Contacts of the helix formed by residues 505 - 513 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501H GLU 3.2 16.5 + - - -
502H MET* 3.4 5.4 - - - -
504H ARG* 1.3 75.6 - - - +
506H MET* 1.3 61.0 + - - +
507H LYS* 3.2 3.4 - - - -
508H LEU* 3.2 9.9 + - - +
509H LEU* 3.1 20.4 + - - +
1430H VAL* 4.6 20.2 - - - -
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Residues in contact with MET 506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502H MET 3.0 14.9 + - - +
503H LEU* 3.3 18.2 - - - +
504H ARG 3.2 3.0 - - - -
505H GLY* 1.3 75.6 - - - +
507H LYS* 1.3 60.6 + - - +
509H LEU* 3.4 9.2 + - - +
510H LYS* 2.9 26.7 + - - +
1110H MET* 6.1 0.2 - - - -
1113H PHE* 5.7 8.5 - - + -
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Residues in contact with LYS 507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504H ARG 4.7 3.9 + - - +
505H GLY 5.0 0.2 - - - -
506H MET* 1.3 78.6 - - - +
508H LEU* 1.3 56.7 + - - +
510H LYS* 2.8 24.1 + - - +
511H LEU* 2.9 12.9 + - - +
1110H MET* 5.1 14.1 - - + -
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Residues in contact with LEU 508 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505H GLY* 3.2 14.7 + - - +
507H LYS* 1.3 79.0 - - - +
509H LEU* 1.3 61.6 + - - +
511H LEU* 3.2 18.1 + - - +
512H TYR* 3.4 14.9 + - - +
1430H VAL* 4.6 22.0 - - + +
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Residues in contact with LEU 509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502H MET 5.6 0.7 - - - +
505H GLY 3.1 12.1 + - - +
506H MET* 3.5 13.2 - - - +
507H LYS 3.2 0.2 - - - -
508H LEU* 1.3 77.2 - - - +
510H LYS* 1.3 56.6 + - - +
513H ALA* 2.9 10.6 + - - -
514H TRP* 2.9 52.8 + - + +
515H GLU* 4.2 11.9 + - + +
518H PHE* 6.4 1.1 - - + -
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Residues in contact with LYS 510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506H MET 2.9 12.9 + - - +
507H LYS* 2.8 15.2 + - - +
509H LEU* 1.3 75.0 - - - +
511H LEU* 1.3 63.3 + - - +
513H ALA* 4.0 6.4 + - - +
515H GLU* 6.4 0.2 - - - -
1110H MET* 4.8 15.5 - - + +
1419H ARG 6.2 0.3 - - - -
1420H SER* 6.1 0.3 - - - -
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Residues in contact with LEU 511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507H LYS 2.9 9.5 + - - +
508H LEU* 3.4 14.6 - - - +
509H LEU 3.2 0.4 - - - -
510H LYS* 1.3 80.7 - - - +
512H TYR* 1.3 58.5 + - + +
513H ALA 3.5 0.2 - - - -
1393H PHE* 4.8 23.5 - - + -
1419H ARG 4.2 9.0 - - - +
1420H SER* 4.9 1.6 - - - -
1422H LEU 3.8 17.5 - - - +
1423H SER* 5.4 1.0 - - - -
1424H ILE* 5.3 11.1 + - + +
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Residues in contact with TYR 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508H LEU 3.4 12.3 + - - +
509H LEU 3.4 0.4 + - - -
511H LEU* 1.3 78.9 - - + +
513H ALA* 1.3 68.3 + - - +
514H TRP* 3.4 15.3 + - + -
1420H SER* 4.4 12.3 - - - +
1422H LEU 5.5 0.4 - - - -
1423H SER* 6.3 1.3 - - - +
1442H PRO* 4.4 22.2 - - + +
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Residues in contact with ALA 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509H LEU 2.9 8.2 + - - -
510H LYS* 4.0 6.2 + - - +
511H LEU 3.5 2.4 - - - -
512H TYR* 1.3 80.3 - - - +
514H TRP* 1.3 55.7 + - - +
515H GLU* 3.3 10.8 + - - +
516H SER* 4.6 5.0 + - - -
1416H HIS 5.4 0.4 - - - +
1420H SER* 3.4 28.4 - - - +
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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