Contacts of the helix formed by residues 524 - 533 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493I GLU* 3.6 39.3 - - + +
496I ALA* 3.8 26.9 - - + -
497I LEU* 3.8 29.8 - - + +
500I TYR* 4.3 7.4 - - + -
520I ILE* 4.1 14.4 - - + -
521I PRO* 4.2 24.1 - - + +
522I GLY 3.3 1.2 - - - +
523I GLU* 1.3 80.7 - - - +
525I GLN* 1.3 56.8 + - - +
526I PRO 3.5 0.7 - - - -
527I LEU* 3.3 10.3 + - + +
528I ALA* 2.9 28.1 + - - +
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Residues in contact with GLN 525 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517I ILE* 2.7 32.7 + - + +
518I SER* 4.2 8.1 + - - +
519I ARG 4.8 0.2 - - - +
520I ILE* 3.4 26.0 + - + +
521I PRO 4.5 0.3 - - - +
522I GLY* 3.2 22.0 - - - +
524I LEU* 1.3 75.3 - - - +
526I PRO* 1.4 65.7 - - + +
528I ALA* 4.5 1.8 - - - +
529I SER* 2.9 34.2 + - - +
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Residues in contact with PRO 526 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522I GLY 3.3 18.2 - - - +
523I GLU* 3.5 15.7 - - - +
524I LEU 3.6 0.2 - - - -
525I GLN* 1.4 91.0 - - + +
527I LEU* 1.3 55.4 + - + +
529I SER* 4.3 3.7 - - - -
530I GLU* 3.4 26.9 + - - +
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Residues in contact with LEU 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465I ARG* 3.8 26.9 - - - +
493I GLU* 3.5 40.8 - - + +
494I HIS* 4.8 14.1 - - + +
497I LEU* 5.1 2.5 - - + -
523I GLU 5.4 1.1 - - - +
524I LEU* 3.3 15.1 + - + +
525I GLN 3.1 0.4 - - - -
526I PRO* 1.3 79.8 - - + +
528I ALA* 1.3 64.9 + - - +
529I SER 3.2 1.6 - - - -
530I GLU* 3.1 14.9 + - + +
531I LEU* 3.2 31.1 + - + +
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Residues in contact with ALA 528 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472I MSE 3.7 10.1 - - - +
497I LEU* 3.7 30.5 - - + +
517I ILE* 3.6 13.0 - - + +
520I ILE* 4.3 13.9 - - + -
524I LEU 2.9 21.8 + - - +
525I GLN 4.4 0.7 - - - +
527I LEU* 1.3 69.8 - - - +
529I SER* 1.3 66.6 + - - +
531I LEU* 3.8 10.9 - - - +
532I SER* 3.3 17.3 + - - -
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Residues in contact with SER 529 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517I ILE* 3.9 17.9 - - - +
525I GLN* 2.9 21.6 + - - -
526I PRO* 4.3 6.1 - - - -
528I ALA* 1.3 77.1 - - - +
530I GLU* 1.3 66.3 + - - +
531I LEU 3.0 3.5 + - - -
532I SER* 2.5 26.3 + - - -
533I LEU* 3.6 13.7 + - - +
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Residues in contact with GLU 530 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465I ARG* 5.1 7.6 + - - +
526I PRO 3.4 19.5 + - - +
527I LEU* 3.1 12.3 + - + +
529I SER* 1.3 84.2 + - - +
531I LEU* 1.3 59.3 + - - +
533I LEU* 4.1 27.0 - - - +
534I LEU* 4.0 17.7 + - - +
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Residues in contact with LEU 531 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465I ARG* 3.4 57.9 - - + +
468I LEU* 4.2 12.1 - - + -
469I ALA* 3.6 14.3 - - - +
472I MSE 3.6 15.5 - - + -
494I HIS* 5.2 3.6 - - + -
497I LEU* 3.8 27.6 - - + -
527I LEU* 3.2 34.8 + - + +
528I ALA* 3.8 2.2 - - - +
529I SER 3.1 0.4 - - - -
530I GLU* 1.3 78.4 - - - +
532I SER* 1.3 63.9 + - - +
533I LEU 3.0 5.8 + - - -
534I LEU* 3.2 24.0 + - + +
536I ILE* 6.1 0.3 - - - +
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Residues in contact with SER 532 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472I MSE 3.4 12.1 - - - +
473I ARG* 3.5 31.1 + - - +
513I PRO* 3.8 29.8 - - - -
517I ILE* 4.0 8.6 - - - +
528I ALA 3.3 9.1 + - - -
529I SER* 2.5 27.6 + - - -
531I LEU* 1.3 78.9 - - - +
533I LEU* 1.3 63.0 + - - +
536I ILE* 5.7 2.3 - - - +
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Residues in contact with LEU 533 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473I ARG* 5.7 3.1 - - - +
529I SER* 3.6 15.4 + - - +
530I GLU* 4.1 30.3 - - - +
531I LEU 3.0 0.8 - - - -
532I SER* 1.3 85.7 + - - +
534I LEU* 1.3 67.3 + - - +
535I LEU 3.9 0.2 - - - -
536I 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
------------------------------------------------------------
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