Contacts of the helix formed by residues 466 - 471 (chain A) in PDB entry 5M5X
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 LEU 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A ALA 3.8 14.8 - - - +
460A LEU* 3.1 38.5 + - + +
461A GLU* 3.4 2.6 - - - +
462A LYS* 3.5 46.3 - - + +
465A GLY* 1.3 71.7 - - - +
467A PHE* 1.3 55.2 + - + +
468A ARG 2.9 0.9 - - - -
469A LYS* 2.7 45.6 + - + +
470A HIS* 3.9 17.6 + - + +
1184B TYR* 5.5 9.0 - - + -
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Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A LEU* 3.9 39.0 - - + -
465A GLY* 2.8 10.4 + - - +
466A LEU* 1.3 80.0 - - + +
468A ARG* 1.3 57.3 + - + +
469A LYS 3.0 1.0 + - - -
470A HIS* 4.8 0.7 - - - +
471A MET* 2.8 61.8 + - + +
472A MET* 3.2 3.0 + - - -
1610A PHE* 6.4 1.3 - + - -
1613A MET* 4.5 15.5 - - + -
1614A SER* 4.9 16.6 - - - +
1618A THR* 3.7 37.5 - - + -
1622A LEU* 5.8 2.5 - - + -
1642A VAL* 6.6 0.2 - - + -
1185B LEU* 3.6 33.9 - - + -
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Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A LYS* 4.9 2.0 - - - +
463A LYS* 3.8 42.1 + - - +
464A GLU* 3.9 20.3 + - - -
465A GLY* 3.3 12.7 + - - +
466A LEU 2.8 1.4 + - - +
467A PHE* 1.3 74.3 - - - +
469A LYS* 1.3 52.1 + - - +
472A MET* 4.2 7.9 - - + +
473A GLY 3.8 11.2 + - - -
1021A ARG* 2.9 39.9 - - - +
1614A SER 4.1 10.6 + - - +
1615A TYR* 2.5 31.1 + - - -
1616A GLU* 4.4 0.6 - - - +
1070B ARG* 2.7 29.2 + - - +
1073B GLU* 3.0 28.1 + - - +
14T A 3.8 16.0 + - - -
15T C 5.0 7.7 + - - -
16T G 5.4 2.0 + - - -
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Residues in contact with LYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A LYS* 3.5 31.4 - - - +
466A LEU* 2.7 29.9 + - + +
468A ARG* 1.3 72.4 - - - +
470A HIS* 1.3 89.4 + - + +
473A GLY 2.7 21.2 - - - +
474A LYS* 4.5 0.5 - - - -
475A ARG* 4.4 21.0 + - - +
1058B GLN* 4.3 3.1 - - - +
1061B LYS* 5.5 4.0 - - - +
1070B ARG* 3.9 16.3 + - - +
13R G 5.2 9.9 - - - +
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Residues in contact with HIS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU* 3.9 19.7 + - + +
467A PHE 3.4 1.2 + - - -
469A LYS* 1.3 111.3 - - + +
471A MET* 1.3 64.7 + - + +
473A GLY 4.4 1.1 - - - -
474A LYS* 3.2 18.7 - - - +
475A ARG* 6.0 1.3 - - + -
1053B ASN* 4.8 5.9 + - - -
1055B LEU* 5.6 3.1 - - + -
1056B THR* 3.5 26.5 + - + +
1058B GLN* 3.1 38.6 + - - +
1181B VAL* 3.3 37.0 - - + +
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Residues in contact with MET 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 2.8 40.8 + - + +
469A LYS 3.8 0.2 - - - -
470A HIS* 1.3 85.0 - - + +
472A MET* 1.3 78.8 + - + +
474A LYS* 3.2 18.5 - - - +
1641A ILE* 3.6 17.4 - - - +
1642A VAL* 4.5 27.6 - - + +
1181B VAL* 3.6 47.1 - - + +
1182B LEU* 4.1 4.3 - - - +
1185B LEU* 3.6 29.4 - - + -
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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