Contacts of the helix formed by residues 505 - 513 (chain G) in PDB entry 6BAA
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 GLY 505 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501G GLU 3.2 14.8 + - - -
502G MET* 3.4 5.8 - - - -
504G ARG* 1.3 75.4 - - - +
506G MET* 1.3 62.7 + - - +
507G LYS* 3.2 3.6 - - - -
508G LEU* 3.2 10.5 + - - +
509G LEU* 3.1 19.6 + - - +
1430G VAL* 4.6 19.7 - - - -
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Residues in contact with MET 506 (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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502G MET 3.0 15.3 + - - +
503G LEU* 3.3 17.9 + - - +
504G ARG 3.2 2.8 - - - -
505G GLY* 1.3 75.6 - - - +
507G LYS* 1.3 60.7 + - - +
509G LEU* 3.4 9.5 + - - +
510G LYS* 2.9 26.7 + - - +
1110G MET* 6.1 0.2 - - - -
1113G PHE* 5.7 8.7 - - + -
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Residues in contact with LYS 507 (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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504G ARG 4.7 3.5 + - - +
505G GLY* 3.2 0.9 - - - -
506G MET* 1.3 79.2 - - - +
508G LEU* 1.3 57.6 + - - +
510G LYS* 2.8 24.7 + - - +
511G LEU* 2.9 13.0 + - - +
1110G MET* 5.1 13.7 - - + -
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Residues in contact with LEU 508 (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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505G GLY* 3.2 15.8 + - - +
507G LYS* 1.3 77.8 - - - +
509G LEU* 1.3 61.1 + - - +
511G LEU* 3.2 17.4 + - - +
512G TYR* 3.4 15.1 + - - +
1430G VAL* 4.6 21.8 - - + +
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Residues in contact with LEU 509 (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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502G MET 5.6 0.4 - - - +
505G GLY 3.1 12.1 + - - +
506G MET* 3.5 13.0 - - - +
508G LEU* 1.3 77.6 - - - +
510G LYS* 1.3 57.6 + - - +
513G ALA* 2.9 10.6 + - - -
514G TRP* 2.9 51.4 + - + +
515G GLU* 4.2 12.2 + - + +
518G PHE* 6.4 0.7 - - + -
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Residues in contact with LYS 510 (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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506G MET 2.9 13.1 + - - +
507G LYS* 2.8 14.4 + - - +
509G LEU* 1.3 74.3 - - - +
511G LEU* 1.3 64.7 + - - +
513G ALA* 4.0 6.6 + - - +
515G GLU* 6.4 0.4 - - - -
1110G MET* 4.8 15.5 - - + +
1419G ARG 6.2 0.3 - - - -
1420G SER* 6.1 0.5 - - - -
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Residues in contact with LEU 511 (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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507G LYS 2.9 10.4 + - - +
508G LEU* 3.4 14.4 - - - +
509G LEU 3.2 0.4 - - - -
510G LYS* 1.3 79.9 - - - +
512G TYR* 1.3 59.4 + - + +
513G ALA 3.9 0.2 + - - -
1393G PHE* 4.8 23.4 - - + -
1419G ARG 4.2 9.2 - - - +
1420G SER* 4.9 1.4 - - - -
1422G LEU 3.8 17.2 - - - +
1423G SER* 5.4 1.2 - - - -
1424G ILE* 5.3 11.3 + - + +
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Residues in contact with TYR 512 (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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508G LEU 3.4 12.7 + - - +
509G LEU 3.4 0.2 + - - -
511G LEU* 1.3 78.9 - - + +
513G ALA* 1.3 67.5 + - - +
514G TRP* 3.4 15.2 + - + -
1420G SER 4.4 11.7 - - - +
1422G LEU 5.5 1.1 - - - -
1423G SER* 6.3 1.3 - - - +
1442G PRO* 4.4 21.7 - - + +
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Residues in contact with ALA 513 (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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509G LEU 2.9 7.9 + - - -
510G LYS* 4.0 6.4 + - - +
511G LEU 3.5 3.0 + - - -
512G TYR* 1.3 79.5 - - - +
514G TRP* 1.3 56.6 + - - +
515G GLU* 3.3 9.7 + - - +
516G SER* 4.6 5.4 + - - -
1420G SER* 3.4 29.8 - - - +
1442G PRO 5.3 0.2 - - - -
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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