Contacts of the helix formed by residues 524 - 533 (chain G) in PDB entry 2R6C
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 524 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493G GLU* 3.8 36.8 - - + +
496G ALA* 4.1 9.9 - - + -
497G LEU* 4.0 29.4 - - + +
500G TYR* 3.9 28.0 - - + -
520G ILE* 3.8 17.3 - - + -
521G PRO* 4.0 18.5 - - + +
522G GLY 3.2 0.8 - - - +
523G GLU* 1.3 81.7 - - - +
525G GLN* 1.3 52.2 + - - +
526G PRO* 3.5 0.9 - - - -
527G LEU* 3.1 11.3 + - + +
528G ALA* 2.8 32.4 + - - +
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Residues in contact with GLN 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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517G ILE* 2.6 31.4 + - + +
518G SER* 4.1 8.9 + - - +
519G ARG 4.6 0.4 - - - +
520G ILE* 3.5 27.2 + - + +
521G PRO 4.7 0.2 - - - -
522G GLY* 3.2 21.3 - - - +
524G LEU* 1.3 73.0 - - - +
526G PRO* 1.4 68.1 - - + +
527G LEU 3.0 1.8 - - - -
528G ALA* 4.3 2.7 - - - +
529G SER* 2.8 36.6 + - - -
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Residues in contact with PRO 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 GLY 3.3 17.3 - - - +
523G GLU* 3.8 11.9 - - - +
524G LEU 3.6 2.2 - - - -
525G GLN* 1.4 90.7 - - + +
527G LEU* 1.3 56.1 + - + +
529G SER* 4.7 2.9 - - - -
530G GLU* 3.4 27.3 - - - +
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Residues in contact with LEU 527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465G ARG* 3.9 26.0 - - - +
493G GLU* 3.3 40.8 - - + +
494G HIS* 5.2 8.5 - - + +
497G LEU* 4.4 14.1 - - + -
523G GLU 5.3 1.3 - - - +
524G LEU* 3.1 13.1 + - + +
525G GLN 3.0 0.4 - - - -
526G PRO* 1.3 80.0 - - + +
528G ALA* 1.3 64.2 + - - +
529G SER 3.2 1.8 - - - -
530G GLU* 3.2 13.8 + - + +
531G LEU* 3.3 28.1 + - + +
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Residues in contact with ALA 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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472G MSE 3.6 14.1 - - - +
497G LEU* 3.7 35.4 - - + -
517G ILE* 3.3 13.6 - - + +
520G ILE* 4.3 15.9 - - + -
524G LEU 2.8 22.7 + - - +
525G GLN* 4.3 1.6 - - - +
527G LEU* 1.3 70.1 - - - +
529G SER* 1.3 63.3 + - - +
531G LEU* 4.0 4.9 - - - -
532G SER* 3.2 13.5 + - - -
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Residues in contact with SER 529 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G ILE* 3.9 19.7 - - - +
525G GLN* 2.8 21.7 + - - -
526G PRO* 4.5 4.7 - - - -
528G ALA* 1.3 77.1 - - - +
530G GLU* 1.3 66.9 + - - +
531G LEU 3.1 3.5 + - - -
532G SER* 2.5 26.4 + - - -
533G LEU* 3.5 14.6 + - - +
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Residues in contact with GLU 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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465G ARG* 5.1 7.1 + - - +
526G PRO 3.4 18.8 - - - +
527G LEU* 3.2 9.3 + - + +
529G SER* 1.3 84.2 + - - +
531G LEU* 1.3 58.3 + - - +
533G LEU* 4.1 25.5 - - - +
534G LEU* 4.0 19.9 + - - +
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Residues in contact with LEU 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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465G ARG* 3.3 57.9 - - + +
468G LEU* 4.0 24.7 - - + -
469G ALA* 3.6 14.9 - - - +
472G MSE 3.6 15.5 - - + -
494G HIS* 4.9 4.5 - - + -
497G LEU* 4.1 13.2 - - + -
527G LEU* 3.3 33.4 + - + +
528G ALA* 4.2 1.8 - - - +
529G SER 3.1 1.0 - - - -
530G GLU* 1.3 76.7 - - - +
532G SER* 1.3 62.4 + - - +
533G LEU 3.1 6.0 + - - -
534G LEU* 3.3 26.7 + - + +
536G ILE* 5.8 0.9 - - - +
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Residues in contact with SER 532 (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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469G ALA* 5.6 0.2 - - - +
472G MSE 3.5 13.0 - - - +
473G ARG* 3.5 32.9 + - - +
513G PRO* 3.9 29.2 - - - -
517G ILE* 3.8 7.8 - - - +
528G ALA 3.2 12.0 + - - -
529G SER* 2.5 26.0 + - - -
531G LEU* 1.3 78.4 - - - +
533G LEU* 1.3 62.1 + - - +
536G ILE* 5.7 1.9 - - - +
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Residues in contact with LEU 533 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473G ARG* 5.5 4.7 - - - +
529G SER* 3.5 16.9 + - - +
530G GLU* 4.2 29.6 - - - +
531G LEU 3.1 1.0 - - - +
532G SER* 1.3 86.7 - - - +
534G LEU* 1.3 67.0 + - - +
535G LEU 3.8 0.7 - - - -
536G ILE* 6.3 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