacts of the helix formed by residues 517 - 526 (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 THR 517 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469D ILE* 4.7 22.6 - - + +
470D ILE* 5.9 0.2 - - - +
515G PHE* 3.7 6.3 + - - +
516G MET* 1.3 71.1 - - - +
518G ARG* 1.4 66.2 + - - +
519G MET* 4.7 1.9 + - + +
520G THR* 3.7 26.6 - - + +
521G ALA* 3.2 17.8 + - - +
10Y GLN* 4.1 9.4 - - - +
11Y SER 5.3 2.6 + - - +
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Residues in contact with ARG 518 (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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516G MET 3.7 1.0 + - - -
517G THR* 1.4 72.6 + - - +
519G MET* 1.3 69.3 + - - +
521G ALA* 3.3 0.4 + - - -
522G LEU* 2.9 33.2 + - + +
10Y GLN* 3.9 17.1 - - + +
18Y GLU* 2.8 33.5 + - - +
21Y ARG* 4.2 13.5 - - - +
24Y LEU* 5.4 2.2 - - - +
25Y PHE* 3.6 29.8 - - + -
173Y TRP* 3.8 25.6 - - + -
180Y GLU* 2.7 40.6 + - - -
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Residues in contact with MET 519 (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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517G THR* 3.7 2.8 + - + +
518G ARG* 1.3 83.3 - - + +
520G THR* 1.3 58.1 + - - +
522G LEU* 3.5 4.4 + - - +
523G LEU* 3.1 45.4 + - + +
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Residues in contact with THR 520 (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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466D LEU* 6.0 7.6 - - + -
517G THR* 3.7 24.3 + - + +
519G MET* 1.3 74.1 - - - +
521G ALA* 1.3 59.2 + - - +
523G LEU* 3.6 10.2 + - + +
524G ALA* 2.9 33.2 + - + +
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Residues in contact with ALA 521 (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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516G MET* 5.0 7.6 - - + +
517G THR 3.2 17.7 + - - +
518G ARG 3.6 4.3 - - - +
520G THR* 1.3 76.8 - - - +
522G LEU* 1.3 54.0 + - - +
524G ALA* 3.9 4.5 - - - +
525G THR* 2.5 39.1 + - - +
170Y PHE* 4.3 8.8 - - + -
173Y TRP* 4.0 32.8 - - + -
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Residues in contact with LEU 522 (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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518G ARG* 2.9 29.9 + - + +
519G MET* 4.1 4.5 - - - +
521G ALA* 1.3 71.8 - - - +
523G LEU* 1.3 58.7 - - + +
525G THR* 3.2 8.1 + - - -
526G LEU* 2.9 38.3 + - + +
24Y LEU* 6.3 3.8 - - + -
28Y GLY* 6.4 1.6 - - - -
32Y VAL* 4.4 24.5 - - + -
173Y TRP* 4.1 22.4 - - + -
174Y LEU* 5.1 7.9 - - + -
177Y GLN* 6.5 0.4 - - - -
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Residues in contact with LEU 523 (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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519G MET* 3.1 43.3 + - + +
520G THR* 3.8 8.3 - - - +
522G LEU* 1.3 72.7 - - + +
524G ALA* 1.3 61.8 + - - +
526G LEU* 3.9 2.8 - - - -
527G PHE* 3.2 24.8 + - - +
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Residues in contact with ALA 524 (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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520G THR* 2.9 24.3 + - + +
521G ALA* 3.9 4.0 - - - +
523G LEU* 1.3 73.0 - - - +
525G THR* 1.3 61.5 + - - +
527G PHE* 3.3 20.6 - - - +
528G PHE* 3.7 14.6 - - - -
170Y PHE* 4.1 17.5 - - + -
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Residues in contact with THR 525 (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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521G ALA* 2.5 25.4 + - - +
522G LEU* 3.5 8.3 - - - -
524G ALA* 1.3 76.4 - - - +
526G LEU* 1.4 61.8 + - + +
527G PHE 3.8 0.5 + - - -
528G PHE* 4.1 10.0 - - - -
529G ILE* 4.4 2.9 - - - +
32Y VAL* 4.1 20.2 - - + -
77Y ILE* 4.6 0.7 - - - +
78Y PHE* 3.9 26.7 - - + -
170Y PHE* 3.1 50.3 - - + +
173Y TRP* 5.8 1.7 - - - -
174Y LEU* 5.9 2.2 - - + -
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Residues in contact with LEU 526 (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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522G LEU* 2.9 22.1 + - + +
523G LEU* 3.9 3.6 - - - +
525G THR* 1.4 81.8 - - + +
527G PHE* 1.4 63.8 + - - +
528G PHE 3.6 2.0 - - - -
529G ILE* 3.4 19.5 + - + +
530G ILE* 4.0 11.4 - - - +
32Y VAL* 3.9 35.4 - - + +
35Y ILE* 3.4 52.0 - - + -
78Y PHE* 4.9 4.7 - - + -
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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
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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